WO2025236011A1 - Compositions for phosphorous-azole exchange chemistry and use thereof to target functional protein sites - Google Patents

Abstract

Compounds comprising phosphorous-azole electrophiles are described. Also described is the use of these compounds in phosphorous-azole exchange (PhAzE) chemistry for labeling the proteome and in developing new covalent therapeutic agents that selectively modify select amino acid residues in biologically active proteins and peptides. The PhAzE compounds can target amino acid residues other than cysteine, such as, for example serine, threonine, tyrosine, and lysine. Covalent modification of serine hydrolases is also described.

Description

Attorney Docket No.: 3436/2 PCT DESCRIPTION COMPOSITIONS FOR PHOSPHOROUS-AZOLE EXCHANGE CHEMISTRY AND USE THEREOF TO TARGET FUNCTIONAL PROTEIN SITES CROSS REFRENCE TO RELATED APPLICATION 5 This application claims the benefit of U.S. Provisional Patent Application Serial No. 63/645,248, filed May 10, 2024, the disclosure of which is incorporated herein by reference in its entirety. TECHNICAL FIELD The presently disclosed subject matter relates to compounds comprising a phospho-azole 10 electrophile and their ability to undergo phosphorous-azole exchange (PhAzE) with amino acid residues, such as tyrosine, lysine, serine, and threonine residues, in peptides and proteins, to provide covalently modified peptides and proteins. BACKGROUND The ability of covalent therapeutics to permanently bind oncogene proteins and out-compete 15 high affinity substrates or protein-protein interactions has inspired the development of new drug compounds in the pharmaceutical industry. Pharmaceutical companies have typically aimed to ligand cysteine residues in the proteome to inhibit biological function and induce cancer cell death towards oncology. The ability to ligand amino acid residues other than cysteine has been limited by chemistry that can selectively target a particular amino acid side chain. 20 The development of sulfur-fluoride exchange (SuFEx) provided an electrophilic warhead that could bind various additional amino acid residues in the proteome, such as tyrosine, lysine, serine, and threonine. Additionally, the Hsu lab pioneered sulfur-triazole exchange (SuTEx) chemistry for use in covalently modifying peptides and proteins. See PCT International Publication Number WO 2020/214336. SuTEx compounds, which principally target tyrosine and lysine residues in the proteome, 25 can provide useful tools for discovering new functions of amino acids in biology and in developing new covalent therapeutics. However, there remains an ongoing need to develop additional chemistry platforms, e.g., to provide additional electrophilic probes and ligands that can more selectively target serine and threonine residues in the proteome. In addition, there is an ongoing need for compounds that can be tailored to 30 covalently modify serine hydrolases more selectively, e.g., thereby providing for the development of therapeutics directed to serine hydrolases without the toxicity associated with acetylcholinesterase inhibition and other proteins covalently modified by fluorophosphonates. SUMMARY This Summary lists several embodiments of the presently disclosed subject matter, and in many 35 cases lists variations and permutations of these embodiments. This Summary is merely exemplary of the numerous and varied embodiments. Mention of one or more representative features of a given - 1 - Attorney Docket No.: 3436/2 PCT embodiment is likewise exemplary. Such an embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the presently disclosed subject matter, whether listed in this Summary or not. To avoid excessive repetition, this Summary does not list or suggest all possible combinations of such features. 5 In some embodiments, the presently disclosed subject matter provides a compound having a structure of Formula (I): wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; X₁ is selected from -Oˉ, -OR₂, -NR₂R₃, alkyl, substituted alkyl, aralkyl, 10 substituted aralkyl, aryl, and substituted aryl; X₂ is selected from -O-, -OR₂ and -NR₂R₃; R₁ is selected from H, halo, alkyl, perhaloalkyl, aralkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; each R₂ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl, or wherein two R₂ groups together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered 15 phosphorus-containing ring, wherein said bivalent group is optionally substituted and/or fused to a substituted or unsubstituted aromatic ring; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and 20 each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, two of Z₁, Z₂, and Z₃ are N, optionally wherein Z₁ and Z₃ are each N or wherein Z₁ and Z₂ are each N. In some embodiments, X₁ and/or X₂ comprise an alkyne moiety, optionally a terminal alkyne moiety, a fluorophore moiety, or a detectable labeling group, optionally 25 wherein: (i) X₁ or X₂ comprises an r₂ group wherein said R₂ group is an unsaturated alkyl group comprising an alkyne moiety, optionally wherein said R₂ is -CH₂-C^CH; (ii) X₁ or X₂ comprises an r₂ group wherein said R₂ group is selected from substituted alkyl, substituted aralkyl, or substituted aryl, wherein said substituted alkyl, substituted aralkyl, or substituted aryl is an alkyl, aralkyl, or aryl that is substituted with an alkyl or alkoxy group comprising an alkyne moiety, optionally where said alkyl or 30 alkoxy group is -CH₂-C^CH or -O-CH₂-C^CH; (iii) X₁ and X₂ each comprise an r₂ group that together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ - 2 - Attorney Docket No.: 3436/2 PCT groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is substituted with an alkyl or alkoxy group comprising an alkyne moiety, optionally wherein said alkyl or alkoxy group is -CH₂-C^CH or -O-CH₂-C^CH; or (iv) X₁ and X₂ each comprise an r₂ group that together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each 5 of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is fused to a substituted aromatic ring, wherein said substituted aromatic ring is an aromatic ring substituted by an alkyl or alkoxy group comprising an alkyne moiety, optionally wherein said alkyl or alkoxy group is -CH_2-C^CH or -O-CH₂-C^CH. In some embodiments, R₁ is selected from H, phenyl, thiophenyl, furanyl, pyridinyl, and 10 substituted phenyl, wherein said substituted phenyl is phenyl substituted with one or more substituent selected from halo, alkoxy, and perhaloalkoxy, optionally wherein R₁ is phenyl substituted with fluoro or -OCF₃. In some embodiments, the compound of Formula (I) comprises a chiral center and/or wherein X₁ and/or X₂ comprises an alkyne moiety, a fluorophore moiety, or a detectable labeling group. In some embodiments, two R₂ together are a bivalent group that is covalently bonded to an 15 oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is optionally substituted and/or fused to a substituted or unsubstituted aromatic ring; further optionally wherein the compound of Formula (I) has a structure of Formula (II) or Formula (III): 20 wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; X₃ is selected from O and NH; X₄ is selected from O and NR₃; R₁ is - 3 - Attorney Docket No.: 3436/2 PCT selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, - NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; each R₅ is independently selected 5 from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, -S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, aryl and substituted aryl; R₁₁ is selected from H, -C(=O)R₄, -CH₂C(=O)R₄, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and 10 substituted aryl; and R₁₂ and R₁₃ are independently selected from H, -C(=O)R₄, -CH₂C(=O)R₄, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, the compound has a structure of Formula (II) wherein X₃ is O and X₄ is NR₃ and the compound has a structure of Formula (IIa): 15 wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted 20 aryl; each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, -S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, aryl and substituted aryl, optionally H, halo, alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, and 25 aryl. In some embodiments, R₃ is alkyl, optionally a linear or branched C1-C6 saturated alkyl group or a C1-C6 alkyl group comprising a terminal alkyne, further optionally wherein R₃ is -CH₂-C^CH or -CH(CH₃)C(CH₃)₃. In some embodiments, R₃ is selected from -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄, optionally wherein R₄ is selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and 30 substituted aryl, further optionally wherein R₄ is C1-C6 alkyl. - 4 - Attorney Docket No.: 3436/2 PCT In some embodiments, R₆ is H, wherein Z₁ and Z₃ are N and Z₂ is CH, and wherein the compound of Formula (IIa) has a structure of Formula (IIa1): wherein R₁, R₃, R₇, R₈, R₉, and R₁₀ are defined as for Formula (IIa). In some embodiments, at least three 5 of R₇, R₈, R₉, and R₁₀ are H, optionally wherein at least R₇, R₈, and R₁₀ are H, Z₁ and Z₃ are N, and Z₂ is CH, and the compound of Formula (IIa1) has a structure of Formula (IIa2): wherein R₁, R₃, and R₉ are defined as for Formula (IIa). In some embodiments, R₉ is alkoxy, optionally -O-CH₂-C^CH, and R₃ is a linear or branched C1-C6 alkyl group, optionally wherein R₃ comprises a 10 chiral carbon atom. In some embodiments, R₃ is ethyl or -CH(CH₃)C(CH₃)₃. In some embodiments, R₉ is H and the compound of Formula (IIa2) has a structure of Formula (IIa3): wherein R₁ is H, aryl, substituted aryl, heteroaryl, or substituted heteroaryl. In some embodiments, R₁ is H, phenyl, furanyl, thiophenyl, pyridinyl, or substituted phenyl, 15 wherein substituted phenyl is phenyl substituted by one or more substituents selected from halo, alkyl, alkoxy, perfluoroalkyl, and perfluoroalkoxy. In some embodiments, R₁ is selected from phenyl, furanyl, fluoro-substituted phenyl, and trifluoromethoxy-substituted phenyl. In some embodiments, the compound is selected from 3-(prop-2-yn-1-yl)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydro-benzo- [e][1,3,2]oxazaphosphinine 2-oxide (RJG-2259A), 2-(3-phenyl-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-20 yl)-3,4-dihydrobenzo[e][1,3,2]oxaza-phosphinine 2-oxide (RJG-2259B), 3-(prop-2-yn-1-yl)-2-(3-(4- - 5 - Attorney Docket No.: 3436/2 PCT (trifluoromethoxy)phenyl)-1H-1,2,4-triazol-1-yl)-3,4-dihydro-benzo[e][1,3,2]oxazaphosphinine 2- oxide (RJG-2275), 2-(3-(2-fluorophenyl)-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4- dihydrobenzo[e][1,3,2]-oxazaphosphinine 2-oxide (RJG-2276), 2-(3-(furan-2-yl)-1H-1,2,4-triazol-1- yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]-oxazaphosphinine 2-oxide (RJG-2279), 3-((S)-3,3- 5 dimethylbutan-2-yl)-2-(3-phenyl-1H-1,2,4-triazol-1-yl)-7-(prop-2-yn-1-yloxy)-3,4- dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (RJG-2284), 3-ethyl-7-(prop-2-yn-1-yloxy)-2-(1H- 1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza-phosphinine 2-oxide (RJG-2292), and 3‐ cyclopropyl‐2‐(7H‐purin‐7‐yl)‐3,4‐dihydrobenzo[e][1,3,2]oxazaphosphinine 2‐oxide (RJG-3130-9). In some embodiments. 10 In some embodiments, the compound is 3‐cyclopropyl‐2‐(7H‐purin‐7‐yl)‐3,4‐ dihydrobenzo[e][1,3,2]oxazaphosphinine 2‐oxide (RJG-3130-9), which has the following structure: . In some embodiments, the compound has a structure of Formula (II) wherein X₃ is O and X₄ is O and the compound has a structure of Formula (IIb): 15 wherein Z₁, Z₂, Z₃, R₁, R₆, R₇, R₈, R₉, and R₁₀ are as defined for Formula (II). In some embodiments, the compound has a structure of Formula (II) wherein X₃ is NH and X₄ is NR₃ and the compound has a structure of Formula (IIc): - 6 - Attorney Docket No.: 3436/2 PCT wherein Z₁, Z₂, Z₃, R₁, R₃, R₆, R₇, R₈, R₉, and R₁₀ are as defined for Formula (II). In some embodiments, the compound has a structure of Formula (III) wherein X₃ is O and X₄ is NR₃ and the compound has a structure of Formula (IIIa): 5 (IIIa), wherein Z₁, Z₂, Z₃, R₁, R₃, R₁₁, R₁₂, and R₁₃ are as defined for Formula (III). In some embodiments, Z₁ and Z₃ are N and Z₂ is CH. In some embodiments, R₁₁ is selected from -C(=O)R₄ and -CH₂C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from alkyl, substituted alkyl,10 aralkyl, substituted aralkyl, aryl, and substituted aryl; optionally wherein R₁₁ is selected from -C(=O)- OH and -CH₂C(=O)-OH. In some embodiments, R₁₂ and R₁₃ are independently selected from H and C1-C6 alkyl, optionally wherein R₁₂ and R₁₃ are independently selected from H and methyl. In some embodiments, R₃ is H. In some embodiments, the compound has a structure of one of Formulas (IIIa1)- (IIIa4): - 7 - Attorney Docket No.: 3436/2 PCT wherein Z₁, Z₂, Z₃, and R₁ are as defined for Formula (III). In some embodiments, X₁ is selected from -Oˉ and -OR₂, and the compound has a structure of 5 Formula (IVa), (IVb), or (IVc): wherein: Z₁, Z₂, Z₃, and R₁ are as defined for Formula (I); each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₃ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and 10 -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted - 8 - Attorney Docket No.: 3436/2 PCT aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, X₁ is selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and wherein the compound has a structure of Formula (IVd), (IVe), or (IVf): 5 wherein: Z₁, Z₂, Z₃, and R₁ are as defined for Formula (I); each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₃ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted 10 aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, the presently disclosed subject matter provides a method of covalently modifying and/or modulating an activity of a protein, optionally a serine hydrolase, further optionally wherein the serine hydrolase is acetylcholinesterase (ACHE), wherein the method comprises contacting 15 a sample comprising a serine hydrolase with a compound of Formula (I), optionally wherein the sample comprises a cell lysate or a live cell, optionally wherein modulating an activity of a serine hydrolase comprises inhibiting the serine hydrolase. In some embodiments, the presently disclosed subject matter provides a method of identifying a reactive amino acid residue of a protein, wherein the reactive amino acid residue is a tyrosine residue, 20 a lysine residue, a serine residue, or a threonine residue, the method comprising: (a) providing a protein sample comprising isolated proteins, living cells, or a cell lysate; (b) contacting the protein sample with a compound of Formula (I) for a period of time sufficient for the compound to react with at least one reactive tyrosine, lysine, serine, or threonine in a protein in the protein sample, thereby forming at least one modified reactive amino acid residue; and (c) analyzing proteins in the protein sample to identify 25 at least one modified reactive amino acid residue, thereby identifying at least one reactive amino acid residue of a protein; wherein the probe compound has a structure of Formula (I): - 9 - Attorney Docket No.: 3436/2 PCT wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; X₁ is selected from -Oˉ, -OR₂, -NR₂R₃, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; X₂ is selected from -O-, -OR₂ and -NR₂R₃; R₁ is selected 5 from H, halo, alkyl, perhaloalkyl, aralkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl, or wherein two R₂ groups together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is optionally 10 substituted and/or fused to a substituted or unsubstituted aromatic ring; and R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; further wherein one of X₁ and X₂ comprises an 15 alkyne moiety; and wherein the at least one modified reactive amino acid residue comprises a structure of Formula (V): where X₁ and X₂ are as defined for formula (I) and X’ is O or NH. In some embodiments, the probe compound is a compound of Formula (IIa): 20 - 10 - Attorney Docket No.: 3436/2 PCT wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, 5 substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, -S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, 10 aryl and substituted aryl, optionally H, halo, alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, and aryl; wherein one of R₃, R₇, R₈, R₉, and R₁₀ comprises an alkyne moiety; and wherein the at least one modified reactive amino acid residue comprises a structure of Formula (V-IIa): wherein R₃, R₆, R₇, R₈, R₉, and R₁₀ are as defined for formula (IIa) and X’ is O or NH. 15 In some embodiments, the analyzing of step (c) comprises tagging the at least one modified reactive amino acid residue with a compound comprising a detectable labeling group, thereby forming at least one tagged reactive amino acid residue, optionally wherein the detectable labeling group comprises biotin or a biotin derivative. In some embodiments, the tagging comprises reacting a terminal alkyne group in the at least one modified reactive amino acid residue with a compound comprising (i) 20 an azide moiety and (ii) the detectable labeling group, optionally wherein the reacting comprises a copper-catalyzed azide-alkyne cycloaddition (CuAAC) coupling reaction. In some embodiments, the analyzing further comprises digesting the protein sample with trypsin to provide a digested protein sample comprising a protein fragment comprising the at least one tagged reactive amino acid residue. In some embodiments, the analyzing further comprises enriching the digested protein sample for the 25 detectable labeling group, optionally wherein the enriching comprises contacting the digested protein sample with a solid support comprising a binding partner of the detectable labeling group. In some embodiments, the analyzing further comprises analyzing the enriched the digested protein sample via liquid chromatography-mass spectrometry. In some embodiments, providing the protein sample further comprises separating the protein 30 sample into a first protein sample and a second protein sample; contacting the protein sample with a probe compound of Formula (I) comprises contacting the first protein sample with a first probe - 11 - Attorney Docket No.: 3436/2 PCT compound of Formula (I) at a first probe concentration for a first period of time and contacting the second protein sample with one of the group consisting of: (b1) a second probe compound of Formula (I) at the first probe concentration for the first period of time, (b2) the first probe compound of Formula (I) at a second probe concentration for the first period of time, and (b3) the first probe compound of 5 Formula (I) at the first probe concentration for a second period of time; thereby forming at least one modified reactive amino acid residue in said first and/or said second protein sample; and analyzing proteins comprises analyzing the first and second protein samples to determine the presence and/or identity of a modified reactive amino acid residue in the first sample and the presence and/or identity of a modified reactive amino acid residue in the second sample. In some embodiments, the protein 10 sample comprises living cells and wherein providing the protein sample further comprises separating the protein sample into a first protein sample and a second protein sample and culturing the first protein sample in a first cell culture medium comprising heavy isotopes prior to the contacting of step (b), optionally wherein the first cell culture medium comprises ¹³C- and/or ¹⁵N-labeled amino acids, further optionally wherein the first cell culture medium comprises ¹³C-,¹⁵N-labeled lysine and arginine; and 15 culturing the second protein sample in a second cell culture medium, wherein said second cell culture medium comprises a naturally occurring isotope distribution, prior to the contacting of step (b). Accordingly, it is an object of the presently disclosed subject matter to provide phosphorous- azole compounds, e.g., of Formula (I), and related methods of identifying reactive amino acid residues and of covalently modifying and/or modulating an activity of a protein, e.g., a serine hydrolase. This 20 and other objects are achieved in whole or in part by the presently disclosed subject matter. An object of the presently disclosed subject matter having been stated above, other objects and advantages of the presently disclosed subject matter will become apparent to those of ordinary skill in the art after a study of the following description of the presently disclosed subject matter and non- limiting Figures and EXAMPLES. 25 BRIEF DESCRIPTION OF THE FIGURES The presently disclosed subject matter will now be described more fully hereinafter with reference to the accompanying Figures, in which representative embodiments are shown. The presently disclosed subject matter can, however, be embodied in different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this 30 disclosure will be thorough and complete, and will fully convey the scope of the embodiments to those skilled in the art. Certain components in the Figures are not necessarily to scale, emphasis instead being placed upon illustrating the principles of the presently disclosed subject matter (in some cases schematically). Figure 1A is a schematic diagram showing the chemical structures of electrophiles used in 35 preliminary proteome labeling studies to determine the reactivity of phosphorous-azole exchange (PhAzE) compounds. The bottom two compound structures, for RJG-2-259A and RJG-2-259B, - 12 - Attorney Docket No.: 3436/2 PCT represent exemplary PhAzE probe compounds, while the top compound structure, for a previously described sulfonyl-triazole exchange (SuTEx) probe compound, HHS-481, is used as a positive control for broad-level proteome labeling. Figure 1B is an image of gel analysis showing proteomic labeling results of the competition of 5 established electrophiles with phosphorous-azole (PhAzE) compound labeling. Colorectal adenocarcinoma cell (Colo205) soluble lysate (1.0 milligrams per milliliter (mg/ml) was treated with dimethyl sulfoxide (DMSO) or 100 micromolar (^M) inhibitor (i.e., iodoacetamide (IAA), as an exemplary cysteine (Cys)-reactive compound; HHS-482-desthiobiotin (482-DB), as an exemplary tyrosine/lysine (Tyr/Lys)-reactive compound; fluorophosphonate-biotin (FP-B), as an exemplary10 active-site, serine-reactive compound; or tandem mass-tag 0 (TMT-0), as an exemplary terminus/lysine- reactive compound) for 30 minutes at 37°C, and then with RJG-2-259A (100 ^M) of sulfonyl-triazole probe (HHS-481) for 30 minutes at 37°C. HHS-481 labeling was very intense. Thus, labeling results with HHS-481 were cut from the image to better visualize PhAzE labeling. Figure 1C is an image of gel analysis showing proteomic labeling results of the competition of 15 established electrophiles with phosphorous-azole (PhAzE) compound labeling. Colorectal adenocarcinoma cell (Colo205) soluble lysate (1.0 milligrams per milliliter (mg/ml) was treated with dimethyl sulfoxide (DMSO) or 100 micromolar (^M) inhibitor (i.e., iodoacetamide (IAA), as an exemplary cysteine (Cys)-reactive compound; HHS-482-desthiobiotin (482-DB), as an exemplary tyrosine/lysine (Tyr/Lys)-reactive compound; fluorophosphonate-biotin (FP-B), as an exemplary20 active-site, serine-reactive compound; or tandem mass-tag 0 (TMT-0), as an exemplary terminus/lysine- reactive compound) for 30 minutes at 37°C, and then with RJG-2-259B (100 ^M) of sulfonyl-triazole probe (HHS-481) for 30 minutes at 37°C. HHS-481 labeling was very intense and labeling results with HHS-481 were cut from the image to better visualize PhAzE labeling. Figure 2 is an image of gel analysis showing the labeling of human embryonic kidney cell 25 (HEK293T) soluble lysate (1.0 milligrams per milliliter (mg/ml)) treated with dimethyl sulfoxide (DMSO, vehicle) or 100 micromolar (^M) electrophilic probe (RJG-2259A or RJG-2-259B) for 30, 60, 120, or 240 minutes (min). Phosphorous-azole exchange (PhAzE) compound structures are shown to the left of the gel image. Figure 3 is an image of gel analysis showing the labeling of mouse brain proteome (soluble 30 fraction) treated with dimethyl sulfoxide (DMSO, vehicle) or a phosphorous-azole (PhAzE) probe (RJG-2259A or RJG-2-259B) at a concentration of 25 micromolar (^M), 50 ^M or 100 ^M for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 2 ^M) for 30 minutes at 37°C. PhAzE and FP-Rh compound structures are shown to the left of the gel image. Figure 4A is a schematic drawing showing the chemical structures of phosphorous-azole 35 exchange (PhAzE) probe compounds used in live cell (in situ) and in vitro labelling profile studies. The structure of a previously described phosphorous-fluoride (PFEx) probe (2273) is also shown. - 13 - Attorney Docket No.: 3436/2 PCT Figure 4B is a graph showing the number of unique labeling sites and tyrosine to lysine ratio (Y/K ratio) for some of the phosphorous-azole exchange (PhAzE) probe compounds shown in Figure 4A following live cell treatment in human embryonic kidney cells (HEK293T cells) for four hours at 37 °C. 5 Figure 4C is a graph showing the number of unique labeling sites and tyrosine to lysine ratio (Y/K ratio) for the phosphorous-azole exchange (PhAzE) probe compounds shown in Figure 4A following in vitro treatment of human embryonic kidney cells (HEK293T cells) for four hours at 37 °C. Results with the phosphorous-fluoride exchange (PFEx) probe (2273) from Figure 4A are also shown. Figure 5A is a schematic diagram showing the number of unique labeling sites determined for 10 two exemplary phosphorous-azole exchange (PhAzE) probes (RJG-2-259A, RJG-2-259B), a phosphorous-fluoride exchange probe (2273), and a sulfonyl-triazole (SuTEx) probe (HHS-475), as well as the overlap between the unique sites labelled by each probe. Figure 5B is a schematic diagram showing the number of unique proteins labeled by two exemplary phosphorous-azole exchange (PhAzE) probes (RJG-2-259A, RJG-2-259B), a phosphorous- 15 fluoride exchange probe (2273), and a sulfonyl-triazole (SuTEx) probe (HHS-475), as well as the overlap between the proteins labelled by each probe. Figure 6A is a schematic drawing showing the chemical structures of fluorophosphonate-biotin (FP-biotin) and donezepil HCl. Figure 6B is a graph showing the inhibition of acetylcholinesterase (AChE) activity by the20 phosphorous-azole exchange (PhAzE) probes shown in Figure 4A, fluorophosphonate-biotin (FP- Biotin), and donezepil HCl. Results are shown as percent (%) inhibition compared to the log of the nanomolar (nM) concentration of the probe compound. Figure 7 is a volcano plot showing the inhibition of fluorophosphonate probe labeling of acetylcholinesterase (AChE) by fluorophosphonate and phosphorous-azole compounds. 25 Figure 8 is a volcano plot showing the inhibition of fluorophosphonate probe labeling of select serine hydrolases by fluorophosphonate and phosphorous-azole compounds. Points enclosed by a box on the left side of the plot represent serine hydrolases selectively inhibited by PhAzE or PFEx compounds, or points in the upper right of the right side of the plot represent a site on Q61206 that is more enriched due to labeling by PhAzE or PFEx compounds. 30 Figure 9 is an image of gel analysis showing the labeling of N2a cell soluble lysate (1.0 milligrams per milliliter (mg/ml)) treated with vehicle or 100 micromolar (^M) non-alkynyl PhAzE ligands (RJG-3044, RJG-3045, RJG-3048, or RJG-3049) for four hours followed by in vitro labeling competition with FP-Rh (1 µM) for 1 hour at room temperature. Figure 10 is a graph of PhAzE IS 75 kDa band inhibition derived from band intensity in the 35 SDS-PAGE experiment in Figure 9 of non-alkynyl PhAzE ligands RJG-3044, RJG-3045, RJG-3048, or RJG-3049 compared to PhAzE ligand RJG-2273. - 14 - Attorney Docket No.: 3436/2 PCT Figure 11 is a graph showing inhibition of acetylcholinesterase (ACHE) by exemplary PhAzE ligands of the presently disclosed subject matter. Figure 12 is a plot of serine hydrolases inhibited by respective ligands determined by LC- MS/MS using Tandem-Mass Tag (TMT) to quantify inhibition for the insoluble fraction of N2a cells 5 treated with 3044 (dark gray circles) or 3045 (light gray circles). Figure 13 is a plot of serine hydrolases inhibited by respective ligands determined by LC- MS/MS using Tandem-Mass Tag (TMT) to quantify inhibition for the soluble fraction of N2a cells treated with 3044 (dark gray circles) or 3045 (light gray circles). Figure 14 is a plot of serine hydrolases inhibited by respective ligands determined by LC- 10 MS/MS using Tandem-Mass Tag (TMT) to quantify inhibition for the insoluble fraction of N2a cells treated with 3048 (dark gray circles) or 3049 (light gray circles). Figure 15 is a plot of serine hydrolases inhibited by respective ligands determined by LC- MS/MS using Tandem-Mass Tag (TMT) to quantify inhibition for the soluble fraction of N2a cells treated with 3048 (dark gray circles) or 3049 (light gray circles). 15 Figure 16 is a plot of acetylcholinesterase inhibited by respective ligands determined by LC- MS/MS using Tandem-Mass Tag (TMT) to quantify inhibition for the soluble fraction of N2a cells treated with 2273, 3044, 3045, 3048, or 3049. Figure 17 is a gel analysis showing the labeling of mouse brain and heart proteomes (insoluble and soluble fractions) from C57BL/6 mice treated with dimethyl sulfoxide (DMSO, vehicle) or a 20 phosphorous-azole (PhAzE) ligand (RJG-3048) at a concentration of 25 mg/kg for four hours and then with fluorophosphonate-rhodamine (FP-Rh, 2 ^M) for 30 minutes at 37°C. Figure 18A is a bar graph showing APEH inhibition in mouse brain and heart proteomes derived from a biochemical assay for APEH inhibition (insoluble and soluble fractions). Black bars: vehicle. Gray bars: 3048. n.s.: not significant (i.e., p ≥ 0.5). **: p < 0.01. Error bars represent the standard error 25 of the mean, Figure 18B is a bar graph showing ACHE inhibition in mouse brain proteome derived from a biochemical assay for AChE inhibition (insoluble and soluble fractions). Black bars: vehicle. Gray bars: 3048. n.s.: not significant (i.e., p ≥ 0.5). ****: p < 0.001. Error bars represent the standard error of the mean. 30 Figure 19 is a gel analysis showing the labeling of an N2a insoluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 micromolar (^M) to 0.001 µM for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Figure 20 is a plot showing ACHE biochemical inhibition of an N2a insoluble fraction treated 35 with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a - 15 - Attorney Docket No.: 3436/2 PCT concentration of 1 to 0.001 micromolar (^M). PhAzE ligand RJG-3130-2 is the only PhAzE ligand in this experiment that exhibits >50% AChE inhibition at 1 µM. Figure 21 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 5 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Figure 22 is a plot showing ACHE biochemical inhibition of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M). ). PhAzE ligand RJG-3130-2 is the only PhAzE ligand 10 in this experiment that exhibits >50% AChE inhibition at 1 µM. Figures 23A-23D are a series of graphs showing APEH or DPP inhibition in SDS-PAGE ABPP or N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous- azole (PhAzE) probes (3044, 3130-2, 3130-3, 3130-4, 3130-5, and 3130-6) at concentrations of 1 to 0.001 micromolar (^M). Figure 23A shows SDS-PAGE ABPP of APEH. Figure 23B shows APEH 15 inhibition in an N2a soluble fraction. Figure 23C shows SDS-PAGE ABPP of DPP. Figure 23D shows DPP inhibition in an N2a soluble fraction. PhAzE ligands RJG-3044 and 3130-2 are potent inhibitors of APEH and DPPs. Other PhAzE ligands have reduced reactivity with APEH and DPPs. Figure 24 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 20 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were AA74-1, talabostat, 3044, 3130-7, 3130-8, and 3130-9. Figure 25 is a plot showing ACHE biochemical inhibition of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a 25 concentration of 1 to 0.001 micromolar (^M). Figure 26 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were AA74-1, talabostat, 3044, 3130-7, 3130-8, and 30 3130-9. The locations of APEH and DPP species (DPPs) are indicated with arrows. Figures 27A-27D are a series of graphs showing APEH or DPP inhibition in SDS-PAGE ABPP or N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous- azole (PhAzE) probes (AA74-1 and talabostat controls, along with 3044, 3130-7, 3130-8, and 3130-9) at concentrations of 1 to 0.001 micromolar (^M). Figure 27A shows SDS-PAGE ABPP of APEH. 35 Figure 27B shows APEH inhibition in an N2a soluble fraction. Figure 27C shows SDS-PAGE ABPP - 16 - Attorney Docket No.: 3436/2 PCT of DPP. Figure 27D shows DPP inhibition in an N2a soluble fraction. PhAzE ligands RJG-3044 and 3130-9 were potent inhibitors of APEH and DPPs. Figure 28 is a gel analysis showing labeling of N2a soluble fractions treated with dimethyl sulfoxide (DMSO, vehicle) or 3130-9 at a concentration of 1 to 0.001 micromolar (^M) for four hours 5 at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Figure 29 is a graph showing a slight inhibition of ACHE with 3130-9 at a concentration of 1 to 0.001 micromolar (^M). Figure 30 is a gel analysis showing labeling of N2a soluble fractions treated with dimethyl sulfoxide (DMSO, vehicle) or 3130-9 at a concentration of 1 to 0.001 micromolar (^M) for four hours 10 at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Figures 31A-31D are a series of graphs showing APEH or DPP inhibition in N2a soluble fractions treated with dimethyl sulfoxide (DMSO, vehicle) or phosphorous-azole (PhAzE) probe 3130- 9 at concentrations of 1 to 0.001 micromolar (^M). Figure 31A shows APEH inhibition. Figure 31B shows APEH inhibition in an N2a soluble fraction. Figure 31C shows DPP inhibition. Figure 31D 15 shows DPP inhibition in an N2a soluble fraction. Figure 32 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3150-1, 3150-2, 3150-3, 3150-4, 20 3150-5, and 3150-6. Figure 33 is a graph showing a lack of inhibition of ACHE with 3150-1, 3150-2, 3150-3, 3150- 4, 3150-5, and 3150-6. Figure 34 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 25 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3150-1, 3150-2, 3150-3, 3150-4, 3150-5, and 3150-6. Figures 35A-35D are a series of graphs showing APEH or DPP inhibition in SDS-PAGE ABPP or N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous- 30 azole (PhAzE) probes (AA74-1 and talabostat controls, along with PhAzE probes 3150-1, 3150-2, 3150-3, 3150-4, 3150-5, and 3150-6) at concentrations of 1 to 0.001 micromolar (^M). Figure 35A shows SDS-PAGE ABPP of APEH. Figure 35B shows APEH inhibition in an N2a soluble fraction. Figure 35C shows SDS-PAGE ABPP of APEH. Figure 35D shows DPP inhibition in an N2a soluble fraction. 35 Figure 36 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 - 17 - Attorney Docket No.: 3436/2 PCT to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3044, 3130-2, 3130-3, 3130-4, 3130-5, 3130-6, 3130-7, 3130-8, 3130-9 as well as AA74-1, talabostat and PhAZe probes as controls AA75-1 and talabostate. 5 Figure 37 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3150-1, 3150-2, 3150-3, 3150-4, 3150-5, and 3150-6. 10 Figure 38 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3048, 3125L-2, 3125L-3, 3049, 31250D-2, and 3125D-3. 15 Figure 39 is a graph showing weak or missing inhibition of ACHE with PhAzE probes 3048, 3125L-2, 3125L-3, 3049, 3125D-2, and 3125D-3. Figure 40 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 20 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3048, 3135L-2, 3135L-3, 3049, 3135D-2, and 3135D-3. Figures 41A-41D are a series of graphs showing APEH or DPP inhibition in SDS-PAGE ABPP or N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous- azole (PhAzE) probes 3048, 3135L-2, 3135L-3, 3049, 3135D-2, and 3135D-3 at concentrations of 1 to 25 0.001 micromolar (^M). Figure 41A shows SDS-PAGE ABPP of APEH. Figure 41 B shows APEH inhibition in an N2a soluble fraction. Figure 41C shows SDS-PAGE ABPP of APEH. Figure 41D shows DPP inhibition in an N2a soluble fraction. Figure 42 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 30 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3048, 3125L-2, 3125L-3, 3049, 3125D-2, and 3125D-3. Figure 43 is a graph showing a lack of inhibition of ACHE with PhAzE probes 3048, 3125L-2, 3125L-3, 3049, 3125D-2, and 3125D-3. 35 Figure 44 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 - 18 - Attorney Docket No.: 3436/2 PCT to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3048, 3125L-2, 3125L-3, 3049, 3125D-2, and 3125D-3. Figures 45A-45D are a series of graphs showing APEH or DPP inhibition in SDS-PAGE ABPP 5 or N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous- azole (PhAzE) probes 3048, 3125L-4 F1, 3125L-4 F2, 3049, 3125D-4 F1, and 3125D-4 F2 at concentrations of 1 to 0.001 micromolar (^M). Figure 45A shows SDS-PAGE ABPP of APEH. Figure 45B shows APEH inhibition in an N2a soluble fraction. Figure 45C shows SDS-PAGE ABPP of APEH. Figure 45D shows DPP inhibition in an N2a soluble fraction. 10 Figure 46 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3129L, 3129D, 3131L, 3131D, 3132, and 3133. 15 Figure 47 is a graph showing a lack of inhibition of ACHE with PhAzE probes 3129L, 3129D, 3131L, 3131D, 3132, and 3133. Figure 48 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 20 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3129L, 3129D, 3131L, 3131D, 3132, and 3133. Figures 49A-49D are a series of graphs showing APEH or DPP inhibition in SDS-PAGE ABPP or N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous- azole (PhAzE) probes 3129L, 3129D, 3131L, 3131D, 3132, and 3133 at concentrations of 1 to 0.001 25 micromolar (^M). Figure 49A shows SDS-PAGE ABPP of APEH. Figure 49B shows APEH inhibition in an N2a soluble fraction. Figure 49C shows SDS-PAGE ABPP of APEH. Figure 45D shows DPP inhibition in an N2a soluble fraction. Figure 50 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 30 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3048L, 3135L-2, 3135L-3, 3049, 3135L-2, 3135L-3, 3048, 3125L-4-1, 3125-L-4-1, 3125L-4-2, 3049, 3125D-4-1, and 3125D-4-2. Figure 51 is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) probes at a concentration of 1 35 to 0.001 micromolar (^M) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, - 19 - Attorney Docket No.: 3436/2 PCT 1 ^M) for one hour at room temperature. Tested were PhAzE probes 3029L, 3129D, 3131L, 3131D, 3132, and 3133. Figure 52 summarizes the results of in situ PhAzE screen employed to optimize the azole leaving group with respect to APEH and DPP selectivity. Shown are various classes of probes employed 5 and their IC₅₀ values for DPP and APEH. As can be seen, purine analog PhAzE probes 3130-8 and 3130-9 displayed selectivity for DPPs over APEH. Generally, however, most PhAzE probes based on 3044 were potent APEH inhibitors, Figures 53A-53C are graphs showing inhibition of proliferation of Mia-Paca-2 cells (Figure 53A) and of A549 cells (Figure 53B) using various PhAzE probes of the presently disclosed subject 10 matter. The structures of the PhAzE probes tested (i.e., 3044, 3130-9, 3150-3, 3048, and 3131L) as well as control 5-FU are presented in Figure 53C. Figures 54A-54C are graphs showing inhibition of proliferation of THP1 cells (Figure 54A) and of RAW264.7 cells (Figure 54B) using various PhAzE probes of the presently disclosed subject matter. The structures of the PhAzE probes tested (i.e., 3044, 3048, 3150-2, and 3130-9) as well as 15 control talabostat are presented in Figure 54C. Figures 55A-55C summarize the results of testing in situ treatment of THP1 cells and comparing the potency and sites labeled by talabostat and 3130-9. THP1 cells were seeded at about 1 x 10⁸ in 50 mL serum-free RPMI. The final amount of DMSO present was 0.1%. Cells were treated for 4 hours at 37 °C. with the indicated compounds. Figure 55A is a gel showing treatment with vehicle, 1 20 μM talabostat, or 1-1000 nM 3130-9. The location of the APEH band is indicated by arrow. Provided are graphs of the inhibitory activities of the various concentrations of 3130-9 as compared to the vehicle control as determined by SDS-PAGE (Figure 55B) and LC-MS/MS (Figure 55C). Figures 56A-56D summarize the results of testing in situ treatment of THP1 cells and comparing the potency and sites labeled by talabostat and 3130-9. THP1 cells were seeded at about 1 x 25 10⁸ in 50 mL serum-free RPMI. The final amount of DMSO present was 0.1%. Cells were treated for 4 hours at 37 °C. with the indicated compounds. Figure 56A is a gel showing treatment with vehicle, 1 μM talabostat, or 1-1000 nM 3130-9. The location of the APP band is indicated by arrow. Provided are graphs of the inhibitory activities of the various concentrations of 3130-9 as compared to the vehicle control as determined by SDS-PAGE (Figure 56B), LC-MS/MS (Figure 56C), and for 3130-9 on the 30 soluble fraction of the THP1 cells (Figure 56D). Figure 57 is a bar graph showing a comparison of DPP inhibition of talabostat (black bars) and 3130-9 (gray bars) in THP1 cells. Shown are inhibitory activities in the soluble (S) and insoluble (I) fractions with respect to APEH, DPP1, DPP2, DPP3, DPP8, DPP9, PREP, and PRCP. Selective inhibition is indicated by the asterisks. As shown in Figure 57, 3130-9 is a comparable, potent inhibitor 35 of DPP2, DPP8, and DPP9, but also inhibits APEH, PREP, and PRCP. - 20 - Attorney Docket No.: 3436/2 PCT Figure 58 is a gel analysis of in situ treatment of THP1s to determine stereoselectivity of 3130- 9. The 3130-9 were separated, with the individual enantiomers referred to as UTXA-2-027 and UTXA- 2-028. Labeling of a THP1 soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated enantiomer probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C 5 and then with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for four hours at 37 °C. The location of the APEH band is indicated by arrow. Figure 59 is a graph of the results of stereoselective APEH inhibition in live THP1 cells.3130- 9 (Biochem and SDS-PAGE) was compared to UTXA-2-027 (Biochem and SDS-PAGE) and UTXA- 2-028 (Biochem and SDS-PAGE). An approximately 20-fold difference in APEH inhibition was 10 observed as determined by IC₅₀ values. Figure 60 is a gel analysis of in situ treatment of THP1s to determine stereoselectivity of 3130- 9. The 3130-9 were separated, with the individual enantiomers (UTXA-2-027 and UTXA-2-028). Labeling of a THP1 soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated enantiomer probes at a concentration of 1 to 0.001 micromolar (^M) for four hours at 37°C and then 15 with fluorophosphonate-rhodamine (FP-Rh, 1 ^M) for four hours at 37 °C. The location of the DPP band is indicated by arrow. An approximately 20-fold difference in DPP inhibition was observed as determined by IC₅₀ values. The IC₅₀ value of the 028 enantiomer was determined to be approximately 230 pM. Figures 61A-61G summarize the results of in situ treatment of THP1s to determine 20 stereoselectivity of 3130-9 for the DPPs. Figure 61A shows the chemical structures of exemplary PhAzE probes of the presently disclosed subject matter. Figure 61B is a graph showing inhibition of THP1 cell proliferation with the exemplary PhAzE probes. Figure 61C is a graph showing inhibition of THP1 cell proliferation with the exemplary PhAzE probes including enantiomeric versions of 3216. Figures 61D-61F is a series of graphs showing that inhibition of proliferation in RAW264.7, MOLM14, 25 and HEK293T cell lines. Figure 61G is a bar graph showing that (R)3130-9 was a more potent inhibitor of cell proliferation in THP1 and RAW264.7 cancer cell lines. n.s.: not significant. ****: p < 0.001. Figures 62A-62F summarize the results of in situ chiral PhAzE screening showing enantioselective inhibition. Figure 62A is a gel analysis showing the labeling of an N2a soluble fraction treated with dimethyl sulfoxide (DMSO, vehicle) or the indicated phosphorous-azole (PhAzE) 30 enantiomers at a concentration of 1 to 0.001 micromolar (μM) for four hours at 37°C and then with fluorophosphonate-rhodamine (FP-Rh, 1 μM) for one hour at room temperature. Tested were (S) and (R) enantiomers of 2273 and 2259A. Figure 62B is a graph showing soluble ACHE inhibition of the various tests. Figures 62C and 62D are graphs showing ACHE inhibition of the various tests. Figures 62E and 62F are graphs showing DPP inhibition of the various tests. 35 Figure 63 is a graph of ACHE inhibition of (S) and (R) enantiomers of 2273 and 2259A. Figure 64 is a graph of FAAH inhibition of (S) and (R) enantiomers of 2273 and 2259A. - 21 - Attorney Docket No.: 3436/2 PCT Figures 65A-65G summarize the results of testing 3130-9 for activity in inhibiting DPP8/9. Figure 65A shows the chemical structure and covalent mechanism of 313-9 binding to the active site serine of DPP9. Figure 65B is a graph showing dose-dependent biochemical assays in live N2a cells. Figure 65C is a bar graph of LC-MS/MS based ABPP showing selective inhibition of DPP8/9. Figure 5 65D is a graph showing that 3130-9 treatment blocked proliferation in THP1, RAW264.7, and A549 cancer cell lines. Figure 65E is a schematic depiction of chiral PhAzE probes and their potential utilities. Figure 65F is a bar graph of LC-MS/MS based ABPP showing enantioselective, ultrapotent inhibition of DPPs. Figure 65G is a bar graph showing that (R)3130-9 was a more potent inhibitor of cell proliferation in THP1 and RAW264.7 cancer cell lines. n.s.: not significant. ****: p < 0.001. 10 Figures 66A and 66B show the results of testing ACHE inhibition with PhAzE compared to PFEx. Figure 66A is a diagram of an exemplary testing strategy for comparing ACHE inhibitory activities of PhAzE probes as compared to PFEx probes. Figure 66B is a graph showing the results of the testing. It was determined that PFEx compound 2273 was the best inhibitor of ACHE probe labeling followed by 2259A and 2279. 15 Figure 67 is a plot showing PhAzE labeling of exemplary serine hydrolases. Tandem-Mass Tag (TMT) was employed to identify exemplary serine hydrolases selectively labeled by PhAzE compounds. These included UniProt Accession No. Q8R146 (Acylamino-acid-releasing enzyme (ACPH)), which hydrolyzes N-terminal peptide bonds of N-acetylated peptides UniProt Accession No. Q8BVG4 (Dipeptidyl peptidase 9 (DPP9)), which cleaves off N-terminal dipeptides from proteins 20 having a Pro or Ala residue at position 2, and Uniprot Accession No. Q61206 (Platelet-activating factor acetylhydrolase IB subunit alpha2 (PA1B2)), which hydrolyzes the acetyl group at the sn-2 position of platelet-activating factor (PAF) and its analogs to modulate the action of PAF. It was determined that PhAzE and PFEx probes labeled UniProt Accession No. Q8R146, but PhAzE probes selectively labeled the other two serine hydrolases. 25 Figure 68 is a summary of PhAzE probe binding to the exemplary serine protease DPP9, which can be labeled 2279, 2292, 3025, and 3026, among others. DETAILED DESCRIPTION In some embodiments, the presently disclosed subject matter utilizes phosphorous-azole exchange (PhAzE) to covalently modify compounds comprising nucleophiles, e.g., nucleophilic 30 functional groups in biomolecules such as proteins or RNA. In some embodiments, the electrophilic warhead of the PhAzE compound comprises a phospho-triazole. By providing increased selectivity and/or reduced activity, in some embodiments, the electrophilic phosphorous of the PhAzE compounds can be capable of reacting with amino acids in the proteome without the inherent toxicity associated with fluorophosphonate compounds or with reduced toxicity compared to fluorophosphonate 35 compounds. The adduct formed between the phosphorous of a PhAzE compound and an amino acid can, in some embodiments, be considered as comparable to the phosphorylation post-translational - 22 - Attorney Docket No.: 3436/2 PCT modification that is responsible for facilitating many biological processes, such as signal transduction. Competition studies were performed using activity-based protein profiling with SDS-PAGE and it was found that fluorophosphonate-biotin and HHS-482-desthiobiotin, which bind active site serines or functional tyrosines and lysines, respectively, compete PhAzE binding sites, suggesting that PhAzE 5 binds serines, threonines, and tyrosines. The binding sites of PhAzE probes were characterized as mostly tyrosine and lysine using tandem liquid chromatography/mass spectrometry (LC-MS/MS). Assignment of serine/threonine adducts with fluorophosphonate probes is historically difficult. In some embodiments, the PhAzE compounds described herein include a phospho center (P=O) bound to a nitrogen and oxygen that are substituted to make a 6-membered ring containing the phosphor 10 center. In some embodiments, the leaving group is a 1,2,4-triazole with or without substitutions (e.g., aryl substitutions) at the 3-position. In some embodiments, an aryl group bound to the 6-membered ring containing the phospho moiety can be unsubstituted or can include a propargyl ether substitution at the 5-position. Substitutions on the nitrogen bound to the phosphor center include propargyl, ethyl, or 3,3- dimethylbutan-2-yl, the latter of which is a chiral center (S-enantiomer). 15 PhAzE compounds are cell permeable. No apparent toxicity/cell death was observed with live cell treatments at concentrations as high as 100 µM. Thus, it appears that PhAzE compounds can be used in live cells or animals with relative safety. Accordingly, the presently disclosed PhAzE compounds can provide several advantages compared to previously described electrophile probes. In particular, although fluorophosphonates are 20 well established in the field of chemical biology as highly stable probes that selectively react with active-site serines in serine hydrolase proteins, they are potent inhibitors of acetylcholinesterase (AChE), limiting their application in drug discovery. As described herein, the presently disclosed PhAzE compounds are significantly less reactive with AChE compared to comparable fluorophosphonates. The PhAzE compounds are also reactive with other amino acid residues, e.g., 25 tyrosine, which is rarely reported with fluorophosphonates. In addition, the leaving group of the PhAzE compounds, e.g., a triazole group, can be modified to target amino acids other than active site serine residues, while other portions of the PhAze compound can be modified to modulate reactivity. For example, in some embodiments, the PhAzE compounds can include phospho center substituents to sterically hinder the electrophilic phosphorous center, e.g., by forming a ring including the phosphor 30 center. Alternatively, steric hindrance can be reduced, e.g., by the use of substituents on the phosphor center that do not form cyclic structures with the phosphorous center, to increase reactivity of the PhAzE compound. In some embodiments, the PhAzE compounds can include a chiral center, thereby providing a scaffold to generate chiral electrophiles to target particular sites based on their chirality. The presently disclosed subject matter will now be described more fully hereinafter with 35 reference to the accompanying Figures and EXAMPLES, in which representative embodiments are shown. The presently disclosed subject matter can, however, be embodied in different forms and should - 23 - Attorney Docket No.: 3436/2 PCT not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the embodiments to those skilled in the art. Certain components in the figures are not necessarily to scale, emphasis instead being placed upon illustrating the principles of the presently disclosed subject matter 5 (in some cases schematically). Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the presently described subject matter belongs. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. 10 Throughout the specification and claims, a given chemical formula or name shall encompass all active optical and stereoisomers, as well as racemic mixtures where such isomers and mixtures exist. I. Definitions The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the presently disclosed subject matter. 15 While the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate explanation of the presently disclosed subject matter. Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including in the claims. For example, the phrase “a protein” refers to one or more proteins, including a plurality of the same protein. Similarly, the phrase “at least one”, 20 when employed herein to refer to an entity, refers to, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, or more of that entity, including but not limited to whole number values between 1 and 100 and greater than 100. Unless otherwise indicated, all numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in 25 all instances by the term “about”. The term “about”, as used herein when referring to a measurable value such as an amount of mass, weight, time, volume, concentration, or percentage, is meant to encompass variations of in some embodiments ±20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, in some embodiments ±0.5%, and in some embodiments ±0.1 % from the specified amount, as such variations are appropriate to perform the disclosed methods and/or employ 30 the disclosed compositions. Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by the presently disclosed subject matter. As used herein, the term “and/or” when used in the context of a list of entities, refers to the entities being present singly or in combination. Thus, for example, the phrase “A, B, C, and/or D” 35 includes A, B, C, and D individually, but also includes any and all combinations and subcombinations of A, B, C, and D. - 24 - Attorney Docket No.: 3436/2 PCT The term “comprising”, which is synonymous with “including” “containing”, or “characterized by”, is inclusive or open-ended and does not exclude additional, unrecited elements and/or method steps. “Comprising” is a term of art that means that the named elements and/or steps are present, but that other elements and/or steps can be added and still fall within the scope of the relevant subject 5 matter. As used herein, the phrase “consisting essentially of” limits the scope of the related disclosure or claim to the specified materials and/or steps, plus those that do not materially affect the basic and novel characteristic(s) of the disclosed and/or claimed subject matter. For example, a pharmaceutical composition can “consist essentially of” a pharmaceutically active agent or a plurality of 10 pharmaceutically active agents, which means that the recited pharmaceutically active agent(s) is/are the only pharmaceutically active agent(s) present in the pharmaceutical composition. It is noted, however, that carriers, excipients, and/or other inactive agents can and likely would be present in such a pharmaceutical composition and are encompassed within the nature of the phrase “consisting essentially of”. 15 As used herein, the phrase “consisting of” excludes any element, step, or ingredient not specifically recited. It is noted that, when the phrase “consists of” appears in a clause of the body of a claim, rather than immediately following the preamble, it limits only the element set forth in that clause; other elements are not excluded from the claim as a whole. With respect to the terms “comprising”, “consisting of”, and “consisting essentially of”, where 20 one of these three terms is used herein, the presently disclosed and claimed subject matter can include the use of either of the other two terms. For example, a composition that in some embodiments comprises a given active agent also in some embodiments can consist essentially of that same active agent, and indeed can in some embodiments consist of that same active agent. The terms “additional therapeutically active compound” and “additional therapeutic agent”, as 25 used in the context of the presently disclosed subject matter, refers to the use or administration of a compound for an additional therapeutic use for a particular injury, disease, or disorder being treated. Such a compound, for example, could include one being used to treat an unrelated disease or disorder, or a disease or disorder which may not be responsive to the primary treatment for the injury, disease, or disorder being treated. 30 As used herein, the terms “administration of” and/or “administering” a compound should be understood to refer to providing a compound of the presently disclosed subject matter to a subject in need of treatment. The term “aqueous solution” as used herein can include other ingredients commonly used, such as sodium bicarbonate described herein, and further includes any acid or base solution used to adjust 35 the pH of the aqueous solution while solubilizing a peptide. - 25 - Attorney Docket No.: 3436/2 PCT The term “binding” refers to the adherence of molecules to one another, such as, but not limited to, enzymes to substrates, ligands to receptors, antibodies to antigens, DNA binding domains of proteins to DNA, and DNA or RNA strands to complementary strands. “Binding partner”, as used herein, refers to a molecule capable of binding to another molecule. 5 The term “biocompatible”, as used herein, refers to a material that does not elicit a substantial detrimental response in the host. As used herein, the terms “biologically active fragment” and “bioactive fragment” of a peptide encompass natural and synthetic portions of a longer peptide or protein that are capable of specific binding to their natural ligand and/or of performing a desired function of a protein, for example, a 10 fragment of a protein of larger peptide which still contains the epitope of interest and is immunogenic. The term “biological sample”, as used herein, refers to samples obtained from a subject, including but not limited to skin, hair, tissue, blood, plasma, cells, sweat, and urine. A “control” cell, tissue, sample, or subject is a cell, tissue, sample, or subject of the same type as a test cell, tissue, sample, or subject. The control may, for example, be examined at precisely or 15 nearly the same time the test cell, tissue, sample, or subject is examined. The control may also, for example, be examined at a time distant from the time at which the test cell, tissue, sample, or subject is examined, and the results of the examination of the control may be recorded so that the recorded results may be compared with results obtained by examination of a test cell, tissue, sample, or subject. The control may also be obtained from another source or similar source other than the test group or a test 20 subject, where the test sample is obtained from a subject suspected of having a condition, disease, or disorder for which the test is being performed. A “test” cell is a cell being examined. A “pathogenic” cell is a cell that, when present in a tissue, causes or contributes to a condition, disease, or disorder in the animal in which the tissue is located (or from which the tissue was obtained). 25 A tissue “normally comprises” a cell if one or more of the cell are present in the tissue in an animal not afflicted with a condition, disease, or disorder. As used herein, the terms “condition”, “disease condition”, “disease”, “disease state”, and “disorder” refer to physiological states in which diseased cells or cells of interest can be targeted with the compositions of the presently disclosed subject matter. 30 As used herein, the term “diagnosis” refers to detecting a risk or propensity to a condition, disease, or disorder. In any method of diagnosis exist false positives and false negatives. Any one method of diagnosis does not provide 100% accuracy. A “disease” is a state of health of an animal wherein the animal cannot maintain homeostasis, and wherein if the disease is not ameliorated then the animal’s health continues to deteriorate. 35 In contrast, a “disorder” in an animal is a state of health in which the animal is able to maintain homeostasis, but in which the animal’s state of health is less favorable than it would be in the absence - 26 - Attorney Docket No.: 3436/2 PCT of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal’s state of health. As used herein, an “effective amount” or “therapeutically effective amount” refers to an amount of a compound or composition sufficient to produce a selected effect, such as but not limited to 5 alleviating symptoms of a condition, disease, or disorder. In the context of administering compounds in the form of a combination, such as multiple compounds, the amount of each compound, when administered in combination with one or more other compounds, may be different from when that compound is administered alone. Thus, an effective amount of a combination of compounds refers collectively to the combination as a whole, although the actual amounts of each compound may vary. 10 The term “more effective” means that the selected effect occurs to a greater extent by one treatment relative to the second treatment to which it is being compared. As used herein, an “essentially pure” preparation of a particular protein or peptide is a preparation wherein in some embodiments at least about 95% and in some embodiments at least about 99%, by weight, of the protein or peptide in the preparation is the particular protein or peptide. 15 In some embodiments, the terms “fragment”, “segment”, or “subsequence” as used herein refers to a portion of an amino acid sequence, comprising at least one amino acid, or a portion of a nucleic acid sequence comprising at least one nucleotide. Thus, in some embodiments, the terms “fragment”, “segment”, and “subsequence” are used interchangeably herein. In some embodiments, the term “fragment” refers to a compound (e.g., a small molecule compound, such as a PhAzE compound as 20 described herein) that can react with a reactive amino acid residue (e.g., a reactive tyrosine or lysine residue in a peptide or protein) to form an adduct comprising a modified amino acid residue. Thus, in some embodiments, the terms “fragment” and “ligand” are used interchangeably. In some embodiments, the term “fragment” refers to that portion of a PhAzE compound that remains covalently attached to the amino acid residue. 25 As used herein, a “ligand” is an entity (e.g., a molecule) that specifically or selectively binds to or “is specifically or selectively reactive with a second entity (e.g., a biomolecule, such as a peptide, protein, nucleic acid, lipid, etc.) when the ligand functions in a binding reaction which is determinative of the presence of the second entity in a heterogenous sample (i.e., a sample comprising a plurality of different entities, such as a plurality of different biomolecules). As used herein, in some embodiments, 30 “ligand” can refer to a synthetic molecule (e.g., a PhAzE compound) that binds to a target compound or molecule, such as a reactive nucleophilic amino acid residue in a peptide or protein. As used herein, a “functional” biological molecule is a biological molecule in a form in which it exhibits a property by which it can be characterized. A functional enzyme, for example, is one that exhibits the characteristic catalytic activity by which the enzyme can be characterized. 35 As used herein “injecting”, “applying”, and administering” include administration of a compound of the presently disclosed subject matter by any number of routes and modes including, but - 27 - Attorney Docket No.: 3436/2 PCT not limited to, topical, oral, buccal, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, vaginal, ophthalmic, pulmonary, vaginal, and rectal approaches. As used herein, the term “linkage” refers to a connection between two groups. The connection 5 can be either covalent or non-covalent, including but not limited to ionic bonds, hydrogen bonding, and hydrophobic/hydrophilic interactions. As used herein, the term “linker” refers to a molecule that joins two other molecules either covalently or noncovalently, such as but not limited to through ionic or hydrogen bonds or van der Waals interactions. 10 The terms “measuring the level of expression” and “determining the level of expression” as used herein refer to any measure or assay which can be used to correlate the results of the assay with the level of expression of a gene or protein of interest. Such assays include measuring the level of mRNA, protein levels, etc. and can be performed by assays such as northern and western blot analyses, binding assays, immunoblots, etc. The level of expression can include rates of expression and can be 15 measured in terms of the actual amount of an mRNA or protein present. Such assays are coupled with processes or systems to store and process information and to help quantify levels, signals, etc. and to digitize the information for use in comparing levels. The term “modulating an activity of” as used herein refers to changing one or more biological activities of a peptide or protein. In some embodiments, the modulating can refer to increasing or 20 decreasing a biological activity (e.g., binding, enzymatic activity, etc.) of a peptide or protein. For example, modulating can refer to inhibiting a biological activity of a peptide or protein or activating a biological activity of a peptide or protein. The term “otherwise identical sample”, as used herein, refers to a sample similar to a first sample, that is, it is obtained in the same manner from the same subject from the same tissue or fluid, 25 or it refers a similar sample obtained from a different subject. The term “otherwise identical sample from an unaffected subject” refers to a sample obtained from a subject not known to have the disease or disorder being examined. The sample may of course be a standard sample. By analogy, the term “otherwise identical” can also be used regarding regions or tissues in a subject or in an unaffected subject. 30 As used herein, “parenteral administration” of a pharmaceutical composition includes any route of administration characterized by physical breaching of a tissue of a subject and administration of the pharmaceutical composition through the breach in the tissue. Parenteral administration thus includes, but is not limited to, administration of a pharmaceutical composition by injection of the composition, by application of the composition through a surgical incision, by application of the composition through 35 a tissue-penetrating non-surgical wound, and the like. In particular, parenteral administration is - 28 - Attorney Docket No.: 3436/2 PCT contemplated to include, but is not limited to, subcutaneous, intraperitoneal, intramuscular, intrasternal injection, and kidney dialytic infusion techniques. The term “pharmaceutical composition” refers to a composition comprising at least one active ingredient, whereby the composition is amenable to investigation for a specified, efficacious outcome 5 in a mammal (for example, without limitation, a human). Those of ordinary skill in the art will understand and appreciate the techniques appropriate for determining whether an active ingredient has a desired efficacious outcome based upon the needs of the artisan. “Pharmaceutically acceptable” means physiologically tolerable, for either human or veterinary application. Similarly, “pharmaceutical compositions” include formulations for human and veterinary 10 use. As used herein, the term “pharmaceutically acceptable carrier” means a chemical composition with which an appropriate compound or derivative can be combined and which, following the combination, can be used to administer the appropriate compound to a subject. As used herein, the term “physiologically acceptable” ester or salt means an ester or salt form 15 of the active ingredient which is compatible with any other ingredients of the pharmaceutical composition, which is not deleterious to the subject to which the composition is to be administered. “Plurality” means at least two. As used herein, the term “mass spectrometry” (MS) refers to a technique for the identification and/or quantitation of molecules in a sample. MS includes ionizing the molecules in a sample, forming 20 charged molecules; separating the charged molecules according to their mass-to-charge ratio; and detecting the charged molecules. MS allows for both the qualitative and quantitative detection of molecules in a sample. The molecules can be ionized and detected by any suitable means known to one of skill in the art. Some examples of mass spectrometry are “tandem mass spectrometry” or “MS/MS,” which are the techniques wherein multiple rounds of mass spectrometry occur, either simultaneously 25 using more than one mass analyzer or sequentially using a single mass analyzer. The term “mass spectrometry” can refer to the application of mass spectrometry to protein analysis. In some embodiments, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) can be used in this context. In some embodiments, intact protein molecules can be ionized by the above techniques, and then introduced to a mass analyzer. Alternatively, protein molecules can be broken 30 down into smaller peptides, for example, by enzymatic digestion by a protease, such as trypsin. Subsequently, the peptides are introduced into the mass spectrometer and identified by peptide mass fingerprinting or tandem mass spectrometry. As used herein, the term “mass spectrometer” is used to refer an apparatus for performing mass spectrometry that includes a component for ionizing molecules and detecting charged molecules. 35 Various types of mass spectrometers can be employed in the methods of the presently disclosed subject matter. For example, whole protein mass spectroscopy analysis can be conducted using time-of-flight - 29 - Attorney Docket No.: 3436/2 PCT (TOF) or Fourier transform ion cyclotron resonance (FT-ICR) instruments. For peptide mass analysis, MALDI time-of-flight instruments can be employed, as they permit the acquisition of peptide mass fingerprints (PMFs) at high pace. Multiple stage quadrupole-time-of-flight and the quadrupole ion trap instruments can also be used. 5 The terms “high throughput protein identification,” “proteomics” and other related terms are used herein to refer to the processes of identification of a large number or (in some cases, all) proteins in a certain protein complement. Post-translational protein modifications and quantitative information can also be assessed by such methods. One example of “high throughput protein identification” is a gel- based process that includes the pre-fractionation and purification of proteins by one-dimensional protein 10 gel electrophoresis. The gel can then be fractionated into several molecular weight fractions to reduce sample complexity, and proteins can be in-gel digested with trypsin. The tryptic peptides are extracted from the gel, further fractionated by liquid chromatography, and analyzed by mass spectrometry. In another approach, a sample can be fractionated without using the gels, for example, by protein extraction followed by liquid chromatography. The proteins can then be digested in-solution, and the 15 proteolytic fragments further fractionated by liquid chromatography and analyzed by mass spectrometry. As used herein, the term “Western blot,” which can be also referred to as “immunoblot”, and related terms refer to an analytical technique used to detect specific proteins in a sample. The technique uses gel electrophoresis to separate the proteins, which are then transferred from the gel to a membrane 20 (typically nitrocellulose or PVDF) and stained, in membrane, with antibodies specific to the target protein. The expression “stable isotope labeling by amino acids in cell culture” (SILAC) is used herein to refer to an approach for incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC comprises metabolic incorporation of a given “light” or “heavy” form 25 of the amino acid into the proteins. For example, SILAC comprises the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, ¹³C, ¹⁵N). In an illustrative SILAC experiment, two cell populations are grown in culture media that are identical, except that one of them contains a “light” and the other a “heavy” form of a particular amino acid (for example, ¹²C and ¹³C labeled L- lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of 30 the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of the amino acid is replaced by its isotope-labeled analog. Since there is little chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave substantially similar to the control cell population grown in the presence of a normal amino acid. 35 The term “prevent” as used herein means to stop something from happening, or taking advance measures against something possible or probable from happening. In the context of medicine, - 30 - Attorney Docket No.: 3436/2 PCT “prevention” generally refers to action taken to decrease the chance of getting a disease or condition. It is noted that “prevention” need not be absolute, and thus can occur as a matter of degree. A “preventive” or “prophylactic” treatment is a treatment administered to a subject who does not exhibit signs, or exhibits only early signs, of a condition, disease, or disorder. A prophylactic or 5 preventative treatment is administered for the purpose of decreasing the risk of developing pathology associated with developing the condition, disease, or disorder. “Polypeptide” refers to a polymer composed of amino acid residues, related naturally occurring structural variants, and synthetic non-naturally occurring analogs thereof linked via peptide bonds, related naturally occurring structural variants, and synthetic non-naturally occurring analogs thereof. 10 “Synthetic peptides or polypeptides” refers to non-naturally occurring peptides or polypeptides. Synthetic peptides or polypeptides can be synthesized, for example, using an automated polypeptide synthesizer. Various solid phase peptide synthesis methods are known to those of skill in the art. The term “protein” typically refers to large polypeptides (e.g., greater than 50 amino acid residues). Conventional notation is used herein to portray polypeptide sequences: the left-hand end of 15 a polypeptide sequence is the amino-terminus; the right-hand end of a polypeptide sequence is the carboxyl-terminus. As used herein, the term “peptide” refers to smaller polypeptides, e.g., having 2 to about 50 amino acid residues (e.g., about 5 to 50 amino acid or 10 to 50 amino acid residues). The term “amino acid residue” refers to a moiety resulting from the incorporation of an amino 20 acid into a polypeptide, e.g., a moiety having the structure -NH-CH(R)-C(=O)-, where R corresponds to the side chain of the amino acid from which the residue originates. The term “proteome” refers to the entire set of proteins expressed by a genome, cell, tissue, or organism at a particular time and/or under particular conditions. As used herein, the term “purified” and like terms relate to an enrichment of a molecule or 25 compound relative to other components normally associated with the molecule or compound in a native environment. The term “purified” does not necessarily indicate that complete purity of the particular molecule has been achieved during the process. A “highly purified” compound as used herein refers to a compound that is in some embodiments greater than 90% pure, that is in some embodiments greater than 95% pure, and that is in some 30 embodiments greater than 98% pure. As used herein, the term “mammal” refers to any member of the class Mammalia, including, without limitation, humans, and nonhuman primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats, and horses; domestic mammals such as dogs and cats; laboratory animals including rodents such as mice, rats and guinea pigs, and the like. The term 35 does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be included within the scope of this term. - 31 - Attorney Docket No.: 3436/2 PCT The term “subject” as used herein refers to a member of species for which treatment and/or prevention of a disease or disorder using the compositions and methods of the presently disclosed subject matter might be desirable. Accordingly, the term “subject” is intended to encompass in some embodiments any member of the Kingdom Animalia including, but not limited to the phylum Chordata 5 (e.g., members of Classes Osteichthyes (bony fish), Amphibia (amphibians), Reptilia (reptiles), Aves (birds), and Mammalia (mammals), and all Orders and Families encompassed therein. The compositions and methods of the presently disclosed subject matter are particularly useful for warm-blooded vertebrates. Thus, in some embodiments the presently disclosed subject matter concerns mammals and birds. More particularly provided are compositions and methods derived from 10 and/or for use in mammals such as humans and other primates, as well as those mammals of importance due to being endangered (such as Siberian tigers), of economic importance (animals raised on farms for consumption by humans) and/or social importance (animals kept as pets or in zoos) to humans, for instance, carnivores other than humans (such as cats and dogs), swine (pigs, hogs, and wild boars), ruminants (such as cattle, oxen, sheep, giraffes, deer, goats, bison, and camels), rodents (such as mice, 15 rats, and rabbits), marsupials, and horses. Also provided is the use of the disclosed methods and compositions on birds, including those kinds of birds that are endangered, kept in zoos, as well as fowl, and more particularly domesticated fowl, e.g., poultry, such as turkeys, chickens, ducks, geese, guinea fowl, and the like, as they are also of economic importance to humans. Thus, also provided is the use of the disclosed methods and compositions on livestock, including but not limited to domesticated swine 20 (pigs and hogs), ruminants, horses, poultry, and the like. A “sample”, as used herein, refers in some embodiments to a biological sample from a subject, including, but not limited to, normal tissue samples, diseased tissue samples, biopsies, blood, saliva, feces, semen, tears, and urine. A sample can also be any other source of material obtained from a subject which contains proteins, cells, tissues, or fluid of interest. A sample can also be obtained from cell or 25 tissue culture. The term “standard”, as used herein, refers to something used for comparison. For example, it can be a known standard agent or compound which is administered and used for comparing results when administering a test compound, or it can be a standard parameter or function which is measured to obtain a control value when measuring an effect of an agent or compound on a parameter or function. 30 Standard can also refer to an “internal standard”, such as an agent or compound which is added at known amounts to a sample and is useful in determining such things as purification or recovery rates when a sample is processed or subjected to purification or extraction procedures before a marker of interest is measured. Internal standards are often a purified marker of interest which has been labeled, such as with a radioactive isotope, allowing it to be distinguished from an endogenous marker. 35 A “subject” of analysis, diagnosis, or treatment is an animal. Such animals include mammals, in some embodiments, humans. - 32 - Attorney Docket No.: 3436/2 PCT As used herein, a “subject in need thereof” is a patient, animal, mammal, or human, who will benefit from the method of this presently disclosed subject matter. The term “substantially pure” describes a compound, e.g., a protein or polypeptide, which has been separated from components which naturally accompany it. Typically, a compound is substantially 5 pure when in some embodiments at least 10%, in some embodiments at least 20%, in some embodiments at least 50%, in some embodiments at least 60%, in some embodiments at least 75%, in some embodiments at least 90%, and in some embodiments at least 99% of the total material (by volume, by wet or dry weight, or by mole percent or mole fraction) in a sample is the compound of interest. Purity can be measured by any appropriate method, e.g., in the case of polypeptides by column 10 chromatography, gel electrophoresis, or HPLC analysis. A compound, e.g., a protein, is also substantially purified when it is essentially free of naturally associated components or when it is separated from the native contaminants which accompany it in its natural state. The term “symptom”, as used herein, refers to any morbid phenomenon or departure from the normal in structure, function, or sensation, experienced by the patient and indicative of disease. In 15 contrast, a “sign” is objective evidence of disease. For example, a bloody nose is a sign. It is evident to the patient, doctor, nurse, and other observers. A “therapeutic” treatment is a treatment administered to a subject who exhibits signs of pathology for the purpose of diminishing or eliminating those signs. A “therapeutically effective amount” of a compound is that amount of compound which is 20 sufficient to provide a beneficial effect to the subject to which the compound is administered. As used herein, the phrase “therapeutic agent” refers to an agent that is used to, for example, treat, inhibit, prevent, mitigate the effects of, reduce the severity of, reduce the likelihood of developing, slow the progression of, and/or cure, a disease or disorder. The terms “treatment” and “treating” as used herein refer to both therapeutic treatment and 25 prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition, prevent the pathologic condition, pursue or obtain beneficial results, and/or lower the chances of the individual developing a condition, disease, or disorder, even if the treatment is ultimately unsuccessful. Those in need of treatment include those already with the condition as well as those prone to have or predisposed to having a condition, disease, or disorder, or those in 30 whom the condition is to be prevented. All genes, gene names, and gene products disclosed herein are intended to correspond to homologs and/or orthologs from any species for which the compositions and methods disclosed herein are applicable. Thus, the terms include, but are not limited to genes and gene products from humans and mice. It is understood that when a gene or gene product from a particular species is disclosed, this 35 disclosure is intended to be exemplary only, and is not to be interpreted as a limitation unless the context in which it appears clearly indicates. - 33 - Attorney Docket No.: 3436/2 PCT As used herein the term “alkyl” refers to C1-C20 inclusive, linear (i.e., “straight-chain”), branched, or cyclic, saturated or at least partially and in some cases fully unsaturated (i.e., alkenyl and alkynyl) hydrocarbon chains, including for example, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tert-butyl, pentyl, hexyl, octyl, ethenyl, propenyl, butenyl, pentenyl, hexenyl, octenyl, butadienyl, 5 propynyl, butynyl, pentynyl, hexynyl, heptynyl, and allenyl groups. “Branched” refers to an alkyl group in which a lower alkyl group, such as methyl, ethyl or propyl, is attached to a linear alkyl chain. In some embodiments, the alkyl group is “lower alkyl.” “Lower alkyl” refers to an alkyl group having 1 to about 8 carbon atoms (i.e., a C1-C8 alkyl), e.g., 1, 2, 3, 4, 5, 6, 7, or 8 carbon atoms. In some embodiments, the alkyl is “higher alkyl.” “Higher alkyl” refers to an alkyl group having about 10 to about 20 carbon 10 atoms, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 carbon atoms. In certain embodiments, “alkyl” refers, in particular, to C1-C8 straight-chain alkyls. In other embodiments, “alkyl” refers, in particular, to C1-C8 branched-chain alkyls. Alkyl groups can optionally be substituted (a “substituted alkyl”) with one or more alkyl group substituents, which can be the same or different. The term “alkyl group substituent” includes but is not 15 limited to alkyl, substituted alkyl, halo, arylamino, acyl, hydroxyl, aryloxyl, alkoxyl, alkylthio, arylthio, aralkyloxyl, aralkylthio, carboxyl, alkoxycarbonyl, oxo, and cycloalkyl. There can be optionally inserted along the alkyl chain one or more oxygen, sulfur or substituted or unsubstituted nitrogen atoms, wherein the nitrogen substituent is hydrogen, lower alkyl (also referred to herein as “alkylaminoalkyl”), or aryl. 20 Thus, as used herein, the term “substituted alkyl” includes alkyl groups, as defined herein, in which one or more atoms or functional groups of the alkyl group are replaced with another atom or functional group, including for example, alkyl, substituted alkyl, halogen, aryl, substituted aryl, alkoxyl, hydroxyl, nitro, amino, alkylamino, dialkylamino, sulfate, and mercapto. The term “aryl” is used herein to refer to an aromatic moiety that can be a single aromatic ring, 25 or multiple aromatic rings that are fused together, linked covalently, or linked to a common group, such as, but not limited to, a methylene or ethylene moiety. The common linking group also can be a carbonyl, as in benzophenone, or oxygen, as in diphenylether, or nitrogen, as in diphenylamine. The term “aryl” specifically encompasses heterocyclic aromatic compounds. The aromatic ring(s) can comprise phenyl, naphthyl, biphenyl, diphenylether, diphenylamine and benzophenone, among others. 30 In particular embodiments, the term “aryl” means a cyclic aromatic comprising about 5 to about 10 carbon atoms, e.g., 5, 6, 7, 8, 9, or 10 carbon atoms, and including 5- and 6-membered hydrocarbon and heterocyclic aromatic rings. The aryl group can be optionally substituted (a “substituted aryl”) with one or more aryl group substituents, which can be the same or different, wherein “aryl group substituent” includes alkyl, 35 substituted alkyl, aryl, substituted aryl, aralkyl, hydroxyl, alkoxyl, aryloxyl, aralkyloxyl, carboxyl, carbonyl, acyl, halo, nitro, alkoxycarbonyl, aryloxycarbonyl, aralkoxycarbonyl, acyloxyl, acylamino, - 34 - Attorney Docket No.: 3436/2 PCT aroylamino, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylthio, alkylthio, alkylene, and -NR’R’’, wherein R’ and R’’ can each be independently hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, and aralkyl. Thus, as used herein, the term “substituted aryl” includes aryl groups, as defined herein, in 5 which one or more atoms or functional groups of the aryl group are replaced with another atom or functional group, including for example, alkyl, substituted alkyl, halogen, aryl, substituted aryl, alkoxyl, hydroxyl, nitro, amino, alkylamino, dialkylamino, sulfate, and mercapto. Specific examples of aryl groups include, but are not limited to, cyclopentadienyl, phenyl, furan, thiophene, pyrrole, pyran, pyridine, imidazole, benzimidazole, isothiazole, isoxazole, pyrazole, 10 pyrazine, triazine, pyrimidine, quinoline, isoquinoline, indole, carbazole, and the like. The term “heteroaryl” refers to aryl groups wherein at least one atom of the backbone of the aromatic ring or rings is an atom other than carbon. Thus, heteroaryl groups have one or more non- carbon atoms selected from the group including, but not limited to, nitrogen, oxygen, and sulfur. As used herein, the term “acyl” refers to an organic carboxylic acid group wherein the -OH of 15 the carboxyl group has been replaced with another substituent, i.e., as represented by -C(=O)R, wherein R is an alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl or substituted aryl group as defined herein). As such, the term “acyl” specifically includes arylacyl groups, such as an acetylfuran and a phenacyl group. Specific examples of acyl groups include acetyl and benzoyl. “Cyclic” and “cycloalkyl” refer to a non-aromatic mono- or multicyclic ring system of about 3 20 to about 10 carbon atoms, e.g., 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms. The cycloalkyl group can be optionally partially unsaturated. The cycloalkyl group also can be optionally substituted with an alkyl group substituent as defined herein, oxo, and/or alkylene. There can be optionally inserted along the cyclic alkyl chain one or more oxygen, sulfur or substituted or unsubstituted nitrogen atoms, wherein the nitrogen substituent is hydrogen, alkyl, substituted alkyl, aryl, or substituted aryl, thus providing a 25 heterocyclic group. Representative monocyclic cycloalkyl rings include cyclopentyl, cyclohexyl, and cycloheptyl. Multicyclic cycloalkyl rings include adamantyl, octahydronaphthyl, decalin, camphor, camphane, and noradamantyl. The terms “heterocycle”, “heterocyclyl” “heterocycloalkyl” or “heterocyclic” refer to cycloalkyl groups (i.e., non-aromatic, cyclic groups as described hereinabove) wherein one or more of 30 the backbone carbon atoms of a cyclic ring is replaced by a heteroatom (e.g., nitrogen, sulfur, or oxygen). Examples of heterocycles include, but are not limited to, tetrahydrofuran, tetrahydropyran, morpholine, dioxane, piperidine, piperazine, and pyrrolidine. Additional examples of heterocycles include, for example, the cyclic forms of sugars, such as ribose, glucose, galactose, and the like. “Alkylene” refers to a straight or branched bivalent aliphatic hydrocarbon group having from 1 35 to about 20 carbon atoms, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 carbon atoms. The alkylene group can be straight, branched or cyclic. The alkylene group also can be optionally - 35 - Attorney Docket No.: 3436/2 PCT unsaturated and/or substituted with one or more “alkyl group substituents.” There can be optionally inserted along the alkylene group one or more oxygen, sulfur or substituted or unsubstituted nitrogen atoms (also referred to herein as “alkylaminoalkyl”), wherein the nitrogen substituent is alkyl as previously described. Exemplary alkylene groups include methylene (-CH₂-); ethylene (-CH₂-CH₂-); 5 propylene (-(CH₂)₃-); cyclohexylene (-C₆H₁₀-); -CH=CH—CH=CH-; -CH=CH-CH₂-; -(CH₂)_q-N(R)- (CH₂)_r-, wherein each of q and r is independently an integer from 0 to about 20, e.g., 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20, and R is hydrogen or lower alkyl; methylenedioxyl (-O-CH₂-O-); and ethylenedioxyl (-O-(CH₂)₂-O-). An alkylene group can have about 2 to about 3 carbon atoms and can further have 6-20 carbons. 10 “Alkoxyl” or “alkoxy” refers to an alkyl-O- group wherein alkyl is as previously described. The term “alkoxyl” as used herein can refer to, for example, methoxyl, ethoxyl, propoxyl, isopropoxyl, butoxyl, t-butoxyl, and pentoxyl. The term “oxyalkyl” can be used interchangably with “alkoxyl”. The terms “aryloxy” and “aryloxyl” refer to an aryl-O-group, wherein aryl is as previously described. The term “aryloxy as used herein can refer to, for example, phenoxy, p-chlorophenoxy, p- 15 fluorophenoxy, p-methylphenoxy, p-methoxyphenoxy, and the like. “Aralkyl” refers to an aryl-alkyl- group wherein aryl and alkyl are as previously described and include substituted aryl and substituted alkyl. Exemplary aralkyl groups include benzyl, phenylethyl, and naphthylmethyl. In some embodiments, the aromatic portion of the aralkyl group can be substituted by one or more aryl group substituents and/or the alkyl portion of the aralkyl group can be substituted 20 by one or more alkyl group substituents and the aralkyl group can be a “substituted aralkyl” group. The term “amino” refers to the -NR’R” group, wherein R’ and R” are each independently selected from the group including H and substituted and unsubstituted alkyl, cycloalkyl, heterocycle, aralkyl, aryl, and heteroaryl. In some embodiments, the amino group is -NH₂. The terms “alkylamino” and “aminoalkyl” refer to a -NHR group where R is alkyl or substituted 25 alkyl. The term “arylamino” refers to a -NHR group where R is aryl or substituted aryl. The term “carbonyl” refers to the -(C=O)- or a double bonded oxygen substituent attached to a carbon atom of a previously named parent group. The terms “carboxylate” and “carboxylic acid” can refer to the groups -C(=O)-O- and -C(=O)- OH, respectively. In some embodiments, “carboxylate” can refer to either the -C(=O)-O- or -C(=O)-OH 30 group. In some embodiments, the term “carboxyl” can also be used to refer to a carboxylate or carboxylic acid group. The term “protecting group” refers to a group that is known in the art of organic synthesis for masking a chemical functional group (e.g., hydroxyl, phenol, carbonyl, carboxyl, thiol, amino, etc.) during chemical group transformations elsewhere in the molecule. For example, in some embodiments, 35 an amino protecting group is a group that can replace a hydrogen atom of an amino group on a molecule and that is stable and non-reactive to reaction conditions to which the protected molecule is to be - 36 - Attorney Docket No.: 3436/2 PCT exposed. Various protecting groups are described, for example, in Wuts (2014) Greene’s Protective Groups in Organic Synthesis, 5th Edition. John Wiley & Sons, Inc., New York, New York, United States of America, along with various protecting and deprotecting reagents for use in adding the protecting groups and removing the protecting groups, respectively. 5 The terms “sulfonyl” as used herein refers to the -S(=O)₂- or -S(=O)₂R group, wherein R is alkyl, substituted alkyl, cycloalkyl, heterocycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, heteroaryl, or substituted heteroaryl. The term “sulfonamide” refers to the -S(=O)₂-N(R)₂ group, wherein each R is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl, or 10 wherein the two Rs together can for a ring with the nitrogen atom (e.g., wherein the two Rs are together an alkylene group, such as a butylene or pentylene group). The term “sulfonate” as used herein refers to a -S(=O)₂-O-R group, wherein R is selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. The terms “halo”, “halide”, or “halogen” as used herein refer to fluoro, chloro, bromo, and iodo 15 groups. The term “perhaloalkyl” refers to an alkyl group wherein all of the hydrogen atoms are replaced by halo. Thus, for example, perhaloalkyl can refer to a “perfluroalkyl” group wherein all of the hydrogen atoms of the alkyl group are replaced by fluoro. Perhaloalkyl groups include, but are not limited to, - CF₃. 20 The terms “hydroxyl” and “hydroxy” refer to the -OH group. The term “oxo” refers to a compound described previously herein wherein a carbon atom is replaced by an oxygen atom. The term “thio” refers to the -S- or -SH group. The terms “alkylthio” and “thioalkyl” refer to a -SR group where R is alkyl or substituted alkyl. 25 The term “arylthiol” refers to a -SR group where R is aryl or substituted aryl. The term “phosphoryl” refers to a trivalent >P(=O)- group. In some embodiments, the phosphorous atom of the phosphoryl group can be covalently attached to three different substituents, where each substituent can be covalently attached to the phosphorous atom via an oxygen, nitrogen, or carbon atom of the substituent. In some embodiments, the phosphorous atom of the phosphoryl group 30 can be covalently attached to two different substituents, where one of the substituents is covalently attached to the phosphorous atom via covalent bonds between the phosphorous atom and two different carbon, nitrogen, and/or oxygen atoms of the substituent, thereby forming a cyclic moiety including atoms from the substituent and the phosphorous atom of the phosphoryl group. The term “cyano” refers to the -CN group. 35 The term “nitro” refers to the -NO₂ group. - 37 - Attorney Docket No.: 3436/2 PCT A wavy line in a chemical structure indicating a chemical bond (as in the wavy line attached to R₆ in the structure below) refers to a bond where the stereochemistry is unknown or is not specified. A wavy line crossing the end of a solid line (as in the wavy line crossing the solid line attached to P in the structure below) refers to the site where the indicated structure is covalently attached to another 5 (unshown) group. II. Phosphorous-Azole Exchange (PhAzE) Chemistry Covalent probes and ligands can serve as useful tools for the global investigation of protein function. For example, activity-based protein profiling (ABPP) utilizes active-site directed chemical 10 probes to measure the functional state of large numbers of enzymes in native biological systems (e.g., cells or tissues). Activity-based probes can comprise a reactive group for targeting a specific enzyme class and a reporter tag (or functional group that can be readily modified to include a reporter tag) for detection, e.g., by in-gel fluorescence scanning or by avidin-enrichment coupled with liquid chromatography mass spectrometry (LCMS), respectively. For example, PCT International Publication 15 Number WO 2020/214336, incorporated herein by reference in its entirety, describes sulfonyl-triazole exchange (SuTEx) probes and their use in ABPP. Fluorophosphonates, such as sarin and soman, have been used as chemical warfare agents. These compounds covalently modify the active-site serine of acetylcholinesterase (AChE), inhibiting it and resulting in cholinergic stress. Excessive accumulation of acetylcholine can result in paralysis of 20 muscles, including in the heart and lungs, resulting in asphyxiation or cardiac arrest. However, fluorophosphonates have also been used as electrophiles for ABPP. For example, the Cravatt group has described ABPP with fluorophosphonate-biotin (FP-Biotin) and fluorophosphonate-rhodamine (FP- Rh) probes for liquid chromatography tandem mass spectrometry (LC-MS/MS) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, respectively. See Liu et al., 1999; 25 and Long & Cravatt, 2011. Interest in profiling serine hydrolases has also led to the development of electrophiles such as carbamates and triazole-ureas that can target particular serine hydrolases, e.g., with “druggable” potential. For example, the discovery of the carbamate monoacylglycerol (MAGL) inhibitor JZL-184 inspired the development of carbamate ABX-1431 as a clinical candidate. See Grams & Hsu, 2022. See 30 also Adibekian et al., 2012. - 38 - Attorney Docket No.: 3436/2 PCT Recently, the use of phosphorous-containing electrophiles has been explored with the development of phosphorous-fluoride exchange (PFEx) chemistry for click chemistry. See Sun et al., 2023. When undergoing covalent reaction with a nucleophile, e.g., the phenolic group, the fluoride atom attached to the phosphorous atom of the PFEx molecules can act as a leaving group and the phosphorous 5 atom can form a new covalent adduct with the nucleophile. According to one aspect, the presently disclosed subject matter provides a new class of phosphorous-containing electrophiles comprising a phosphorous atom directly attached to the nitrogen atom of an aromatic heterocycle, e.g., a triazole or imidazole. The use of these compounds in phosphorous-azole exchange (PhAzE) chemistry is described herein (e.g., as probes for proteomics and 10 as ligands for covalently modifying peptides and proteins to study or modify their biological activity). The ability to modify the azole leaving group of the PhAzE compound, e.g., by modifying the substituents attached to the azole, provides enhanced ability to tune the reactivity and selectivity of PhAzE compounds. II.A. Compositions 15 In some embodiments, the presently disclosed subject matter provides a PhAzE compound comprising a phosphorous atom of a phosphoryl group covalently attached to the nitrogen atom of a substituted or unsubstituted nitrogen-containing heteroaryl group. In some embodiments, the nitrogen- containing heteroaryl group is a five-membered heteroaryl group (e.g., a triazole, imidazole, pyrazole, or tetrazole). In some embodiments, the nitrogen-containing heteroaryl group is a substituted or 20 unsubstituted triazole group and the PhAzE compound is a phosphorous-triazole compound. In some embodiments, the nitrogen-containing heteroaryl group is a substituted or unsubstituted 1,2,3-triazole or a substituted or unsubstituted 1,2,4-triazole. In some embodiments, the presently disclosed subject matter provides a compound having a structure of Formula (I): 25 wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; X₁ is selected from the group comprising or consisting of -Oˉ (i.e., an oxyanion), -OR₂, -NR₂R₃, alkyl (e.g., C1-C6 alkyl), substituted alkyl, aralkyl (e.g., benzyl), substituted aralkyl, aryl, and substituted aryl; X₂ is selected from the group comprising or consisting of -O-, -OR₂ 30 and -NR₂R₃; R₁ is selected from the group comprising or consisting of H, halo (e.g., F, Cl, or Br), alkyl - 39 - Attorney Docket No.: 3436/2 PCT (e.g., C1-C6 alkyl), perhaloalkyl (e.g., -CF₃), aralkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; each R₂ is selected from the group comprising or consisting of H, alkyl (e.g., C1-C6 alkyl), substituted alkyl, cycloalkyl (e.g., cyclopropyl), aralkyl, substituted aralkyl, aryl, and substituted aryl, or wherein two R₂ groups together are a bivalent group (e.g., an alkylene or aralkylene group) that is 5 covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is optionally substituted and/or fused to a substituted or unsubstituted aromatic ring; R₃ is selected from the group comprising or consisting of H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from the group comprising or consisting of alkyl, 10 substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from the group comprising or consisting of H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, R₁ is selected from the group comprising or consisting of H, aryl, substituted aryl, heteroaryl, and substituted heteroaryl. In some embodiments, two of Z₁, Z₂, and Z₃ are N. In some embodiments, Z₁ and Z₃ are each 15 N. In some embodiments, Z₁ and Z₂ are each N. In some embodiments, one of Z₁, Z₂, and Z₃ is N. In some embodiments, Z₃ is N. In some embodiments, the compound of Formula (I) comprises a detectable group or a group that can be functionalized (e.g., using Click chemistry) to contain a detectable group. In some embodiments, X₁ and/or X₂ comprise an alkyne moiety, a fluorophore moiety, a detectable labeling 20 group (e.g., an affinity labeling group) or a combination thereof. In some embodiments, X₁ or X₂ comprises an R₂ group wherein said R₂ group is an unsaturated alkyl group comprising an alkyne moiety. For example, in some embodiments, R₂ comprises a terminal alkyne moiety. In some embodiments, R₂ is -CH₂-C^CH. In some embodiments, X₁ or X₂ comprises an R₂ group wherein said R₂ group is selected from substituted alkyl, substituted aralkyl, or substituted aryl, wherein said 25 substituted alkyl, substituted aralkyl, or substituted aryl is an alkyl, aralkyl, or aryl that is substituted with an alkyl or alkoxy group comprising an alkyne moiety (e.g., a terminal alkyne moiety). In some embodiments, the alkyl or alkoxy group is -CH₂-C^CH or -O-CH₂-C^CH. In some embodiments, X₁ and X₂ each comprise an R₂ group that together are a bivalent group (e.g., an alkylene or aralkylene group) that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby 30 forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is substituted with an alkyl or alkoxy group comprising an alkyne moiety (e.g., a terminal alkyne moiety). In some embodiments, the bivalent group is substituted with a group selected from -CH₂-C^CH and -O-CH₂- C^CH. In some embodiments, X₁ and X₂ each comprise an R₂ group that together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby 35 forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is fused to a substituted aromatic ring (e.g., a substituted phenyl group), wherein said substituted aromatic ring is an - 40 - Attorney Docket No.: 3436/2 PCT aromatic ring substituted by an alkyl or alkoxy group comprising an alkyne moiety (e.g., a terminal alkyne moiety). In some embodiments, the alkyl or alkoxy group is -CH₂-C^CH or -O-CH₂-C^CH. In some embodiments, R₁ is selected from the group comprising or consisting of H, halo, alkyl, perhaloalkyl, aralkyl, phenyl, thiophenyl, furanyl, pyridinyl, substituted phenyl, substituted thiophenyl, 5 substituted furanyl, and substituted pyridinyl. In some embodiments, R₁ is selected from the group comprising or consisting of H, phenyl, thiophenyl, furanyl, pyridinyl, and substituted phenyl. When R₁ is substituted phenyl, the substituted phenyl can be substituted with one to five substituents, which can be the same or different. In some embodiments, the substituents can be selected from the “aryl group substituents” described hereinabove. In some embodiments, the substituted phenyl is phenyl substituted 10 with one or more (i.e., 1, 2, 3, 4, or 5) substituents selected from the group comprising or consisting of halo, alkoxy, and perhaloalkoxy. In some embodiments, R₁ is phenyl substituted with fluoro or -OCF₃. In some embodiments, the compound of Formula (I) comprises a chiral center and/or wherein X₁ and/or X₂ comprises an alkyne moiety, a fluorophore moiety, or a detectable labeling group. In some embodiments, the alkyne moiety comprises a group selected from -C^CH, -alkylene-C^CH, -O- 15 alkylene-C^CH (e.g., -O-CH₂-C^CH), and -C(=O)-NH-alkylene-C^CH (e.g., C(=O)-NH-CH₂-C^CH). In some embodiments, the alkylene group is a C₁-C₅ alkylene group. Suitable fluorophores that can be used to provide the fluorophore moiety can be selected from the group including, but not limited to, rhodamine, rhodol, fluorescein, thiofluorescein, aminofluorescein, carboxyfluorescein, chlorofluorescein, methylfluorescein, sulfofluorescein, 20 aminorhodol, carboxyrhodol, chlororhodol, methylrhodol, sulforhodol; aminorhodamine, carboxyrhodamine, chlororhodamine, methylrhodamine, sulforhodamine, thiorhodamine, cyanine, indocarbocyanine, oxacarbocyanine, thiacarbocyanine, merocyanine, cyanine 2, cyanine 3, cyanine 3.5, cyanine 5, cyanine 5.5, cyanine 7, oxadiazole derivatives, pyridyloxazole, nitrobenzoxadiazole, benzoxadiazole, pyren derivatives, cascade blue, oxazine derivatives, Nile red, Nile blue, cresyl violet, 25 oxazine 170, acridine derivatives, proflavin, acridine orange, acridine yellow, arylmethine derivatives, auramine, crystal violet, malachite green, tetrapyrrole derivatives, porphin, phtalocyanine, bilirubin 1- dimethylaminonaphthyl-5-sulfonate, 1-anilino-8-naphthalene sulfonate, 2-p-touidinyl-6-naphthalene sulfonate, 3-phenyl-7-isocyanatocoumarin, N-(p-(2-benzoxazolyl)phenyl)maleimide, stilbenes, pyrenes, 6-FAM (Fluorescein), 6-FAM (NHS Ester), 5(6)-FAM, 5-FAM, Fluorescein dT, 5-TAMRA- 30 cadavarine, 2-aminoacridone, HEX, JOE (NHS Ester), MAX, TET, ROX, and TAMRA. In some embodiments, the fluorophore moiety can be obtained from a compound library. In some cases, the compound library comprises ChemBridge fragment library, Pyramid Platform Fragment-Based Drug Discovery, Maybridge fragment library, FRGx from AnalytiCon, TCI-Frag from AnCoreX, Bio Building Blocks from ASINEX, BioFocus 3D from Charles River, Fragments of Life (FOL) from 35 Emerald Bio, Enamine Fragment Library, IOTA Diverse 1500, BIONET fragments library, Life Chemicals Fragments Collection, OTAVA fragment library, Prestwick fragment library, Selcia - 41 - Attorney Docket No.: 3436/2 PCT fragment library, TimTec fragment-based library, Allium from Vitas-M Laboratory, or Zenobia fragment library. In some embodiments, the detectable labeling moiety is selected from the group comprising a member of a specific binding pair (e.g., biotin:streptavidin, antigen-antibody, nucleic acid:nucleic acid), 5 a bead, a resin, a solid support, or a combination thereof. In some embodiments, the detectable labeling group is a biotin moiety, a streptavidin moiety, bead, resin, a solid support, or a combination thereof. In some embodiments, the detectable labeling moiety comprises biotin or a derivative thereof (e.g., desthiobiotin). In some embodiments, the detectable labeling moiety comprises a heavy isotope (i.e., 1³C). 10 In some embodiments, two R₂ together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring. In some embodiments, the bivalent group is substituted and/or fused to a substituted or unsubstituted aromatic ring. In some embodiments, the compound of Formula (I) has a structure of Formula (II) or Formula (III): 15 wherein: each of Z₁, Z₂, and Z₃ are independently CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; X₃ is O or NH; X₄ is O or NR₃; R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, substituted alkyl, 20 cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, - 42 - Attorney Docket No.: 3436/2 PCT substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, -S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, aryl and substituted aryl; R₁₁ is selected from H, -C(=O)R₄, -CH₂C(=O)R₄, 5 alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and R₁₂ and R₁₃ are independently selected from H, -C(=O)R₄, -CH₂C(=O)R₄, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, the compound has a structure of Formula (II) wherein X₃ is O and X₄ is NR₃ and the compound has a structure of Formula (IIa): 10 wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, 15 substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, -S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, 20 aryl and substituted aryl, optionally H, halo, alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, and aryl. In some embodiments, R₃ is alkyl. In some embodiments, R₃ is a linear or branched C1-C6 saturated alkyl group or a C1-C6 alkyl group comprising a terminal alkyne. In some embodiments, R₃ is -CH₂-C^CH or -CH(CH₃)C(CH₃)₃. In some embodiments, R₃ is cycloalkyl (e.g., cyclopropyl) or 25 substituted alkyl (e.g., an ester and/or thioalkyl substituted alkyl group). In some embodiments, R₃ comprises a chiral center. In some embodiments, R₃ is selected from -S(=O)R₄, -S(=O)₂R₄, and - C(=O)R₄. In some embodiments, R₄ is selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, R₄ is C1-C6 alkyl. - 43 - Attorney Docket No.: 3436/2 PCT In some embodiments, R₆ is H, Z₁ and Z₃ are N and Z₂ is CH, and the compound of Formula (IIa) has a structure of Formula (IIa1): wherein R₁, R₃, R₇, R₈, R₉, and R₁₀ are defined as for Formula (IIa). 5 In some embodiments, at least three of R₇, R₈, R₉, and R₁₀ are H. In some embodiments, at least R₇, R₈, and R₁₀ are H, Z₁ and Z₃ are N, and Z₂ is CH, and the compound of Formula (IIa1) has a structure of Formula (IIa2): wherein R₁, R₃, and R₉ are defined as for Formula (IIa). In some embodiments, R₉ is alkoxy (e.g., C1- 10 C6 alkoxy). In some embodiments, R₉ is -O-CH₂-C^CH. In some embodiments, R₉ is -O-CH₂-C^CH and R₃ is a linear or branched C1-C6 alkyl group, optionally wherein R₃ comprises a chiral carbon atom. In some embodiments, R₃ is ethyl or -CH(CH₃)C(CH₃)₃. In some embodiments, R₉ is H and the compound of Formula (IIa2) has a structure of Formula (IIa3): 15 wherein R₁ is H, aryl, substituted aryl, heteroaryl, or substituted heteroaryl. In some embodiments, R₁ is selected from the group comprising or consisting of H, phenyl, furanyl, thiophenyl, pyridinyl, or substituted phenyl, wherein substituted phenyl is phenyl substituted - 44 - Attorney Docket No.: 3436/2 PCT by one or more substituents selected from the group comprising or consisting of halo, alkyl, alkoxy, perfluoroalkyl, and perfluoroalkoxy. In some embodiments, R₁ is selected from phenyl, furanyl, fluoro- substituted phenyl, and trifluoromethoxy-substituted phenyl. In some embodiments, the compound of Formula (I), Formula (II), or Formula (IIa) is selected 5 from the group comprising or consisting of: i.e., 3-(prop-2-yn-1-yl)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydro-benzo-[e][1,3,2]oxazaphosphinine 2- oxide (also referred to herein as RJG-2-259A, RJG-2259A, 2259A, and PhAzE-1); 10 i.e., 2-(3-phenyl-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza- phosphinine 2-oxide (also referred to herein as RJG-2-259B; RJG-2259B, 2259B, and PhAzE-2); i.e., 3-(prop-2-yn-1-yl)-2-(3-(4-(trifluoromethoxy)phenyl)-1H-1,2,4-triazol-1-yl)-3,4-dihydro- benzo[e][1,3,2]oxazaphosphinine 2-oxide (also referred to herein as RJG-2-275, RJG-2275, 2275, and 15 PhAzE-3); i.e., 2-(3-(2-fluorophenyl)-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]- oxazaphosphinine 2-oxide (also referred to herein as RJG-2-276, RJG-2276, 2276, and PhAzE-4); 20 i.e., 2-(3-(furan-2-yl)-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]- oxazaphosphinine 2-oxide (also referred to herein as RJG-2-279, RJG-2279, 2279, and PhAzE-5); - 45 - Attorney Docket No.: 3436/2 PCT i.e., 3-((S)-3,3-dimethylbutan-2-yl)-2-(3-phenyl-1H-1,2,4-triazol-1-yl)-7-(prop-2-yn-1-yloxy)-3,4- dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (also referred to herein as RJG-2-284, RJG-2284, 2284, and (S)-PhAzE-6); and 5 i.e., 3-ethyl-7-(prop-2-yn-1-yloxy)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza- phosphinine 2-oxide (also referred to herein as RJG-2-292, RJG-2292, 2292, and PhAzE-7). In some embodiments, the compound of Formula (I), Formula (II), or Formula (IIa) is selected from: 10 i.e., 2-(4-bromo-1H-imidazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (PhAzE-8); i.e., 3-(prop-2-yn-1-yl)-2-(4-(trifluoromethyl)-1H-imidazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]- 15 oxazaphosphinine 2-oxide (PhAzE-9); i.e., 3-cyclopropyl-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (PhAzE-10, also referred to here as RJG-3044 or 3044); - 46 - Attorney Docket No.: 3436/2 PCT i.e., 3-(cyclopropylmethyl)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2- oxide (PhAzE-11, also referred to here as RJG-3045 or 3045); i.e., methyl (2R)-4-(methylthio)-2-(2-oxido-2-(1H-1,2,4-triazol-1-yl)benzo[e][1,3,2]oxazaphosphinin- 5 3(4H)-yl)butanoate (PhAzE-12, also referred to here as RJG-3048 or 3048); i.e., methyl (2S)-4-(methylthio)-2-(2-oxido-2-(1H-1,2,4-triazol-1-yl)benzo[e][1,3,2]oxazaphosphinin- 3(4H)-yl)butanoate (PhAzE-13, also referred to here as RJG-3049 or 3049); and 10 i.e., 3‐cyclopropyl‐2‐(7H‐purin‐7‐yl)‐3,4‐dihydrobenzo[e][1,3,2]oxazaphosphinine 2‐oxide (RJG- 3130-9, also referred to herein as 3130-9). In some embodiments, the compound of Formula (I), Formula (II), or Formula (IIa) is an azole of the following general Formula: 15 wherein the azole group is selected from the group consisting of: - 47 - Attorney Docket No.: 3436/2 PCT 3130-7 3130-8 3130-9 In some embodiments, the azole has the general structure: 5 wherein each X is independently selected from the group consisting of C, N, O, and S. In some embodiments, one or more of the Xs can be substituted. By way of example and not limitation, when any given X is a C, the C may have a substituent attached thereto. In some embodiments, the substituent is selected from the group consisting of H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl, -S(=O)R, -S(=O)₂R, and -C(=O)R, wherein R is in some embodiments selected from 10 alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, the compound of Formula (I), Formula (II), or Formula (IIa) is an azole of the following general Formula: 15 wherein the R group is selected from the group consisting of: , 3150-1 3150-2 3150-3 3150-4 3150-5 3150-6 In some embodiments, the compound of Formula (I), Formula (II), or Formula (IIa) is an azole 20 of the following general Formula: - 48 - Attorney Docket No.: 3436/2 PCT wherein the azole group is selected from the group consisting of: 3048 3135L-2 3135L-3 3049 3135D-2 3135D-3 5 In some embodiments, the compound of Formula (I), Formula (II), or Formula (IIa) is an azole of the following general Formula: wherein the azole group is selected from the group consisting of: 10 15 - 49 - Attorney Docket No.: 3436/2 PCT In some embodiments, the compound of Formula (I), Formula (II), or Formula (IIa) is an azole of the following general Formula: wherein the R group is selected from the group consisting of: 5 3129L 3129D 3131L 3131D 3132 3133 In some embodiments, the compound has a general structure as follows: , wherein the compound is a specific stereoisomer selected from the group consisting of UTXA-2-027 10 and UTXA-2-208: UTXA-2-027 UTXA-2-208 In some embodiments, the compound has a structure selected from the group consisting of: 15 In some embodiments, the compound has a general structure as follows: - 50 - Attorney Docket No.: 3436/2 PCT , 2259A wherein the compound is a specific stereoisomer selected from the group consisting of (S)-2259A (R)- 2259A. 5 In some embodiments, the compound has a structure as follows: , wherein X₁ is O or S, and X₂, X₃, Z₁, Z₂, Z₃, and R₁ are defined as herein. In some embodiments, the compound has a structure of Formula (II) wherein X₃ is O and X₄ is O and the compound has a structure of Formula (IIb): 10 wherein Z₁, Z₂, Z₃, R₁, R₆, R₇, R₈, R₉, and R₁₀ are as defined for Formula (II). In some embodiments, the compound has a structure of Formula (II) wherein X₃ is NH and X₄ is NR₃ and the compound has a structure of Formula (IIc): 15 wherein Z₁, Z₂, Z₃, R₁, R₃, R₆, R₇, R₈, R₉, and R₁₀ are as defined for Formula (II). In some embodiments, the compound has a structure of Formula (III) wherein X₃ is O and X₄ is NR₃ and the compound has a structure of Formula (IIIa): - 51 - Attorney Docket No.: 3436/2 PCT wherein Z₁, Z₂, Z₃, R₁, R₃, R₁₁, R₁₂, and R₁₃ are as defined for Formula (III). In some embodiments, Z₁ and Z₃ are N and Z₂ is CH. In some embodiments, R₁₁ is selected from -C(=O)R₄ and -CH₂C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, - 5 NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, R₄ is OH and R₁₁ is selected from -C(=O)-OH and -CH₂C(=O)-OH. In some embodiments, R₁₂ and R₁₃ are independently selected from H and C1-C6 alkyl. In some embodiments, R₁₂ and R₁₃ are independently selected from H and methyl. In some embodiments both R₁₂ and R₁₃ are 10 CH₃. In some embodiments, one of R₁₂ and R₁₃ is CH_3, and the other is H. In some embodiments, both R₁₂ and R₁₃ are H. In some embodiments, R₃ is H. In some embodiments, the compound of Formula (IIIa) comprises a group representing a phosphorous atom-containing heterocycle where the other atoms of the heterocycle are based on the structure of an amino acid. For example, when R₃ is -C(=O)-OH and both R₁₂ and R₁₃ are H, the 15 compound comprises a group representing a serine-based phosphorous atom-containing heterocycle. See the structure of Formula (IIIa1), below. When R₃ is -C(=O)-OH, one of R₁₂ and R₁₃ is H, and one of R₁₂ and R₁₃ is CH₃, the compound comprises a group representing a threonine-based phosphorous atom-containing heterocycle. See the structure of Formula (IIIa2), below. When R₃ is -C(=O)-OH, and both of R₁₂ and R₁₃ are CH₃, the compound comprises a group representing an unnatural threonine- 20 based phosphorous atom-containing heterocycle. See the structure of Formula (IIIa3), below. When R₃ is -CH₂-C(=O)-OH and both R₁₂ and R₁₃ are H, the compound comprises a group representing a phosphorous atom-containing heterocycle based on an aspartic acid with a reduced carboxylic acid. See the structure of Formula (IIIa4), below. In some embodiments, the compound has a structure of one of Formulas (IIIa1)-(IIIa4): - 52 - Attorney Docket No.: 3436/2 PCT wherein Z₁, Z₂, Z₃, and R₁ are as defined for Formula (III). In some embodiments, X₁ and X₂ in the compound of Formula (I) do not form a cyclic structure 5 together with the phosphorous atom. In some embodiments, X₁ is selected from -Oˉ and -OR₂, and the compound of Formula (I) has a structure of Formula (IVa), (IVb), or (IVc): wherein: Z₁, Z₂, Z₃, and R₁ are as defined for Formula (I); each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₃ is selected from 10 H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted - 53 - Attorney Docket No.: 3436/2 PCT aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, X₁ is selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and the compound of Formula (I) has a structure of Formula (IVd), (IVe), or 5 (IVf): wherein Z₁, Z₂, Z₃, and R₁ are as defined for Formula (I); each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₃ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and 10 -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. In some embodiments, a pharmaceutically acceptable salt or solvate of one of the presently disclosed compounds is provided. 15 The presently disclosed PhAzE compounds can be prepared as described in Scheme 2 in EXAMPLE 1, below. More particularly Scheme 2 below shows the preparation of PhAzE compounds comprising six-membered phosphorous-containing rings, e.g., such as compounds of Formula (II). However, the aminophenol of General Procedure B can be substituted with natural or unnatural amino acids and/or with mixtures of alcohol and/or amines to prepare additional phosphoramidocholidates that 20 can then be reacted with an azole to prepare other PhAzE compounds as described herein. II.B. Pharmaceutical Compositions and Administration The presently disclosed subject matter also relates, in some embodiments, to pharmaceutical compositions comprising, consisting essentially of, or consisting of one or more PhAzE compounds of the presently disclosed subject matter and a pharmaceutically acceptable carrier, diluent, and/or 25 excipient. Pharmaceutical compositions comprising the present compounds are administered to a subject in need thereof by any number of routes including, but not limited to, topical, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means. As such, in some embodiments - 54 - Attorney Docket No.: 3436/2 PCT the presently disclosed compositions are administered by injecting the composition subcutaneously, intraperitoneally, into adipose tissue, and/or intramuscularly into the subject. In accordance with some embodiments, a method for treating a subject in need of such treatment is provided. The method comprises administering a pharmaceutical composition comprising at least one 5 compound of the presently disclosed subject matter to a subject in need thereof. Compounds identified by the methods of the presently disclosed subject matter can be administered with known compounds or other medications as well. The pharmaceutical compositions useful for practicing the presently disclosed subject matter may be administered to deliver a dose of between 1 ng/kg/day and 100 mg/kg/day. 10 The presently disclosed subject matter encompasses the preparation and use of pharmaceutical compositions comprising a compound useful for treatment of the diseases and disorders disclosed herein as an active ingredient. Such a pharmaceutical composition may consist of the active ingredient alone, in a form suitable for administration to a subject, or the pharmaceutical composition may comprise the active ingredient and one or more pharmaceutically acceptable carriers, one or more additional 15 ingredients, or some combination of these. The active ingredient may be present in the pharmaceutical composition in the form of a physiologically acceptable ester or salt, such as in combination with a physiologically acceptable cation or anion, as is well known in the art. As used herein, the term “physiologically acceptable” ester or salt means an ester or salt form of the active ingredient which is compatible with any other ingredients of the pharmaceutical 20 composition, which is not deleterious to the subject to which the composition is to be administered. The compositions of the presently disclosed subject matter may comprise at least one active peptide, one or more acceptable carriers, and optionally other peptides or therapeutic agents. For in vivo applications, the compositions of the presently disclosed subject matter may comprise a pharmaceutically acceptable salt. Suitable acids which are capable of forming such salts 25 with the compounds of the presently disclosed subject matter include inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, phosphoric acid and the like; and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, anthranilic acid, cinnamic acid, naphthalene sulfonic acid, sulfanilic acid and the like. Pharmaceutically acceptable carriers include physiologically tolerable or acceptable diluents, 30 excipients, solvents, or adjuvants. The compositions are in some embodiments sterile and nonpyrogenic. Examples of suitable carriers include, but are not limited to, water, normal saline, dextrose, mannitol, lactose or other sugars, lecithin, albumin, sodium glutamate, cysteine hydrochloride, ethanol, polyols (propylene glycol, polyethylene glycol, glycerol, and the like), vegetable oils (such as olive oil), injectable organic esters such as ethyl oleate, ethoxylated isosteraryl alcohols, polyoxyethylene sorbitol 35 and sorbitan esters, microcrystalline cellulose, aluminum methahydroxide, bentonite, kaolin, agar-agar and tragacanth, or mixtures of these substances, and the like. - 55 - Attorney Docket No.: 3436/2 PCT In some embodiments wherein a composition of the presently disclosed subject matter is desired to induce an immune response, the compositions of the presently disclosed subject matter can further comprise an adjuvant. In some embodiments, the at least one adjuvant is selected from the group consisting of montanide ISA-51 (Seppic, Inc.), QS-21 (Aquila Pharmaceuticals, Inc.), tetanus helper 5 peptides, GM-CSF, cyclophosamide, bacillus Calmette-Guerin (BCG), corynbacterium parvum, levamisole, azimezone, isoprinisone, dinitrochlorobenezene (DNCB), keyhole limpet hemocyanins (KLH), Freunds adjuvant (complete and incomplete), mineral gels, aluminum hydroxide (Alum), lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, diphtheria toxin (DT). The pharmaceutical compositions may also contain minor amounts of nontoxic auxiliary 10 pharmaceutical substances or excipients and/or additives, such as wetting agents, emulsifying agents, pH buffering agents, antibacterial and antifungal agents (such as parabens, chlorobutanol, phenol, sorbic acid, and the like). Suitable additives include, but are not limited to, physiologically biocompatible buffers (e.g., tromethamine hydrochloride), additions (e.g., 0.01 to 10 mole percent) of chelants (such as, for example, DTPA or DTPA-bisamide) or calcium chelate complexes (as for example calcium 15 DTPA or CaNaDTPA-bisamide), or, optionally, additions (e.g., 1 to 50 mole percent) of calcium or sodium salts (for example, calcium chloride, calcium ascorbate, calcium gluconate or calcium lactate). If desired, absorption enhancing or delaying agents (such as liposomes, aluminum monostearate, or gelatin) may be used. The compositions can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as 20 emulsions. Pharmaceutical compositions according to the presently disclosed subject matter can be prepared in a manner fully within the skill of the art. The compositions of the presently disclosed subject matter, pharmaceutically acceptable salts thereof, or pharmaceutical compositions comprising these compounds can be so that the compounds can have a physiological effect. Administration can occur enterally or parenterally; for example, orally, 25 rectally, intracisternally, intravaginally, intraperitoneally, locally (e.g., with powders, ointments, or drops), or as a buccal or nasal spray or aerosol. Parenteral administration is preferred. Particularly preferred parenteral administration methods include intravascular administration (e.g., intravenous bolus injection, intravenous infusion, intra-arterial bolus injection, intra-arterial infusion, and catheter instillation into the vasculature), peri- and intra-target tissue injection, subcutaneous injection or 30 deposition including subcutaneous infusion, intramuscular injection, and direct application to the target area, for example by a catheter or other placement device. Where the administration is by injection or direct application, the injection or direct application can be in a single dose or in multiple doses. Where the administration of the compound is by infusion, the infusion can be a single sustained dose over a prolonged period of time or multiple infusions. 35 The formulations of the pharmaceutical compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology. In general, such preparatory methods - 56 - Attorney Docket No.: 3436/2 PCT include the step of bringing the active ingredient into association with a carrier or one or more other accessory ingredients, and then, if necessary or desirable, shaping or packaging the product into a desired single- or multi-dose unit. It will be understood by the skilled artisan that such pharmaceutical compositions are generally 5 suitable for administration to animals of all sorts. Subjects to which administration of the pharmaceutical compositions of the presently disclosed subject matter is contemplated include, but are not limited to, humans and other primates, mammals including commercially relevant mammals such as cattle, pigs, horses, sheep, cats, and dogs, birds including commercially relevant birds such as chickens, ducks, geese, and turkeys. 10 A pharmaceutical composition of the presently disclosed subject matter may be prepared, packaged, or sold in bulk, as a single unit dose, or as a plurality of single unit doses. As used herein, a “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject or a convenient fraction of such a dosage 15 such as, for example, one-half or one-third of such a dosage. The relative amounts of the active ingredient, the pharmaceutically acceptable carrier, and any additional ingredients in a pharmaceutical composition of the presently disclosed subject matter will vary, depending upon the identity, size, and condition of the subject treated and further depending upon the route by which the composition is to be administered. By way of example, the composition may 20 comprise between 0.1% and 100% (w/w) active ingredient. In addition to the active ingredient, a pharmaceutical composition of the presently disclosed subject matter may further comprise one or more additional pharmaceutically active agents. Particularly contemplated additional agents include anti-emetics and scavengers such as cyanide and cyanate scavengers. 25 Controlled- or sustained-release formulations of a pharmaceutical composition of the presently disclosed subject matter may be made using conventional technology. As used herein, “additional ingredients” include, but are not limited to, one or more of the following: excipients; surface active agents; dispersing agents; inert diluents; granulating and disintegrating agents; binding agents; lubricating agents; sweetening agents; flavoring agents; coloring 30 agents; preservatives; physiologically degradable compositions such as gelatin; aqueous vehicles and solvents; oily vehicles and solvents; suspending agents; dispersing or wetting agents; emulsifying agents, demulcents; buffers; salts; thickening agents; fillers; emulsifying agents; antioxidants; antibiotics; antifungal agents; stabilizing agents; and pharmaceutically acceptable polymeric or hydrophobic materials. Other “additional ingredients” which may be included in the pharmaceutical 35 compositions of the presently disclosed subject matter are known in the art and described, for example in Gennaro, 1985; Gennaro, 1990; or Gennaro, 2003; each of which is incorporated herein by reference. - 57 - Attorney Docket No.: 3436/2 PCT Typically, dosages of the compound of the presently disclosed subject matter which may be administered to an animal, in some embodiments a human, range in amount from 1 μg to about 100 g per kilogram of body weight of the animal. While the precise dosage administered will vary depending upon any number of factors, including but not limited to, the type of animal and type of disease state 5 being treated, the age of the animal and the route of administration. In some embodiments, the dosage of the compound will vary from about 1 mg to about 10 g per kilogram of body weight of the animal. In another aspect, the dosage will vary from about 10 mg to about 1 g per kilogram of body weight of the animal. The compound may be administered to an animal as frequently as several times daily, or it may 10 be administered less frequently, such as once a day, once a week, once every two weeks, once a month, or even less frequently, such as once every several months or even once a year or less. The frequency of the dose will be readily apparent to the skilled artisan and will depend upon any number of factors, such as, but not limited to, the type of cancer being diagnosed, the type and severity of the condition or disease being treated, the type and age of the animal, etc. 15 Suitable preparations include injectables, either as liquid solutions or suspensions, however, solid forms suitable for solution in, suspension in, liquid prior to injection, may also be prepared. The preparation may also be emulsified, or the polypeptides encapsulated in liposomes. The active ingredients are often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water saline, dextrose, glycerol, ethanol, or 20 the like and combinations thereof. In addition, if desired, the vaccine preparation may also include minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants. The presently disclosed subject matter also includes a kit comprising the composition of the presently disclosed subject matter and an instructional material which describes administering the 25 composition to a subject. In some embodiments, this kit comprises a (in some embodiments sterile) solvent suitable for dissolving or suspending the composition of the presently disclosed subject matter prior to administering the compound to the subject. As used herein, an “instructional material” includes a publication, a recording, a diagram, or any other medium of expression which can be used to communicate the usefulness of a composition of 30 the presently disclosed subject matter in the kit for effecting alleviation of the various diseases or disorders recited herein. Optionally, or alternately, the instructional material may describe one or more methods of using the compositions for diagnostic or identification purposes or of alleviation the diseases or disorders in a cell or a tissue of a mammal. The instructional material of the kit of the presently disclosed subject matter may, for example, be affixed to a container which contains a composition of 35 the presently disclosed subject matter or be shipped together with a container which contains the - 58 - Attorney Docket No.: 3436/2 PCT composition. Alternatively, the instructional material may be shipped separately from the container with the intention that the instructional material and the compound be used cooperatively by the recipient. The presently disclosed subject matter also related to methods for using the compositions of the presently disclosed subject matter for various purposes. For example, in some embodiments the 5 presently disclosed subject matter also relates to methods for treating and/or preventing diseases, disorders, and/or conditions associated with inflammation. II.C. Dosages An effective dose of a composition of the presently disclosed subject matter is administered to a subject in need thereof. A “treatment effective amount” or a “therapeutic amount” is an amount of a 10 therapeutic composition sufficient to produce a measurable response (e.g., a biologically or clinically relevant response in a subject being treated, such as but not limited to a reduction in scarring and/or fibrosis, particularly as compared to the same subject had the subject not received the composition). Actual dosage levels of active ingredients in the compositions of the presently disclosed subject matter can be varied so as to administer an amount of the active compound(s) that is effective to achieve the 15 desired therapeutic response for a particular subject. The selected dosage level will depend upon the activity of the composition, the route of administration, combination with other drugs or treatments, the severity of the disease, disorder, and/or condition being treated, and the condition and prior medical history of the subject being treated. However, it is within the skill of the art to start doses of the compositions of the presently disclosed subject matter at levels lower than required to achieve the 20 desired therapeutic effect and to gradually increase the dosage until the desired effect is achieved. The potency of a composition can vary, and therefore a “treatment effective amount” can vary. However, using the methods described herein, one skilled in the art can readily assess the potency and efficacy of a composition of the presently disclosed subject matter and adjust the therapeutic regimen accordingly. After review of the disclosure of the presently disclosed subject matter presented herein, one of 25 ordinary skill in the art can tailor the dosages to an individual subject, taking into account the particular formulation, method of administration to be used with the composition, and particular disease, disorder, and/or condition treated. Further calculations of dose can consider subject height and weight, severity and stage of symptoms, and the presence of additional deleterious physical conditions. Such adjustments or variations, as well as evaluation of when and how to make such adjustments or 30 variations, are well known to those of ordinary skill in the art of medicine. II.D. Routes of Administration Suitable methods for administration of the compositions of the presently disclosed subject matter include, but are not limited to intravenous administration, oral delivery, and delivery directly to a target tissue or organ (e.g., a topical application and/or a site of injury such as but not limited to a 35 muscle injury). Exemplary routes of administration include parenteral, enteral, intravenous, intraarterial, intracardiac, intrapericardial, intraosseal, intracutaneous, subcutaneous, intradermal, - 59 - Attorney Docket No.: 3436/2 PCT subdermal, transdermal, intrathecal, intramuscular, intraperitoneal, intrasternal, parenchymatous, oral, sublingual, buccal, inhalational, and intranasal. The selection of a particular route of administration can be made based at least in part on the nature of the formulation and the ultimate target site where the compositions of the presently disclosed subject matter are desired to act. In some embodiments, the 5 method of administration encompasses features for regionalized delivery or accumulation of the compositions at the site in need of treatment. In some embodiments, the compositions are delivered directly into the site to be treated. By way of example and not limitation, in some embodiments a composition of the presently disclosed subject matter is administered to the subject via a route selected from the group consisting of intraperitoneal, intramuscular, intravenous, and intranasal, or any 10 combination thereof. The methods described herein use pharmaceutical compositions comprising the molecules described above, together with one or more pharmaceutically acceptable excipients or vehicles, and optionally other therapeutic and/or prophylactic ingredients. Such excipients include liquids such as water, saline, glycerol, polyethylene glycol, hyaluronic acid, ethanol, cyclodextrins, modified 15 cyclodextrins (i.e., sufobutyl ether cyclodextrins), etc. Suitable excipients for non-liquid formulations are also known to those of skill in the art. Pharmaceutically acceptable salts can be used in the compositions of the present invention and include, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. 20 Additionally, auxiliary substances, such as wetting or emulsifying agents, biological buffering substances, surfactants, and the like, may be present in such vehicles. A biological buffer can be virtually any solution which is pharmacologically acceptable and which provides the formulation with the desired pH, i.e., a pH in the physiologically acceptable range. Examples of buffer solutions include saline, phosphate buffered saline, Tris buffered saline, Hank’s buffered saline, and the like. 25 Depending on the intended mode of administration, the pharmaceutical compositions may be in the form of a liquid, suspension, cream, ointment, lotion, or the like, preferably in unit dosage form suitable for single administration of a precise dosage. The compositions can in some embodiments include one or more pharmaceutically acceptable carriers and, in addition, may include other pharmaceutical agents, adjuvants, diluents, buffers, etc. 30 III. Methods for Covalently Modifying Proteins Small molecules can serve as versatile tools for perturbing the functions of peptides and proteins in biological systems. Many human proteins currently lack selective chemical ligands; and there are several classes of proteins that are currently considered as undruggable. In some embodiments, the presently disclosed PhAzE compounds can be used as covalent ligands to expand the landscape of 35 proteins amenable to targeting by small molecules. In some instances, PhAzE compounds provide covalent ligands that combine features of recognition and reactivity, thereby providing for the targeting - 60 - Attorney Docket No.: 3436/2 PCT of sites on proteins that are difficult to address by reversible binding interactions alone and/or with other types of covalent ligands. For example, Scheme 1, below, shows the reaction of a PhAzE compound (e.g., a PhAzE ligand) with a protein having a reactive tyrosine (Y) or lysine (K). The PhAzE compound comprises a 5 phosphorous electrophile, i.e., a phosphoryl group directed attached to a nitrogen atom of a nitrogen- containing heteroaryl group (e.g., a triazole). The nitrogen-containing heteroaryl group acts as a leaving group (LG) in the reaction of the PhAzE compound with the nucleophilic phenol or amine of the side chain of the tyrosine or lysine, resulting in a modified protein where a modified tyrosine or lysine residue is covalently attached to the phosphorous atom from the PhAzE compound. The group - 10 P(=O)(X₁)(X₂) from the PhAzE compound, which is now covalently attached to protein, can be referred to herein as an “adduct group” (or “AG”) or “fragment.” AGs of PhAzE ligands can include a variety of optionally substituted alkyl, cycloalkyl (including heterocyclic), aryl (including heteroaryl), and aralkyl groups, while PhAzE “probes” can contain an AG group that comprise an alkyne group (e.g., a terminal alkyne group), a fluorophore moiety, another detectable moiety (e.g., an affinity label), or a 15 combination thereof. In some embodiments, the alkyne group of an AG of a protein modified with a PhAzE probe can be contacted with an alkyne-reactive group (e.g., an azide) to attach a detectable group to the modified protein. p_{rotein with} r_{eactive tyrosine protein with modified tyrosine residue} Z_{1, Z2, and Z3 each = N or CH where at least one of Z1, Z2, and Z3 is N or CH} p_{rotein with reactive lysine} p_{rotein with modified lysine residue Z1, Z2, and Z3 each = N or CH} + w_{here at least one of Z1, Z2, and Z3 is N or CH} Scheme 1: PhAzE Reactions with Proteins with Reactive Tyrosines or Lysines. 20 In some embodiments, a PhAzE ligand of the presently disclosed subject matter can compete with a PhAzE probe compound described herein for binding with a reactive amino acid residue, e.g., a - 61 - Attorney Docket No.: 3436/2 PCT reactive tyrosine and/or lysine residue. In some embodiments, the ligand molecule comprises a fragment moiety that facilitates interaction of the compound with a particular amino acid residue of interest, e.g., a reactive tyrosine and/or lysine residue. In some cases, the ligand comprises a fragment moiety that facilitates hydrophobic interaction, hydrogen bonding, or a combination thereof. In some embodiments, 5 the ligand can comprise a fragment moiety that can increase or decrease steric hinderance at the electrophilic phosphorous, thereby modifying the reactivity of the ligand. The presently disclosed PhAzE ligands are typically non-naturally occurring and/or form non-naturally occurring adducts after reaction with a biological target, e.g., a protein. In some embodiments, the presently disclosed subject matter provides a method of covalently 10 modifying a protein or peptide in a sample, wherein the method comprises contacting the sample with a PhAzE compound (i.e., a compound of Formula (I) or one of its sub-formula described hereinabove). In some embodiments, the sample is a biological sample. In some embodiments, the modifying comprises covalently modifying a lysine, tyrosine, serine or threonine residue in the protein or peptide. In some embodiments, the PhAzE compound is a PhAzE ligand, such as PhAzE-10, PhAzE-11, PhAzE- 15 12, or PhAzE-13. In some embodiments, covalently modifying the protein or peptide modulates a biological activity of the protein or peptide. In some embodiments, modifying the protein or peptide inhibits or activates a biological activity of the protein or peptide. For example, in some embodiments, the protein is an enzyme and covalently modifying the enzyme with the compound inhibits the enzyme. In some 20 embodiments, modulating the activity of a protein comprises enhancing or reducing the ability of the protein to interact with other compounds, such as other proteins. Thus, in some embodiments, the modulation results in reducing the protein-protein interactions of the protein comprising the reactive amino acid. In some embodiments, modulating the activity of a protein comprising a comprises inhibiting, blocking (partially or substantially completely) or disrupting a protein-RNA interaction, a 25 protein-DNA interaction, a protein-lipid interaction, and/or a protein-metabolite interaction of the protein. Thus, in accordance with some embodiments of the presently disclosed subject matter, the presently disclosed ligands can serve as tools for the global investigation of protein function. Exemplary proteins that can be covalently modified using a PhAzE compound are listed in Table 2, below. In some embodiments, the protein is macrophage migration inhibitory factor (MIF). In some 30 embodiments, the PhAzE compound covalently modifies threonine 8 of MIF. In some embodiments, the protein is a serine hydrolase. Thus, in some embodiments, the presently disclosed subject matter provides a method of covalently modifying and/or inhibiting a serine hydrolase. In some embodiments, the method comprises contacting a sample comprising a serine hydrolase with a PhAzE compound as described herein. In some embodiments, the serine hydrolase is35 AChE. In some embodiments, the serine hydrolase is selected from the group comprising acylamino- acid releasing enzyme (ACPH; UniProt ID Q8R146), dipeptidyl peptidase 9 (DPP9; UniProt ID - 62 - Attorney Docket No.: 3436/2 PCT Q8BVG4), and platelet-activating factor acetylhydrolase IB subunit alpha 2 (PA1B2; UniProt ID Q61206). In some embodiments, the PhAzE compound modifies ACPH at serine 36. In some embodiments, the PhAzE compound modifies DPP9 at serine 730. In some embodiments, the PhAzE compound modifies PA1B2 at serine 48. 5 In some embodiments, the sample comprises an isolated protein. In some embodiments, the sample comprises a cell lysate, a biological fluid (e.g., saliva, ascites, blood, urine, etc.) or a live cell. In some embodiments, the sample comprising living cells comprises an organ, or a living organism (e.g., a subject, such as a human or other mammal). IV. Methods for Identifying Reactive Amino Acid Residues 10 In some embodiments, the presently disclosed subject matter provides a method of identifying a reactive amino acid residue of a protein, the method comprising: providing a protein sample comprising isolated proteins, living cells, or a cell lysate; (b) contacting the protein sample with a compound of Formula (I) (or a sub-formula thereof, e.g., Formula (II), (III), or (IV)) for a period of time sufficient for the compound to react with at least one reactive amino acid residue (e.g., a tyrosine, 15 lysine, serine, or threonine) in a protein in the protein sample, thereby forming at least one modified reactive amino acid residue; and (c) analyzing proteins in the protein sample to identify at least one modified reactive amino acid residue, thereby identifying at least one reactive amino acid residue of a protein; wherein the probe compound has a structure of Formula (I): 20 wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; X₁ is selected from -Oˉ, -OR₂, -NR₂R₃, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; X₂ is selected from -O-, -OR₂ and -NR₂R₃; R₁ is selected from H, halo, alkyl, perhaloalkyl, aralkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, cycloalkyl, aralkyl, 25 substituted aralkyl, aryl, and substituted aryl, or wherein two R₂ groups together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is optionally substituted and/or fused to a substituted or unsubstituted aromatic ring; and R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, 30 and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted - 63 - Attorney Docket No.: 3436/2 PCT aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; further wherein one of X₁ and X₂ comprises an alkyne moiety; and wherein the at least one modified reactive amino acid residue comprises a structure of Formula (V): 5 where X₁ and X₂ are as defined for formula (I) and X’ is O or NH. In some embodiments, the reactive amino acid residue is a tyrosine residue, a lysine residue, a serine residue, or a threonine residue. In some embodiments, the probe compound is a compound of Formula (IIa): 10 wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted 15 aryl; each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, -S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, aryl and substituted aryl, optionally H, halo, alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, and 20 aryl; wherein one of R₃, R₇, R₈, R₉, and R₁₀ comprises an alkyne moiety; and wherein the at least one modified reactive amino acid residue comprises a structure of Formula (V-IIa): - 64 - Attorney Docket No.: 3436/2 PCT wherein R₃, R₆, R₇, R₈, R₉, and R₁₀ are as defined for formula (IIa) and X’ is O or NH. In some embodiments, the probe compound is selected from the group comprising PhAzE-1, PhAzE-2, PhAzE- 3, PhAzE-4, PhAzE-5, PhAzE-6, PhAzE-7, PhAzE-8, and PhAzE-9. 5 In some embodiments, the analyzing of step (c) further comprisies tagging the at least one modified reactive amino acid residue with a compound comprising a detectable labeling group, thereby forming at least one tagged reactive amino acid residue comprising said detectable labeling group. In some embodiments, the detectable labeling group comprises biotin or a biotin derivative. In some embodiments, the biotin derivative is desthiobiotin. 10 In some embodiments, the tagging comprises reacting an alkyne group of at least one tagged reactive amino acid residue with a compound comprising both an azide moiety (or other alkyne-reactive group) and a detectable labeling group (e.g., biotin or a biotin derivative). In some embodiments, the compound comprising the azide moiety and the detectable labeling group further comprises an alkylene linker, which in some embodiments, can comprise a polyether group, such as an oligomer of methylene 15 glycol, ethylene glycol or propylene glycol (e.g., a group having the formula –(O-C₂H₄-)_x-). In some embodiments, the tagging comprises performing a copper-catalyzed azide-alkyne cycloaddition (CuAAC) coupling reaction. In some embodiments, the analyzing further comprises digesting the protein sample to provide a digested protein sample comprising a protein fragment comprising the at least one tagged reactive 20 amino acid residue comprising the detectable group. In some embodiments, the digesting is performed with a peptidase. In some embodiments, the digesting is performed with trypsin. In some embodiments, the analyzing further comprises enriching the digested protein sample for the detectable labeling group. For example, in some embodiments, the enriching comprises contacting the digested protein sample with a solid support comprising a binding partner of the 25 detectable labeling group. In some embodiments, when the detectable labeling group comprises biotin or a derivative thereof, the solid support comprises streptavidin. In some embodiments, the analyzing further comprises analyzing the digested protein sample (e.g., the enriched digested protein sample) via liquid chromatography-mass spectrometry or via a gel-based assay. In some embodiments, providing the protein sample further comprises separating the protein 30 sample into a first protein sample and a second protein sample. Then, in the contacting step, the first protein sample can be contacted with a first probe compound (e.g., a probe compound of Formula (I)) - 65 - Attorney Docket No.: 3436/2 PCT at a first probe concentration for a first period of time and the second protein sample can be contacted with a second probe compound (e.g., a second probe compound of Formula (I) having a different structure than that of the first probe compound) at the same probe concentration (i.e., at the first probe concentration) for the same time period (i.e., for the first period of time. Alternatively, the second 5 protein sample can be contacted with the same probe compound as the first protein sample, but at a different probe concentration (i.e., a second probe concentration) or for a different period of time. In some embodiments, analyzing proteins comprises analyzing the first and second protein samples to determine the presence and/or identity of a modified reactive amino acid residue in the first sample and the presence and/or identity of a modified reactive amino acid residue in the second sample. In some 10 embodiments, the identities and/or amounts of identified modified reactive amino acid residues from the first and second protein samples are compared. In some embodiments, the protein sample comprises living cells. In some embodiments, providing the protein sample further comprises separating the protein sample into a first protein sample and a second protein sample and culturing the first protein sample in a first cell culture medium 15 comprising heavy isotopes prior to the contacting of step (b) and culturing the second protein sample in a second cell culture medium, wherein the second culture medium comprises a naturally occurring isotope distribution prior to the contacting of step (b). In some embodiments, the first cell culture medium comprises ¹³C- and/or ¹⁵N-labeled amino acids. In some embodiments, the first cell culture medium comprises ¹³C-,¹⁵N-labeled lysine and arginine. 20 In some embodiments, e.g., if the protein sample does not comprise living cells, the probe compound can comprise a detectable labeling group comprising a heavy isotope (e.g., a ¹³C label) or the method can comprise tagging the at least one modified amino acid residue with a detectable labeling group comprising a heavy isotope. In some embodiments, the protein sample is separated into a first and a second protein sample 25 and one of the first and the second protein sample is cultured in the presences of an inhibitor of a protein of interest (e.g., a serine hydrolase). In some embodiments, the presently disclosed subject matter provides a modified protein or protein fragment that comprises one or more amino acid residues comprising a structure of Formula (V) or (V-IIa). 30 V. Cells, Analytical Techniques, and Instrumentation In some embodiments, one or more of the methods disclosed herein comprise a sample (e.g., a cell sample, cell lysate sample or a biological organism). In some embodiments, the sample for use with the methods described herein is obtained from cells of an animal. In some instances, the animal cell includes a cell from a marine invertebrate, fish, insects, amphibian, reptile, or mammal. In some 35 instances, the mammalian cell is a primate, ape, equine, bovine, porcine, canine, feline, or rodent. In some instances, the mammal is a primate, ape, dog, cat, rabbit, ferret, or the like. In some cases, the - 66 - Attorney Docket No.: 3436/2 PCT rodent is a mouse, rat, hamster, gerbil, hamster, chinchilla, or guinea pig. In some embodiments, the bird cell is from a canary, parakeet or parrots. In some embodiments, the reptile cell is from a turtles, lizard or snake. In some cases, the fish cell is from a tropical fish. In some cases, the fish cell is from a zebrafish (e.g. Danino rerio). In some cases, the worm cell is from a nematode (e.g. C. elegans). In some 5 cases, the amphibian cell is from a frog. In some embodiments, the arthropod cell is from a tarantula or hermit crab. In some embodiments, the sample for use with the methods described herein is obtained from a mammalian cell. In some instances, the mammalian cell is an epithelial cell, connective tissue cell, hormone secreting cell, a nerve cell, a skeletal muscle cell, a blood cell, or an immune system cell. 10 Exemplary mammalian cell lines include, but are not limited to, 293A cells, 293FT cells, 293F cells, 293H cells, HEK 293 cells, CHO DG44 cells, CHO-S cells, CHO-K1 cells, and PC12 cells. In some embodiments, the sample for use with the methods described herein is obtained from cells of a tumor cell line. In some instances, the sample is obtained from cells of a solid tumor cell line. In some instances, the solid tumor cell line is a sarcoma cell line. In some instances, the solid tumor cell 15 line is a carcinoma cell line. In some embodiments, the sarcoma cell line is obtained from a cell line of alveolar rhabdomyosarcoma, alveolar soft part sarcoma, ameloblastoma, angiosarcoma, chondrosarcoma, chordoma, clear cell sarcoma of soft tissue, dedifferentiated liposarcoma, desmoid, desmoplastic small round cell tumor, embryonal rhabdomyosarcoma, epithelioid fibrosarcoma, epithelioid hemangioendothelioma, epithelioid sarcoma, esthesioneuroblastoma, Ewing sarcoma, 20 extrarenal rhabdoid tumor, extraskeletal myxoid chondrosarcoma, extraskeletal osteosarcoma, fibrosarcoma, giant cell tumor, hemangiopericytoma, infantile fibrosarcoma, inflammatory myofibroblastic tumor, Kaposi sarcoma, leiomyosarcoma of bone, liposarcoma, liposarcoma of bone, malignant fibrous histiocytoma (MFH), malignant fibrous histiocytoma (MFH) of bone, malignant mesenchymoma, malignant peripheral nerve sheath tumor, mesenchymal chondrosarcoma, 25 myxofibrosarcoma, myxoid liposarcoma, myxoinflammatory fibroblastic sarcoma, neoplasms with perivascular epitheioid cell differentiation, osteosarcoma, parosteal osteosarcoma, neoplasm with perivascular epitheioid cell differentiation, periosteal osteosarcoma, pleomorphic liposarcoma, pleomorphic rhabdomyosarcoma, PNET/extraskeletal Ewing tumor, rhabdomyosarcoma, round cell liposarcoma, small cell osteosarcoma, solitary fibrous tumor, synovial sarcoma, and telangiectatic 30 osteosarcoma. In some embodiments, the carcinoma cell line is obtained from a cell line of adenocarcinoma, squamous cell carcinoma, adenosquamous carcinoma, anaplastic carcinoma, large cell carcinoma, small cell carcinoma, anal cancer, appendix cancer, bile duct cancer (i.e., cholangiocarcinoma), bladder cancer, brain tumor, breast cancer, cervical cancer, colon cancer, cancer of Unknown Primary (CUP), 35 esophageal cancer, eye cancer, fallopian tube cancer, gastroenterological cancer, kidney cancer, liver cancer, lung cancer, medulloblastoma, melanoma, oral cancer, ovarian cancer, pancreatic cancer, - 67 - Attorney Docket No.: 3436/2 PCT parathyroid disease, penile cancer, pituitary tumor, prostate cancer, rectal cancer, skin cancer, stomach cancer, testicular cancer, throat cancer, thyroid cancer, uterine cancer, vaginal cancer, or vulvar cancer. In some instances, the sample is obtained from cells of a hematologic malignant cell line. In some instances, the hematologic malignant cell line is a T-cell cell line. In some instances, B-cell cell 5 line. In some instances, the hematologic malignant cell line is obtained from a T-cell cell line of: peripheral T-cell lymphoma not otherwise specified (PTCL-NOS), anaplastic large cell lymphoma, angioimmunoblastic lymphoma, cutaneous T-cell lymphoma, adult T-cell leukemia/lymphoma (ATLL), blastic NK-cell lymphoma, enteropathy-type T-cell lymphoma, hematosplenic gamma-delta T-cell lymphoma, lymphoblastic lymphoma, nasal NK/T-cell lymphomas, or treatment-related T-cell 10 lymphomas. In some instances, the hematologic malignant cell line is obtained from a B-cell cell line of: acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute monocytic leukemia (AMoL), chronic lymphocytic leukemia (CLL), high-risk chronic lymphocytic leukemia (CLL), small lymphocytic lymphoma (SLL), high-risk small 15 lymphocytic lymphoma (SLL), follicular lymphoma (FL), mantle cell lymphoma (MCL), Waldenstrom’s macroglobulinemia, multiple myeloma, extranodal marginal zone B cell lymphoma, nodal marginal zone B cell lymphoma, Burkitt’s lymphoma, non-Burkitt high grade B cell lymphoma, primary mediastinal B-cell lymphoma (PMBL), immunoblastic large cell lymphoma, precursor B- lymphoblastic lymphoma, B cell prolymphocytic leukemia, lymphoplasmacytic lymphoma, splenic 20 marginal zone lymphoma, plasma cell myeloma, plasmacytoma, mediastinal (thymic) large B cell lymphoma, intravascular large B cell lymphoma, primary effusion lymphoma, or lymphomatoid granulomatosis. In some embodiments, the sample for use with the methods described herein is obtained from a tumor cell line. Exemplary tumor cell lines include, but are not limited to, 600MPE, AU565, BT-20, 25 BT-474, BT-483, BT-549, Evsa-T, Hs578T, MCF-7, MDA-MB-231, SkBr3, T-47D, HeLa, DU145, PC3, LNCaP, A549, H1299, NCI-H460, A2780, SKOV-3/Luc, Neuro2a, RKO, RKO-AS45-1, HT-29, SW1417, SW948, DLD-1, SW480, Capan-1, MC/9, B72.3, B25.2, B6.2, B38.1, DMS 153, SU.86.86, SNU-182, SNU-423, SNU-449, SNU-475, SNU-387, Hs 817.T, LMH, LMH/2A, SNU-398, PLHC-1, HepG2/SF, OCI-Ly1, OCI-Ly2, OCI-Ly3, OCI-Ly4, OCI-Ly6, OCI-Ly7, OCI-Ly10, OCI-Ly18, OCI- 30 Ly19, U2932, DB, HBL-1, RIVA, SUDHL2, TMD8, MEC1, MEC2, 8E5, CCRF-CEM, MOLT-3, TALL-104, AML-193, THP-1, BDCM, HL-60, Jurkat, RPMI 8226, MOLT-4, RS4, K-562, KASUMI- 1, Daudi, GA-10, Raji, JeKo-1, NK-92, and Mino. In some embodiments, the sample for use in the methods is from any tissue or fluid from an individual. Samples include, but are not limited to, tissue (e.g. connective tissue, muscle tissue, nervous 35 tissue, or epithelial tissue), whole blood, dissociated bone marrow, bone marrow aspirate, pleural fluid, peritoneal fluid, central spinal fluid, abdominal fluid, pancreatic fluid, cerebrospinal fluid, brain fluid, - 68 - Attorney Docket No.: 3436/2 PCT ascites, pericardial fluid, urine, saliva, bronchial lavage, sweat, tears, ear flow, sputum, hydrocele fluid, semen, vaginal flow, milk, amniotic fluid, and secretions of respiratory, intestinal or genitourinary tract. In some embodiments, the sample is a tissue sample, such as a sample obtained from a biopsy or a tumor tissue sample. In some embodiments, the sample is a blood serum sample. In some embodiments, 5 the sample is a blood cell sample containing one or more peripheral blood mononuclear cells (PBMCs). In some embodiments, the sample contains one or more circulating tumor cells (CTCs). In some embodiments, the sample contains one or more disseminated tumor cells (DTC, e.g., in a bone marrow aspirate sample). In some embodiments, the samples are obtained from the individual by any suitable means of 10 obtaining the sample using well-known and routine clinical methods. Procedures for obtaining tissue samples from an individual are well known. For example, procedures for drawing and processing tissue sample such as from a needle aspiration biopsy is well-known and is employed to obtain a sample for use in the methods provided. Typically, for collection of such a tissue sample, a thin hollow needle is inserted into a mass such as a tumor mass for sampling of cells that, after being stained, will be examined 15 under a microscope. In some embodiments, the sample is a biological organism. In some embodiments, the biological organism is a rodent, e.g., a mouse or a rat. In some embodiments, the biological organism is a primate, e.g., a monkey. In some embodiments, the biological organism is a bacteria or a fungi. VI. Sample Preparation and Analysis 20 In some embodiments, the sample (e.g., cell sample, cell lysate sample, or comprising isolated proteins) is a sample solution. In some instances, the sample solution comprises a solution such as a buffer (e.g. phosphate buffered saline) or a media. In some embodiments, the media is an isotopically labeled media. In some instances, the sample solution is a cell solution. In some embodiments, the sample (e.g., cell sample, cell lysate sample, or comprising isolated 25 proteins) is incubated with one or more compound probes for analysis of protein-probe interactions. In some instances, the sample (e.g., cell sample, cell lysate sample, or comprising isolated proteins) is further incubated in the presence of an additional compound probe prior to addition of the one or more probes. In other instances, the sample (e.g., cell sample, cell lysate sample, or comprising isolated proteins) is further incubated with a non-probe small molecule ligand, in which the non-probe small 30 molecule ligand does not contain a photoreactive moiety and/or an alkyne group. In such instances, the sample is incubated with a probe and non-probe small molecule ligand for competitive protein profiling analysis. In some cases, the sample is compared with a control. In some cases, a difference is observed between a set of probe protein interactions between the sample and the control. In some instances, the 35 difference correlates to the interaction between the small molecule fragment and the proteins. - 69 - Attorney Docket No.: 3436/2 PCT In some embodiments, one or more methods are utilized for labeling a sample (e.g. cell sample, cell lysate sample, or comprising isolated proteins) for analysis of probe protein interactions. In some instances, a method comprises labeling the sample (e.g. cell sample, cell lysate sample, or comprising isolated proteins) with an enriched media. In some cases, the sample (e.g. cell sample, cell lysate 5 sample, or comprising isolated proteins) is labeled with isotope-labeled amino acids, such as ¹³C or ¹⁵N- labeled amino acids. In some cases, the labeled sample is further compared with a non-labeled sample to detect differences in probe protein interactions between the two samples. In some instances, this difference is a difference of a target protein and its interaction with a small molecule ligand in the labeled sample versus the non-labeled sample. In some instances, the difference is an increase, decrease 10 or a lack of protein-probe interaction in the two samples. In some instances, the isotope-labeled method is termed SILAC, stable isotope labeling using amino acids in cell culture. In some embodiments, a method comprises incubating a sample (e.g. cell sample, cell lysate sample, or comprising isolated proteins) with a labeling group (e.g., an isotopically labeled labeling group) to tag one or more proteins of interest for further analysis. In such cases, the detectable labeling 15 group comprises a biotin, a streptavidin, bead, resin, a solid support, or a combination thereof, and further comprises a linker that is optionally isotopically labeled. As described above, the linker can be about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more residues in length and might further comprise a cleavage site, such as a protease cleavage site (e.g., TEV cleavage site). In some cases, the labeling group is a biotin-linker moiety, which is optionally isotopically labeled with ¹³C and ¹⁵N atoms at one or more20 amino acid residue positions within the linker. In some cases, the biotin-linker moiety is a isotopically- labeled TEV-tag. In some embodiments, an isotopic reductive dimethylation (ReDi) method is utilized for processing a sample. In some cases, the ReDi labeling method involves reacting peptides with formaldehyde to form a Schiff base, which is then reduced by cyanoborohydride. This reaction 25 dimethylates free amino groups on N-termini and lysine side chains and monomethylates N-terminal prolines. In some cases, the ReDi labeling method comprises methylating peptides from a first processed sample with a “light” label using reagents with hydrogen atoms in their natural isotopic distribution and peptides from a second processed sample with a “heavy” label using deuterated formaldehyde and cyanoborohydride. Subsequent proteomic analysis (e.g., mass spectrometry analysis) 30 based on a relative peptide abundance between the heavy and light peptide version might be used for analysis of probe-protein interactions. In some embodiments, isobaric tags for relative and absolute quantitation (iTRAQ) method is utilized for processing a sample. In some cases, the iTRAQ method is based on the covalent labeling of the N-terminus and side chain amines of peptides from a processed sample. In some cases, reagent such 35 as 4-plex or 8-plex is used for labeling the peptides. - 70 - Attorney Docket No.: 3436/2 PCT In some embodiments, the probe-protein complex is further conjugated to a chromophore, such as a fluorophore. In some instances, the probe-protein complex is separated and visualized utilizing an electrophoresis system, such as through a gel electrophoresis, or a capillary electrophoresis. Exemplary gel electrophoresis includes agarose based gels, polyacrylamide based gels, or starch based gels. In 5 some instances, the probe-protein is subjected to a native electrophoresis condition. In some instances, the probe-protein is subjected to a denaturing electrophoresis condition. In some instances, the probe-protein after harvesting is further fragmentized to generate protein fragments. In some instances, fragmentation is generated through mechanical stress, pressure, or chemical means. In some instances, the protein from the probe-protein complexes is fragmented by a 10 chemical means. In some embodiments, the chemical means is a protease. Exemplary proteases include, but are not limited to, serine proteases such as chymotrypsin A, penicillin G acylase precursor, dipeptidase E, DmpA aminopeptidase, subtilisin, prolyl oligopeptidase, D-Ala-D-Ala peptidase C, signal peptidase I, cytomegalovirus assemblin, Lon-A peptidase, peptidase Clp, Escherichia coli phage KIF endosialidase CIMCD self-cleaving protein, nucleoporin 145, lactoferrin, murein tetrapeptidase 15 LD-carboxypeptidase, or rhomboid-1; threonine proteases such as ornithine acetyltransferase; cysteine proteases such as TEV protease, amidophosphoribosyltransferase precursor, gamma-glutamyl hydrolase (Rattus norvegicus), hedgehog protein, DmpA aminopeptidase, papain, bromelain, cathepsin K, calpain, caspase-1, separase, adenain, pyroglutamyl-peptidase I, sortase A, hepatitis C virus peptidase 2, sindbis virus-type nsP2 peptidase, dipeptidyl-peptidase VI, or DeSI-1 peptidase; aspartate 20 proteases such as beta-secretase 1 (BACE1), beta-secretase 2 (BACE2), cathepsin D, cathepsin E, chymosin, napsin-A, nepenthesin, pepsin, plasmepsin, presenilin, or renin; glutamic acid proteases such as AfuGprA; and metalloproteases such as peptidase_M48. In some instances, the fragmentation is a random fragmentation. In some instances, the fragmentation generates specific lengths of protein fragments, or the shearing occurs at particular 25 sequence of amino acid regions. In some instances, the protein fragments are further analyzed by a proteomic method such as by liquid chromatography (LC) (e.g. high performance liquid chromatography), liquid chromatography- mass spectrometry (LC-MS), matrix-assisted laser desorption/ionization (MALDI-TOF), gas chromatography-mass spectrometry (GC-MS), capillary electrophoresis-mass spectrometry (CE-MS), 30 or nuclear magnetic resonance imaging (NMR). In some embodiments, the LC method is any suitable LC methods well known in the art, for separation of a sample into its individual parts. This separation occurs based on the interaction of the sample with the mobile and stationary phases. Since there are many stationary/mobile phase combinations that are employed when separating a mixture, there are several different types of 35 chromatography that are classified based on the physical states of those phases. In some embodiments, the LC is further classified as normal-phase chromatography, reverse-phase chromatography, size- - 71 - Attorney Docket No.: 3436/2 PCT exclusion chromatography, ion-exchange chromatography, affinity chromatography, displacement chromatography, partition chromatography, flash chromatography, chiral chromatography, and aqueous normal-phase chromatography. In some embodiments, the LC method is a high performance liquid chromatography (HPLC) 5 method. In some embodiments, the HPLC method is further categorized as normal-phase chromatography, reverse-phase chromatography, size-exclusion chromatography, ion-exchange chromatography, affinity chromatography, displacement chromatography, partition chromatography, chiral chromatography, and aqueous normal-phase chromatography. In some embodiments, the HPLC method of the present disclosure is performed by any standard 10 techniques well known in the art. Exemplary HPLC methods include hydrophilic interaction liquid chromatography (HILIC), electrostatic repulsion-hydrophilic interaction liquid chromatography (ERLIC) and reverse phase liquid chromatography (RPLC). In some embodiments, the LC is coupled to a mass spectroscopy as a LC-MS method. In some embodiments, the LC-MS method includes ultra-performance liquid chromatography-electrospray 15 ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-QTOF-MS), ultra-performance liquid chromatography-electro spray ionization tandem mass spectrometry (UPLC-ESI-MS/MS), reverse phase liquid chromatography-mass spectrometry (RPLC-MS), hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS), hydrophilic interaction liquid chromatography-triple quadrupole tandem mass spectrometry (HILIC-QQQ), electrostatic repulsion-hydrophilic interaction 20 liquid chromatography-mass spectrometry (ERLIC-MS), liquid chromatography time-of-flight mass spectrometry (LC-QTOF-MS), liquid chromatography-tandem mass spectrometry (LC-MS/MS), multidimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS). In some instances, the LC-MS method is LC/LC-MS/MS. In some embodiments, the LC-MS methods of the present disclosure are performed by standard techniques well known in the art. 25 In some embodiments, the GC is coupled to a mass spectroscopy as a GC-MS method. In some embodiments, the GC-MS method includes two-dimensional gas chromatography time-of-flight mass spectrometry (GC*GC-TOFMS), gas chromatography time-of-flight mass spectrometry (GC-QTOF- MS) and gas chromatography-tandem mass spectrometry (GC-MS/MS). In some embodiments, CE is coupled to a mass spectroscopy as a CE-MS method. In some30 embodiments, the CE-MS method includes capillary electrophoresis-negative electrospray ionization- mass spectrometry (CE-ESI-MS), capillary electrophoresis-negative electrospray ionization- quadrupole time of flight-mass spectrometry (CE-ESI-QTOF-MS) and capillary electrophoresis- quadrupole time of flight-mass spectrometry (CE-QTOF-MS). In some embodiments, the nuclear magnetic resonance (NMR) method is any suitable method 35 well known in the art for the detection of one or more cysteine binding proteins or protein fragments disclosed herein. In some embodiments, the NMR method includes one dimensional (1D) NMR - 72 - Attorney Docket No.: 3436/2 PCT methods, two dimensional (2D) NMR methods, solid state NMR methods and NMR chromatography. Exemplary 1D NMR methods include ¹Hydrogen, ¹³Carbon, ¹⁵Nitrogen, ¹⁷Oxygen, ¹⁹Fluorine, 3¹Phosphorus, ³⁹Potassium, ²³Sodium, ³³Sulfur, ⁸⁷Strontium, ²⁷Aluminium, ⁴³Calcium, ³⁵Chlorine, 3⁷Chlorine, ⁶³Copper, ⁶⁵Copper, ⁵⁷Iron, ²⁵Magnesium, ¹⁹⁹Mercury or ⁶⁷Zinc NMR method, distortionless 5 enhancement by polarization transfer (DEPT) method, attached proton test (APT) method and 1D- incredible natural abundance double quantum transition experiment (INADEQUATE) method. Exemplary 2D NMR methods include correlation spectroscopy (COSY), total correlation spectroscopy (TOCSY), 2D-INADEQUATE, 2D-adequate double quantum transfer experiment (ADEQUATE), nuclear overhauser effect spectroscopy (NOSEY), rotating-frame NOE spectroscopy (ROESY), 10 heteronuclear multiple-quantum correlation spectroscopy (HMQC), heteronuclear single quantum coherence spectroscopy (HSQC), short range coupling and long range coupling methods. Exemplary solid state NMR method include solid state ¹³Carbon NMR, high resolution magic angle spinning (HR- MAS) and cross polarization magic angle spinning (CP-MAS) NMR methods. Exemplary NMR techniques include diffusion ordered spectroscopy (DOSY), DOSY-TOCSY and DOSY-HSQC. 15 In some embodiments, the results from the mass spectroscopy method are analyzed by an algorithm for protein identification. In some embodiments, the algorithm combines the results from the mass spectroscopy method with a protein sequence database for protein identification. In some embodiments, the algorithm comprises ProLuCID algorithm, Probity, Scaffold, SEQUEST, or Mascot. In accordance with the presently disclosed subject matter, as described above or as discussed 20 in the EXAMPLES below, there can be employed conventional chemical, cellular, histochemical, biochemical, molecular biology, microbiology, recombinant DNA, and clinical techniques which are known to those of skill in the art. Such techniques are explained fully in the literature. See for example, Sambrook & Russell, 2001; Glover, 1985; Gait, 1984; Harlow & Lane, 1988; Roe et al., 1996; Ausubel et al., 2002; and Ausubel et al., 2003. 25 VII. Kits/Articles of Manufacture Disclosed herein, in certain embodiments, are kits and articles of manufacture for use with one or more methods described herein. In some embodiments, described herein is a kit for generating a protein comprising a detectable group and/or a fragment of a ligand compound described herein. In some embodiments, such kit includes a probe or ligand as described herein, small molecule fragments 30 or libraries, and/or controls, and reagents suitable for carrying out one or more of the methods described herein. In some instances, the kit further comprises samples, such as a cell sample, and suitable solutions such as buffers or media. In some embodiments, the kit further comprises recombinant proteins for use in one or more of the methods described herein. In some embodiments, additional components of the kit comprises a carrier, package, or container that is compartmentalized to receive one or more 35 containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in a method described herein. Suitable containers include, for example, bottles, - 73 - Attorney Docket No.: 3436/2 PCT vials, plates, syringes, and test tubes. In one embodiment, the containers are formed from a variety of materials such as glass or plastic. The articles of manufacture provided herein contain packaging materials. Examples of pharmaceutical packaging materials include, but are not limited to, bottles, tubes, bags, containers, and 5 any packaging material suitable for a selected formulation and intended mode of use. For example, the container(s) include probes, ligands, control compounds, and one or more reagents for use in a method disclosed herein. The presently disclosed kits and articles of manufacture optionally include an identifying description or label or instructions relating to its use in the methods described herein. For example, a 10 kit typically includes labels listing contents and/or instructions for use, and package inserts with instructions for use. A set of instructions will also typically be included. In some embodiments, a label is on or associated with the container. In some embodiments, a label is on a container when letters, numbers or other characters forming the label are attached, molded or etched into the container itself; a label is associated with a container when it is present within a receptacle or carrier that also holds the 15 container, e.g., as a package insert. In some embodiments, a label is used to indicate that the contents are to be used for a specific therapeutic application. The label also indicates directions for use of the contents, such as in the methods described herein. EXAMPLES The following EXAMPLES provide illustrative embodiments. In light of the present disclosure 20 and the general level of skill in the art, those of skill will appreciate that the following EXAMPLES are intended to be exemplary only and that numerous changes, modifications, and alterations can be employed without departing from the scope of the presently disclosed subject matter. Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative EXAMPLES, make and utilize the compounds of 25 the presently disclosed subject matter and practice the methods of the presently disclosed subject matter. The following EXAMPLES therefore particularly point out embodiments of the presently disclosed subject matter and are not to be construed as limiting in any way the remainder of the disclosure. EXAMPLE 1 Synthesis and Characterization of PhAzE Compounds 30 All chemicals used were reagent grade and used as supplied, except where noted. N,N- Dimethylformamide (DMF), dichloromethane (CH₂Cl₂), toluene and tetrahydrofuran (THF) were used without any further purification steps. Analytical thin layer chromatography (TLC) was performed on Merck silica gel 60 F254 plates (0.25 mm). Flash column chromatography was carried out using forced flow of the indicated solvent on Silica Gel 60 (230-400 mesh) purchased from Fisher Scientific. 35 Compounds were visualized by UV-irradiation. ¹H and ¹³C NMR spectra were recorded on a Varian Inova 500 (500 MHz), 600 (600 MHz), or Bruker Avance III 800 (800 MHz) spectrometers in CDCl₃, - 74 - Attorney Docket No.: 3436/2 PCT Acetone-d₆, or DMSO-d₆ with chemical shifts referenced to internal standards (CDCl₃: 7.26 ppm ¹H, 77.16 ppm ¹³C ; (CD₃)₂CO: 2.05 ppm ¹H, 29.84 and 206.26 ppm ¹³C; (CD₃)₂CO: 2.50ppm ¹H, 40.00 ppm ¹³C) unless stated otherwise. Splitting patterns are indicated as s, singlet; d, doublet; t, triplet; q, quartet; m, multiplet; br, broad singlet for 1 H-NMR data. NMR chemical shifts (δ) are reported in ppm 5 and coupling constants (J) are reported in Hz. High resolution mass spectral (HRMS) data were obtained by an Agilent 6545B LC/Q-TOF (Agilent Technologies, Santa Clara, California, United States of America). Chemical Suppliers: Chemicals were purchased from the following suppliers: Propargylamine (Fisher Scientific); Water, Acetonitrile, Dichloromethane, Acetone, Ethyl acetate, n-Heptane, Hexanes,10 Formic acid (OPTIMA®), Acetic acid (OPTIMA®), and Sodium sulfate (Fisher Chemical); 4-bromo- 1H-imidazole, 5-trifluoromethyl-1H-imidazole, methyl trifluoro-methanesulfonate, 4- (chlorosulfonyl)benzoic acid, 3-phenyl-1H-pyrazole, 3-(4-methoxyphenyl)-1H-pyrazole, 3-(4- fluorophenyl)-1H-pyrazole, 4-(4-fluorophenyl)-1H-imidazole, 4-phenyl-1H-imidazole, and 4-bromo- 1H-imidazole (Combi-Blocks); N,N-Diisopropylethylamine, 4-Phenylpiperidine, and 1,2,4-1H-15 Triazole (Acros Organics); 4’-methoxybiphenyl-4-sulfonyl chloride, 5-phenyl-2H-tetrazole, 5-(4- methoxy-phenyl)-2H-tetrazole, and 5-(4-fluorophenyl)-2H-tetrazole (Alfa Aesar); Cyclopropylamine, 4-methoxybenzenesulfonyl chloride, cyclopropane-sulfonyl chloride, and 1H-pyrazole (Oakwood Chemicals); 4’-methoxy-[1,1’-biphenyl]-4-sulfonyl chloride (1ClickChemistry); and 4- trifluoromethyl-1H-imidazole (Enamine). 20 Synthesis and Experimental Data for Cyclic Phosphoramidotriazoles: Scheme 2: Synthesis of Cyclic Phosphoroamidotriazoles Phosphoroamidotriazoles were prepared according to the route shown in Scheme 2, above. The first two steps (General Procedure A and General Procedure B) were performed as described in Sun et 25 al., 2023. General Procedure A: To a solution of amine (1.00 equiv) in MeOH (0.8 M) at room temperature was added salicylaldehyde (1.00 equiv). The reaction was stirred at room temperature for 2 hours. Once complete, the reaction was diluted with MeOH to 0.4 M and cooled to 0 °C. Sodium - 75 - Attorney Docket No.: 3436/2 PCT borohydride (1.00 equiv) was slowly added. The resulting mixture was stirred for 10 minutes at 0 °C then warmed to room temperature. Once complete, the reaction was poured into ice-cold water and extracted with ethyl acetate three times. The crude material was purified by flash chromatography eluting with ethylacetate-hexane to afford the desired aminophenol. 5 General Procedure B: To a solution of aminophenol (1.00 equiv) in CH₂Cl₂ (0.2 M), cooled to – 78 °C, was slowly added phosphorous oxychloride (1.00 equiv) followed by Et₃N (2.00 equiv). The reaction was slowly warmed to room temperature and stirred for one hour. The reaction was diluted with CH₂Cl₂ and washed with NH₄Cl (sat., aq.). The organic phase was dried over anhydrous Na₂SO₄ and concentrated in vacuo. The crude material was purified by flash chromatography eluting with ethyl 10 acetate-hexanes to afford the desired cyclic phosphoramidochloridate. General Procedure C: To a solution of phosphoramidochloridate (1.00 equiv) in CH₂Cl₂ (0.2 M) was added azole (1.00 equiv) and EtN(iPr)₂ (1.00 equiv). The reaction was stirred overnight. The reaction was concentrated in vacou and the crude material purified by flash chromatography with ethyl acetate-hexanes to afford the desired cyclic phosphoramidoazole. 15 Characterization of Phosphoramidoazole (PhAzE) Probes: 3-(prop-2-yn-1-yl)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (PhAzE-1) White solid (78%, 88 mg) ¹H NMR (600 MHz, cdcl₃) δ 8.73 (d, J = 0.9 Hz, 1H), 8.04 (d, J = 1.9 Hz, 20 1H), 7.29 (dddt, J = 7.6, 5.9, 2.4, 1.3 Hz, 1H), 7.21 – 7.16 (m, 2H), 7.05 (dd, J = 8.0, 1.0 Hz, 1H), 4.95 (ddd, J = 14.6, 4.0, 1.1 Hz, 1H), 4.32 (dd, J = 23.3, 14.6 Hz, 1H), 4.20 (ddd, J = 18.0, 6.6, 2.5 Hz, 1H), 3.92 (td, J = 17.7, 2.5 Hz, 1H), 2.14 (t, J = 2.5 Hz, 1H).³¹P NMR (243 MHz, cdcl₃) δ -9.53.¹³C NMR (201 MHz, cdcl₃) δ 154.9 (d, J = 17.5 Hz), 149.7 (d, J = 8.4 Hz), 149.3 (d, J = 10.5 Hz), 129.4, 129.0 (d, J = 15.2 Hz), 127.1, 125.2, 124.7 (d, J = 3.5 Hz), 121.9 (d, J = 7.2 Hz), 118.7 (d, J = 9.2 Hz), 76.2 25 (d, J = 4.1 Hz), 74.1, 73.7 (d, J = 3.7 Hz), 49.6, 48.5 (d, J = 22.4 Hz), 37.5 (d, J = 4.7 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 275.0692, Found 275.0695. 2-(3-phenyl-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza- phosphinine 2-oxide (PhAzE-2) 30 White solid (66%, 96 mg) ¹H NMR (600 MHz, cdcl₃) δ 8.73 (d, J = 0.9 Hz, 1H), 8.07 – 8.01 (m, 2H), 7.42 – 7.38 (m, 3H), 7.32 – 7.29 (m, 1H), 7.24 (dd, J = 7.7, 2.0 Hz, 1H), 7.20 (td, J = 7.4, 1.2 Hz, 1H), 7.08 (dd, J = 8.2, 1.1 Hz, 1H), 5.06 (ddt, J = 14.5, 4.0, 1.0 Hz, 1H), 4.34 (dd, J = 23.8, 14.6 Hz, 1H), - 76 - Attorney Docket No.: 3436/2 PCT 4.21 (ddd, J = 18.0, 6.4, 2.5 Hz, 1H), 3.96 (ddd, J = 18.0, 17.1, 2.5 Hz, 1H), 2.12 (t, J = 2.5 Hz, 1H). 3¹P NMR (243 MHz, cdcl₃) δ -9.16.¹³C NMR (201 MHz, CDCl₃) δ 165.6 (d, J = 17.0 Hz), 149.9 (d, J = 10.2 Hz), 149.8 (d, J = 9.0 Hz), 130.1, 130.0, 129.3, 129.0, 128.7, 127.0, 127.0, 126.6, 125.1, 124.7 (d, J = 3.6 Hz), 122.3 (d, J = 6.8 Hz), 118.8 (d, J = 8.9 Hz), 76.3 (d, J = 4.3 Hz), 74.1, 73.7 (d, J = 5.0 5 Hz), 49.7, 48.5 (d, J = 23.2 Hz), 37.5 (d, J = 5.0 Hz).¹³C NMR (201 MHz, cdcl₃) δ 165.58 (d, J = 17.0 Hz), 149.88 (d, J = 10.2 Hz), 149.82 (d, J = 9.0 Hz), 130.12, 130.03, 129.34, 128.96, 128.71, 127.03, 126.98, 126.58, 125.09, 124.65 (d, J = 3.6 Hz), 122.32 (d, J = 6.8 Hz), 118.75 (d, J = 8.9 Hz), 76.30 (d, J = 4.3 Hz), 74.06, 73.69 (d, J = 5.0 Hz), 49.67, 48.52 (d, J = 23.2 Hz), 37.52 (d, J = 5.0 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 351.1005, Found 351.1008. 10 3-(prop-2-yn-1-yl)-2-(3-(4-(trifluoromethoxy)phenyl)-1H-1,2,4-triazol-1-yl)-3,4- dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (PhAzE-3) White solid (67%, 121 mg) ¹H NMR (600 MHz, cdcl₃) δ 8.73 (d, J = 0.9 Hz, 1H), 8.08 – 8.04 (m, 2H), 7.32 (t, J = 7.7 Hz, 1H), 7.25 – 7.20 (m, 5H), 7.08 (dd, J = 8.1, 1.1 Hz, 1H), 5.04 (dd, J = 14.6, 3.9 Hz, 15 1H), 4.35 (dd, J = 23.6, 14.6 Hz, 1H), 4.23 (ddd, J = 18.0, 6.5, 2.5 Hz, 1H), 3.96 (ddd, J = 18.0, 17.3, 2.5 Hz, 1H), 2.12 (t, J = 2.5 Hz, 1H).¹⁹F NMR (564 MHz, cdcl₃) δ -57.79.³¹P NMR (243 MHz, cdcl₃) δ -9.36.¹³C NMR (201 MHz, cdcl₃) δ 164.5 (d, J = 17.1 Hz), 150.6, 150.1 (d, J = 10.2 Hz), 149.8 (d, J = 8.6 Hz), 129.4, 128.7, 128.6, 128.2, 127.0, 125.2, 124.7, 122.2 (d, J = 7.2 Hz), 121.3, 121.1, 118.8 (d, J = 9.2 Hz), 76.3 (d, J = 4.0 Hz), 74.1, 49.7, 48.5 (d, J = 25.0 Hz), 37.6 (d, J = 4.6 Hz). ESI-TOF 20 (HRMS) m/z [M+H]⁺ 435.0828, Found 435.0833. 2-(3-(2-fluorophenyl)-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]- oxazaphosphinine 2-oxide ( White solid (51%, 78 mg) ¹H NMR (600 MHz, cdcl₃) δ 8.78 (d, J = 0.9 Hz, 1H), 7.99 (td, J = 7.6, 1.8 25 Hz, 1H), 7.38 (dddd, J = 8.3, 7.0, 4.9, 1.9 Hz, 1H), 7.30 (t, J = 7.7 Hz, 1H), 7.22 (dd, J = 7.7, 1.9 Hz, 1H), 7.19 (td, J = 7.5, 1.1 Hz, 2H), 7.13 (ddd, J = 10.9, 8.3, 1.1 Hz, 1H), 7.07 (dd, J = 8.2, 1.1 Hz, 1H), 5.10 (dd, J = 14.5, 3.6 Hz, 1H), 4.34 (dd, J = 24.2, 14.5 Hz, 1H), 4.21 (ddd, J = 18.0, 6.3, 2.5 Hz, 1H), 4.01 – 3.93 (m, 1H).¹⁹F NMR (564 MHz, cdcl₃) δ -111.78 (ddd, J = 10.8, 7.5, 5.0 Hz).³¹P NMR (243 MHz, cdcl₃) δ -9.15.¹³C NMR (201 MHz, cdcl₃) δ 160.7 (d, J = 256.4 Hz), 149.5 (d, J = 9.9 Hz), 131.6 30 (d, J = 8.3 Hz), 130.6, 129.3, 127.0, 125.1, 124.3 (d, J = 3.7 Hz), 122.4 (d, J = 7.2 Hz), 118.7 (d, J = - 77 - Attorney Docket No.: 3436/2 PCT 9.3 Hz), 116.7 (d, J = 21.3 Hz), 74.1, 49.8, 37.5 (d, J = 4.5 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 369.0911, Found 369.0913. 2-(3-(furan-2-yl)-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza- phosphinine 2-oxide (PhAzE-5) 5 Clear oil (74%, 206 mg) ¹H NMR (400 MHz, CDCl₃) δ 8.69 (d, J = 0.9 Hz, 1H), 7.50 – 7.44 (m, 1H), 7.25 (d, J = 7.3 Hz, 2H), 7.21 – 7.11 (m, 2H), 7.04 (dd, J = 8.2, 1.1 Hz, 1H), 6.97 (dd, J = 3.4, 0.8 Hz, 1H), 6.45 (dd, J = 3.4, 1.8 Hz, 1H), 5.01 (dd, J = 14.7, 4.1 Hz, 1H), 4.28 (dd, J = 24.3, 14.7 Hz, 1H), 4.15 (ddd, J = 17.9, 6.6, 2.5 Hz, 1H), 3.93 (ddd, J = 17.9, 16.6, 2.5 Hz, 1H), 2.14 (t, J = 2.5 Hz, 1H). 10 ³¹P NMR (162 MHz, CDCl₃) δ -8.91 (t, J = 21.0 Hz).¹³C NMR (101 MHz, CDCl₃) δ 158.5 (d, J = 17.5 Hz), 149.9 (d, J = 10.2 Hz), 149.6 (d, J = 8.0 Hz), 145.4, 144.0, 129.3 (d, J = 1.5 Hz), 127.0, 125.0, 122.4, 122.4, 118.6, 118.5, 111.5 (d, J = 25.5 Hz), 77.4, 76.27 (d, J = 4.4 Hz), 74.1, 49.4, 37.5. ESI- TOF (HRMS) m/z [M+H]⁺ 341.0798, Found 341.0799. 3-((S)-3,3-dimethylbutan-2-yl)-2-(3-phenyl-1H-1,2,4-triazol-1-yl)-7-(prop-2-yn-1-yloxy)-3,4- 15 dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide ((S)-PhAzE-6) White solid (14%, 80 mg) ¹H NMR (600 MHz, cdcl₃) δ 8.73 (d, J = 0.9 Hz, 1H), 8.72 (d, J = 0.9 Hz, 1H), 8.13 – 8.10 (m, 1H), 8.10 – 8.07 (m, 2H), 7.42 (ddd, J = 6.3, 3.6, 1.6 Hz, 6H), 7.09 (dd, J = 11.9, 8.3 Hz, 2H), 6.81 – 6.74 (m, 4H), 4.99 (d, J = 15.6 Hz, 1H), 4.86 (dd, J = 14.7, 5.9 Hz, 1H), 4.67 (t, J 20 = 2.2 Hz, 4H), 4.18 (ddd, J = 26.7, 15.2, 3.7 Hz, 2H), 3.83 (s, 1H), 3.57 (dq, J = 11.8, 7.1 Hz, 1H), 2.54 (q, J = 2.3 Hz, 2H), 1.20 (d, J = 7.0 Hz, 2H), 1.12 (d, J = 7.1 Hz, 4H), 0.98 (s, 11H), 0.79 (s, 7H). ³¹P NMR (243 MHz, cdcl₃) δ -4.75, -6.04 (ddd, J = 26.5, 11.6, 5.9 Hz). ¹³C NMR (201 MHz, CDCl₃) δ 165.5 (t, J = 16.2 Hz), 158.3, 151.1 (d, J = 7.4 Hz), 150.9 (d, J = 7.9 Hz), 150.2 (d, J = 8.9 Hz), 149.9 (d, J = 10.5 Hz), 130.2 (d, J = 7.2 Hz), 130.1, 128.7, 128.7, 127.2, 127.1, 127.0, 126.6, 117.2 (d, J = 6.0 25 Hz), 111.8, 111.7, 105.5 (d, J = 8.4 Hz), 105.4 (d, J = 8.8 Hz), 78.0, 78.0, 76.3, 76.3, 56.3, 36.3 (d, J = 2.1 Hz), 36.2 (d, J = 4.8 Hz), 27.6, 27.2, 14.1 (d, J = 3.5 Hz), 12.6. ESI-TOF (HRMS) m/z [M+H]⁺ 451.1894, Found 451.1919. 3-ethyl-7-(prop-2-yn-1-yloxy)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza- phosphinine 2-oxide (PhAzE-7) - 78 - Attorney Docket No.: 3436/2 PCT Clear oil (87%, 482 mg) ¹H NMR (600 MHz, cdcl₃) δ 8.73 (s, 1H), 8.05 (d, J = 1.8 Hz, 1H), 7.09 (d, J = 8.5 Hz, 1H), 6.80 (dd, J = 8.5, 2.5 Hz, 1H), 6.67 (d, J = 2.5 Hz, 1H), 4.76 (dd, J = 14.2, 4.8 Hz, 1H), 4.66 (d, J = 2.4 Hz, 2H), 4.21 (dd, J = 22.6, 14.2 Hz, 1H), 3.35 – 3.24 (m, 2H), 2.53 (t, J = 2.4 Hz, 1H), 5 1.12 (t, J = 7.2 Hz, 4H). ³¹P NMR (243 MHz, cdcl₃) δ -9.08. ¹³C NMR (201 MHz, CDCl₃) δ 158.2, 155.0 (d, J = 17.0 Hz), 150.2 (d, J = 8.0 Hz), 149.4 (d, J = 10.2 Hz), 127.5, 115.3 (d, J = 7.5 Hz), 112.3, 105.2 (d, J = 9.4 Hz), 77.9, 76.3, 56.3, 48.5, 43.1 (d, J = 3.7 Hz), 13.2 (d, J = 2.6 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 319.0955, Found 319.0956. 2-(4-bromo-1H-imidazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza-phosphinine 10 2-oxide (PhAzE-8) Clear oil (38%, 227 mg) ¹H NMR (400 MHz, cdcl₃) δ 7.70 (d, J = 1.6 Hz, 1H), 7.33 (dddd, J = 8.2, 5.2, 3.8, 1.3 Hz, 1H), 7.24 – 7.18 (m, 2H), 7.06 (d, J = 8.2 Hz, 1H), 7.02 (t, J = 1.6 Hz, 1H), 4.59 – 4.39 (m, 2H), 4.25 (ddd, J = 18.1, 9.0, 2.5 Hz, 1H), 3.89 (ddd, J = 18.1, 12.9, 2.4 Hz, 1H), 2.32 (t, J = 2.5 Hz, 15 1H).³¹P NMR (162 MHz, cdcl₃) δ -8.70 (p, J = 12.0 Hz).¹³C NMR (201 MHz, CDCl₃) δ 149.2 (d, J = 8.8 Hz), 139.5 (d, J = 5.1 Hz), 130.1, 127.3, 125.8, 122.2 (d, J = 7.4 Hz), 119.2 (d, J = 8.0 Hz), 118.6 (d, J = 15.2 Hz), 118.2 (d, J = 6.8 Hz), 76.5 (d, J = 3.8 Hz), 74.7, 48.7, 37.4 (d, J = 5.8 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 351.9845, Found 351.9844. 3-(prop-2-yn-1-yl)-2-(4-(trifluoromethyl)-1H-imidazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]- 20 oxazaphosphinine 2-oxide ( Clear oil (42%, 293 mg) ¹H NMR (400 MHz, CDCl₃) δ 7.83 – 7.79 (m, 1H), 7.44 – 7.40 (m, 1H), 7.32 (dddd, J = 9.1, 6.1, 1.8, 1.1 Hz, 1H), 7.22 (qd, J = 4.2, 0.9 Hz, 2H), 7.08 – 7.04 (m, 1H), 4.61 – 4.37 (m, 2H), 4.27 (ddd, J = 18.1, 8.9, 2.5 Hz, 1H), 3.88 (ddd, J = 18.1, 13.6, 2.5 Hz, 1H), 2.30 (t, J = 2.5 25 Hz, 1H). ¹⁹F NMR (377 MHz, CDCl₃) δ -63.53. ³¹P NMR (162 MHz, cdcl₃) δ -9.02 (p, J = 12.1 Hz). 1³C NMR (201 MHz, CDCl₃) δ 149.0 (d, J = 8.8 Hz), 140.4 (d, J = 5.1 Hz), 130.2, 127.3, 126.0, 122.1 (d, J = 7.8 Hz), 121.0 (q, J = 267.3 Hz), 119.5 (dt, J = 7.8, 3.9 Hz), 119.2 (d, J = 8.0 Hz), 76.3 (d, J = 3.6 Hz), 74.8, 48.8, 37.5 (d, J = 5.8 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 342.0614, Found 342.0643. 3-cyclopropyl-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide 30 (PhAzE-10) - 79 - Attorney Docket No.: 3436/2 PCT Clear oil (%,mg) ¹H NMR (400 MHz, CDCl₃) δ 8.78 (d, J = 0.9 Hz, 1H), 8.06 (d, J = 1.9 Hz, 1H), 7.30 – 7.24 (m, 2H), 7.20 – 7.13 (m, 2H), 7.01 (dd, J = 8.1, 1.1 Hz, 1H), 4.82 (ddd, J = 14.6, 6.3, 1.1 Hz, 1H), 4.39 (dd, J = 21.3, 14.6 Hz, 1H), 2.34 (ttd, J = 6.8, 3.6, 1.4 Hz, 1H), 1.19 (dddd, J = 10.4, 6.7, 5.5, 5 3.6 Hz, 1H), 0.77 (dtd, J = 9.8, 6.8, 5.5 Hz, 1H), 0.67 (dtdd, J = 9.8, 6.7, 5.1, 1.6 Hz, 1H), 0.54 – 0.46 (m, 1H). ³¹P NMR (162 MHz, CDCl₃) δ -9.18 (dd, J = 21.9, 6.3 Hz).¹³C NMR (201 MHz, CDCl₃) δ 129.3, 126.9, 125.1, 122.7 (d, J = 6.6 Hz), 118.5 (d, J = 8.2 Hz), 51.7 (d, J = 2.9 Hz), 29.6 (d, J = 4.0 Hz), 7.9, 5.9 (d, J = 6.6 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 277.0849, Found 277.0856. 3-(cyclopropylmethyl)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphos-phinine 2- 10 oxide (PhAzE-11) Clear oil (%,mg) ¹H NMR (400 MHz, CDCl₃) δ 8.72 (d, J = 0.9 Hz, 1H), 8.03 (d, J = 1.9 Hz, 1H), 7.29 – 7.23 (m, 1H), 7.20 – 7.12 (m, 2H), 7.01 (dd, J = 8.2, 1.1 Hz, 1H), 4.95 (ddt, J = 14.7, 4.7, 0.9 Hz, 1H), 4.38 (dd, J = 22.7, 14.7 Hz, 1H), 3.20 – 3.03 (m, 2H), 0.85 (dddd, J = 12.6, 7.7, 6.0, 2.9 Hz, 1H), 15 0.49 (dddd, J = 9.1, 8.1, 5.7, 4.6 Hz, 1H), 0.43 – 0.34 (m, 1H), 0.20 (ddt, J = 9.5, 5.6, 4.7 Hz, 1H), 0.06 (ddt, J = 9.5, 5.7, 4.7 Hz, 1H).³¹P NMR (162 MHz, CDCl₃) δ -8.53 – -9.00 (m).¹³C NMR (201 MHz, CDCl₃) δ 154.8 (d, J = 17.2 Hz), 149.7 (d, J = 8.2 Hz), 149.3 (d, J = 10.2 Hz), 129.2, 126.9, 124.9, 122.6 (d, J = 7.5 Hz), 118.6 (d, J = 8.7 Hz), 53.3 (d, J = 3.6 Hz), 49.7, 9.2 (d, J = 2.9 Hz), 4.2, 3.3. ESI- TOF (HRMS) m/z [M+H]⁺ 291.1005, Found 291.1012. 20 methyl (2R)-4-(methylthio)-2-(2-oxido-2-(1H-1,2,4-triazol-1-yl)benzo[e][1,3,2] oxazaphos-phinin- 3(4H)-yl)butanoate (PhAzE-12) Clear oil (%,mg) ¹H NMR (400 MHz, CDCl₃) δ 8.75 (dd, J = 7.4, 0.9 Hz, 1H), 8.07 (t, J = 1.9 Hz, 1H), 7.35 – 7.28 (m, 1H), 7.18 (dt, J = 4.2, 1.0 Hz, 2H), 7.09 (ddd, J = 5.7, 4.9, 2.5 Hz, 1H), 4.83 (ddd, J = 25 29.2, 15.1, 4.0 Hz, 1H), 4.71 – 4.56 (m, 1H), 4.38 – 4.10 (m, 1H), 3.61 (s, 2H), 3.46 (s, 1H), 2.53 – 2.34 (m, 1H), 2.28 – 2.06 (m, 2H), 2.04 (s, 1H), 1.92 (s, 2H). ³¹P NMR (162 MHz, CDCl₃) δ -7.84 (dt, J = - 80 - Attorney Docket No.: 3436/2 PCT 23.3, 10.9 Hz). ¹³C NMR (201 MHz, CDCl₃) δ 171.4 (d, J = 4.3 Hz), 170.2, 155.0 (d, J = 17.3 Hz), 154.8 (d, J = 17.1 Hz), 149.9 (d, J = 8.8 Hz), 149.7 (d, J = 11.3 Hz), 149.3 (d, J = 10.9 Hz), 129.6, 129.4, 126.8, 126.7, 125.3, 125.2, 123.8 (d, J = 7.2 Hz), 123.1 (d, J = 6.0 Hz), 118.7 (d, J = 8.8 Hz), 118.7 (d, J = 8.1 Hz), 57.3 (d, J = 5.2 Hz), 56.7 (d, J = 3.9 Hz), 52.8, 52.7, 45.9, 44.4, 30.3, 30.2, 28.2, 5 27.9 (d, J = 4.9 Hz), 15.6, 15.0. ESI-TOF (HRMS) m/z [M+H]⁺ 383.0937, Found 383.0939. methyl (2S)-4-(methylthio)-2-(2-oxido-2-(1H-1,2,4-triazol-1-yl)benzo[e][1,3,2]oxazaphos-phinin- 3(4H)-yl)butanoate (PhAzE-13) Clear oil (%,mg) ¹H NMR (400 MHz, CDCl₃) δ 8.75 (dd, J = 7.3, 1.0 Hz, 1H), 8.07 (t, J = 1.9 Hz, 1H), 10 7.31 (dtd, J = 9.4, 4.6, 1.8 Hz, 1H), 7.17 (dt, J = 4.2, 1.0 Hz, 2H), 7.09 (dd, J = 8.0, 4.8 Hz, 1H), 4.83 (ddd, J = 29.2, 15.0, 4.0 Hz, 1H), 4.70 – 4.56 (m, 1H), 4.39 – 4.10 (m, 1H), 3.60 (s, 2H), 3.46 (s, 1H), 2.53 – 2.36 (m, 1H), 2.28 – 2.06 (m, 2H), 2.04 (s, 1H), 1.91 (s, 2H). ³¹P NMR (162 MHz, CDCl₃) δ - 7.84 (dt, J = 22.8, 10.6 Hz).¹³C NMR (201 MHz, CDCl₃) δ 171.4 (d, J = 3.9 Hz), 170.2, 155.0 (d, J = 17.6 Hz), 154.8 (d, J = 17.5 Hz), 149.9 (d, J = 8.8 Hz), 149.7 (d, J = 11.0 Hz), 149.3 (d, J = 10.9 Hz), 15 129.6, 129.4, 126.8, 126.7, 125.3, 125.2, 123.8 (d, J = 7.3 Hz), 123.1 (d, J = 6.3 Hz), 118.7 (d, J = 8.7 Hz), 118.7 (d, J = 8.4 Hz), 57.3 (d, J = 5.2 Hz), 56.6, 52.8, 52.7, 45.9, 44.4, 30.3, 30.2, 28.2, 27.9 (d, J = 4.7 Hz), 15.6, 15.0. ESI-TOF (HRMS) m/z [M+H]⁺ 383.0937, Found 383.0935. 2-fluoro-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (PFEx-1) 20 Prepared according to published methods. See Sun et al., 2023. White solid (86%, 400 mg) ¹H NMR (600 MHz, cdcl₃) δ 7.30 (t, J = 7.5 Hz, 1H), 7.18 – 7.13 (m, 2H), 7.07 (d, J = 8.2 Hz, 1H), 4.61 (dd, J = 15.0, 4.1 Hz, 1H), 4.34 (ddd, J = 21.4, 15.1, 2.0 Hz, 1H), 4.25 (ddd, J = 17.9, 7.8, 2.5 Hz, 2H), 3.98 (dddd, J = 18.1, 15.8, 4.5, 2.5 Hz, 1H), 2.36 (t, J = 2.5 Hz, 1H). ¹⁹F NMR (564 MHz, cdcl₃) δ -70.33 (d, J = 1018.4 Hz).³¹P NMR (243 MHz, cdcl₃) δ -6.15 (ddt, J = 1019.0, 15.2, 7.8 Hz).¹³C NMR (201 25 MHz, CDCl₃) δ 149.77 (d, J = 8.1 Hz), 129.41, 127.13, 125.03, 121.17 (d, J = 8.3 Hz), 119.17 (d, J = 9.5 Hz), 74.06, 48.70, 37.64 (d, J = 5.1 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 226.0428, Found 226.0476. 3-cyclopropyl-2-(9H-purin-9-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (RJG-3130-9) - 81 - Attorney Docket No.: 3436/2 PCT White solid (60%, 190mg) ¹H NMR (400 MHz, CDCl3) δ 9.19 (d, J = 1.5 Hz, 1H), 8.90 (s, 1H), 8.61 (s, 1H), 7.30 – 7.22 (m, 4H), 7.18 (td, J = 7.4, 1.2 Hz, 1H), 7.03 (dd, J = 8.0, 1.2 Hz, 1H), 5.37 (dd, J = 14.3, 5.0 Hz, 1H), 4.33 (dd, J = 23.5, 14.3 Hz, 1H), 2.43 (ttd, J = 6.9, 3.6, 5 1.3 Hz, 1H), 1.30 – 1.14 (m, 1H), 0.76 – 0.63 (m, 2H), 0.56 – 0.44 (m, 1H)..³¹P NMR (162 MHz, CDCl3) δ -9.65 – -9.96 (m). ¹³C NMR (201 MHz, CDCl3) δ 153.66, 153.05, 149.50, 149.39, 147.74 (d, J = 5.6 Hz), 135.38 (d, J = 10.9 Hz), 129.20, 126.85, 125.19, 124.32 (d, J = 6.7 Hz), 118.66 (d, J = 7.5 Hz), 51.54 (d, J = 4.9 Hz), 29.78 (d, J = 5.4 Hz), 7.54 (d, J = 2.5 Hz), 6.16 (d, J = 5.6 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 328.0958, Found 328.0956. 10 2-(4-bromo-1H-imidazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphos- phinine 2-oxide (RJG-3-025, PhAzE-8) Clear oil (38%, 227 mg) ¹H NMR (400 MHz, cdcl3) δ 7.70 (d, J = 1.6 Hz, 1H), 7.33 (dddd, J = 8.2, 5.2, 3.8, 1.3 Hz, 1H), 7.24 – 7.18 (m, 2H), 7.06 (d, J = 8.2 Hz, 1H), 7.02 (t, J = 1.6 Hz, 15 1H), 4.59 – 4.39 (m, 2H), 4.25 (ddd, J = 18.1, 9.0, 2.5 Hz, 1H), 3.89 (ddd, J = 18.1, 12.9, 2.4 Hz, 1H), 2.32 (t, J = 2.5 Hz, 1H).³¹P NMR (162 MHz, cdcl3) δ -8.70 (p, J = 12.0 Hz). ¹³C NMR (201 MHz, CDCl₃) δ 149.2 (d, J = 8.8 Hz), 139.5 (d, J = 5.1 Hz), 130.1, 127.3, 125.8, 122.2 (d, J = 7.4 Hz), 119.2 (d, J = 8.0 Hz), 118.6 (d, J = 15.2 Hz), 118.2 (d, J = 6.8 Hz), 76.5 (d, J = 3.8 Hz), 74.7, 48.7, 37.4 (d, J = 5.8 Hz). ESI-TOF (HRMS) m/z [M+H]⁺ 351.9845, 20 Found 351.9844. 3-(prop-2-yn-1-yl)-2-(4-(trifluoromethyl)-1H-imidazol-1-yl)-3,4-dihydrobenzo[e][1,3,2] oxazaphosphinine 2-oxide (RJG-31026, PhAzE-9) Clear oil (42%, 293 mg) ¹H NMR (400 MHz, CDCl3) δ 7.83 – 7.79 (m, 1H), 7.44 – 7.40 (m, 25 1H), 7.32 (dddd, J = 9.1, 6.1, 1.8, 1.1 Hz, 1H), 7.22 (qd, J = 4.2, 0.9 Hz, 2H), 7.08 – 7.04 (m, 1H), 4.61 – 4.37 (m, 2H), 4.27 (ddd, J = 18.1, 8.9, 2.5 Hz, 1H), 3.88 (ddd, J = 18.1, 13.6, 2.5 - 82 - Attorney Docket No.: 3436/2 PCT Hz, 1H), 2.30 (t, J = 2.5 Hz, 1H).¹⁹F NMR (377 MHz, CDCl3) δ -63.53.³¹P NMR (162 MHz, cdcl3) δ -9.02 (p, J = 12.1 Hz).¹³C NMR (201 MHz, CDCl3) δ 149.0 (d, J = 8.8 Hz), 140.4 (d, J = 5.1 Hz), 130.2, 127.3, 126.0, 122.1 (d, J = 7.8 Hz), 121.0 (q, J = 267.3 Hz), 119.5 (dt, J = 7.8, 3.9 Hz), 119.2 (d, J = 8.0 Hz), 76.3 (d, J = 3.6 Hz), 74.8, 48.8, 37.5 (d, J = 5.8 Hz). ESI- 5 TOF (HRMS) m/z [M+H]⁺ 342.0614, Found 342.0643. EXAMPLE 2 Biological Methods Cell culture. Cell lines were cultured at 37 °C with 5% CO₂ with manufacturer recommended media supplemented with 10% fetal bovine serum (US Source, Omega Scientific) and 1% L-glutamine 10 (Fisher Scientific): HEK293T: DMEM; Colo205: RPMI. Cells were collected or treated for experimental use when they reached ∼90% confluency. The media was aspirated, cells washed with cold PBS (2×) and scraped from plates. The cells were pelleted by centrifugation at 400g for 5 min, snap-frozen using liquid nitrogen and stored at −80 °C until further use. Gel-Based Chemical Proteomic Assay: Cell pellets were lysed in PBS by sonication and 15 fractionated (100,000g, 45 min, 4 °C) to generate soluble and membrane fractions. Protein concentrations were determined using the Bio-Rad DC protein assay and adjusted to 1 mg ml^-1 in PBS. Proteome samples (49 µl aliquots) were treated with PhAzE or PFEx probes at the indicated concentrations (1 µl, 50× stock in DMSO) for 1 h at room temperature. Probe-labeled samples were conjugated by copper-catalyzed azide-alkyne cycloaddition (CuAAC) to rhodamine-azide (1 µl of 20 1.25 mM stock; final concentration of 25 µM) using tris(2-carboxyethyl)phosphine (TCEP; 1 µl of fresh 50 mM stock in water, final concentration of 1 mM), tris[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]amine (TBTA, 3 µl of a 1.7 mM 4:1 t-butanol/DMSO stock, final concentration of 100 µM) and copper sulfate (CuSO₄, 1 µl of 50 mM stock, final concentration of 1 mM). Samples were reacted for 1 h at room temperature, quenched with 17 µl of 4x SDS–PAGE loading buffer and ß-mercaptoethanol (ßME) and 25 quenched samples (30 µl) analyzed by SDS–PAGE and in-gel fluorescence scanning. Live cell evaluation of probes: Cells grown to ~90% confluency in 10 cm plates were treated with DMSO vehicle or probe (10 µl of 1,000× DMSO stock) in serum-free media for the indicated concentrations and times at 37 °C with 5% CO₂. After treatment, cells were washed with cold PBS twice before collection and preparation for gel-based chemical proteomic evaluation as described above. For 30 LC–MS studies, protein concentrations were normalized to 2.3 mg ml^-1 and 432 µl (for 1 mg final protein amount) were used for sample preparation as detailed below. Preparation of proteomes for tandem mass tag LC-MS/MS chemical proteomics: For in situ treatments, live cells were treated with 100 µM probe (37 °C, 5% CO₂) for 4 hours, harvested, then diluted and aliquots of Colo205 soluble proteome (1 mg) utilized for LC-MS/MS sample preparation. 35 For in vitro treatments, soluble proteome (1 mg) was incubated with 100 µM probe (4hr, 37 °C). Copper-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC) and chloroform/methanol extractions - 83 - Attorney Docket No.: 3436/2 PCT were used to remove click reagents as previously described. See Franks et al., 2017; Hahm et al., 2020. Following resuspension in 6M Urea/ 25mM AmBic, proteins were reduced by dithiothreitol and alkylated with iodoacetamide as previously described. See Franks et al., 2017. Denaturing reagents were removed via chloroform/methanol extraction. Proteins were digested overnight with Tryp-Lys-C in 5 25mM AmBic (7.5 µg, 37 °C). Streptavidin enrichment of modified peptides: PhAzE-modified peptides were enriched with avidin agarose and eluted using 150 µL of 50% ACN + 0.1% formic acid (3X) and stored at -80 °C until analysis. FP-Biotin Competition and On-Bead Digestion: Soluble proteome (1 mg) was incubated with 10 100 µM PhAzE ligand (4 hours, 37 °C) followed by incubation with 5 µM FP-biotin (1 hour, room temperature). Chloroform/methanol extractions were used to excess reagents as previously described. See Franks et al., 2017. Following resuspension in 6M Urea/ 25mM AmBic, proteins were reduced by dithiothreitol and alkylated with iodoacetamide as previously described. See Franks et al., 2017. FP- biotin-modified proteins were enriched with avidin agarose. Beads were resuspended in 200 µL 200 15 mM EPPS buffer, pH 8.5. Proteins were digested overnight with Trypsin/Lys-C (2 µg, 37 °C). Supernatant was transferred to a biospin column and isolated via centrifugation (1,400 g x 3 min). The beads were washed with another 150 µL of 200 mM EPPS buffer, pH 8.5, then dried via SpeedVac. Dried peptides were re-suspended in 50 µL 0.1% TFA in water and de-salted via STAGE tip. Peptides were eluted with 4:1 MeCN:H₂O (0.1% TFA) and dried via SpeedVac. 20 FP-Biotin Enriched Peptide TMT labeling: Dried peptides were re-suspended in 10 µL 200 mM EPPS, pH 8.5 then transferred to TMTSIXPLEX™ reagents at a 2:1 w/w ratio of label to peptide. The final solution contains 15 µL (2:1 EPPS:MeCN). The reaction was incubated for 1 hour at room temperature with shaking at 500 rpm. The TMT reaction was quenched with 6% hydroxylamine (15 min, RT) and channels were mixed 1:1. Samples were dried using a SpeedVac and reconstituted in 50 25 µL 0.1% TFA in water and de-salted via STAGE tip. Peptides were eluted with 4:1 MeCN:H₂O (0.1% TFA) and dried via SpeedVac. Dry, TMT-labeled samples were re-suspended in 25 µL 0.1% TFA in water (Mobile Phase A) and stored at -80 °C until analysis. LC-MS/MS analysis of samples: Nano-electrospray ionization–LC–MS/MS analyses were performed using an Ultimate 3000 RSLC nanoSystem-Orbitrap Q Exactive Plus mass spectrometer 30 (Thermo Scientific) as previously described (see Franks et al., 2017) except LC conditions were modified to use the following gradient (A, 0.1% formic acid/H₂O; B, 80% MeCN, 0.1% formic acid in H₂O): 0–1.48 min 1% B, 400 nL min^-1; 1.48–2:00 min 1% B, 300  nL min^-1; 2–90 min 16% B; 90–146 25% B; 146–147 min 95% B; 147–153 min 95% B; 153–154 min 1% B; 154.0–154.1 min 1% B, 400 nL min^-1; 154.1–180 min 1% B, 400  nL min^-1. A top ten data-dependent acquisition MS method was 35 used. - 84 - Attorney Docket No.: 3436/2 PCT LC-MS/MS data analysis: Identification of peptides and proteins from tandem mass spectrometry analyses was accomplished using the Byonic software package (Protein Metrics Inc.; see Bern et al., 2012). Data were searched against a modified human protein database (UniProt human protein database, angiotensin I and vasoactive intestinal peptide standards; 40,660 proteins) with the 5 following parameters: up to three missed cleavages to account for a lysine probe modification, 10 ppm precursor mass tolerance, 20 ppm fragment mass tolerance, too high (narrow) ‘precursor isotope off by x’, precursor and charge assignment computed from MS1, maximum of one precursor per MS2, 0.01 smoothing width, 1% protein false discovery rate, variable (common) methionine oxidation (+15.9949 Da) and fixed cysteine carbamidomethylation (+57.021464 Da). PhAzE probe modifications 10 of tyrosine, lysine and other amino acids were included as a variable (common) modification of +619.2883 Da. Search results were filtered for a Byonic score of >300 (unless otherwise specified), a Delta Mod score of >20, and a precursor mass error between −5 and +5 ppm. A Byonic score of 300 was applied for a more inclusive initial evaluation of the search results and thereby consider more possible probe-modified sites. 15 Analysis and comparison of probe-modified amino acid sites: To compare amino acid residues modified by electrophilic probes, protein and peptide identifications were accomplished as described above with variable (common) modification of +619.2883 Da on the following amino acid residues: cysteine, aspartic acid, glutamic acid, histidine, lysine, methionine, asparagine, glutamine, arginine, serine, threonine, tryptophan and tyrosine. For these amino acid comparisons, carbamidomethylation 20 (+57.021464 Da) of cysteines was searched as a variable/common modification to allow for the potential of probe modification on cysteines. Venn diagrams for comparisons were generated using InteractiVenn.net. See Bern et al., 2012. For amino acid comparisons, a Byonic score cutoff of 300 was used to minimize false positive identifications of modified residues, which were confirmed by manual evaluation to be incorrect assignments. 25 ACHE Activity Assay: This procedure was adapted from published protocols. See Hammand & Forster, 1989; and Ellman et al., 1961. N2a soluble cell proteomes were diluted to 0.25 mg ml⁻¹ in assay buffer (100 mM NaH₂PO₄, pH 7.0) and 100 µL was added to each well of a 96 well plate. Compound stock solutions were diluted in DMSO and 1 µL of 100X stock solution was added to respective wells and incubated for 4 hours at 37 °C. Then, 40 µL of a substrate solution containing 4.94 30 mM DTNB and 7.47 mM acetyl thiocholine in assay buffer was added to each well. The reaction was incubated at room temperature for 3 hours. Absorbance was measured at 414 nm on a BMG Labtech CLARIOSTAR® brand plate reader (BMG Labtech, Cary, North Carolina, United States of America). EXAMPLE 3 PhAzE Labeling 35 PhAzE compounds were prepared as described hereinabove in EXAMPLE 1. For initial protein labeling studies with the PhAzE compounds, the ability of two exemplary PhAzE compounds, RJG-2- - 85 - Attorney Docket No.: 3436/2 PCT 259A (also referred to herein as 2259A and PhAzE-1) and RJG-2-259B (also referred to herein as 2259B and PhAzE-2) to compete with known electrophilic compounds was studied in Colo205 soluble lysate. More particularly, the soluble lysate was first treated with an labeling inhibitor, i.e., iodoacetamide (IAA), as an example of a cysteine-reactive electrophile; HHS-482-desthiobiotin (482- 5 DB), as an example of a tyrosine/lysine reactive electrophile; fluorophosphonate-biotin (FP-B), as an example of an active-site serine-reactive electrophile; and tandem mass-tag 0 (TMT-0), as an example of an N-terminus/lysine-reactive electrophile). The competitive labeling activity of the two PhAzE compounds was compared to the activity of a SuTEx probe compound (HHS-481), a compound which can provide relatively broad proteome labeling. The chemical structures of the PhAzE probes and the 10 SuTEx probe are shown in Figure 1A. Labelling with HHS-481 was intense. Accordingly, the gel lanes for HHS-481 labelling was excised so that portions of the gel showing labeling with the PhAzE compounds could be imaged without the HHS-481 labeling results. See Figures 1B and 1C. While not as reactive as HHS-481, RJG-2-259A displayed decent labeling. RJG-2-259B appeared to be slightly more reactive than RJG-2-259A. Without being bound to any one theory, it is believed that the oxygen 15 and nitrogen atoms attached to the phosphorous center of these PhAzE compounds likely decrease their reactivity. It appeared that IAA enhanced labeling with the PhAzE compounds at about 23kDa, while 482-DB and FP-DB competed for labeling with the PhAzE compounds. The results in in Colo205 soluble lysate suggested potential PhAzE adducts formed with tyrosine, lysine, serine, and threonine residues. 20 A kinetic assay was performed to determine timing for PhAzE adduct formation in HEK293T soluble lysate. Labeling increased with time for studies performed from 30 minutes to 4 hours. See Figure 2. As observed in the Colo205 lysate studies, the PhAzE compounds were less reactive than an exemplary SuTEx compound, HHS-481, presumably due to the heteroatoms attached to the phosphorous. 25 Fluorophosphonates are inherently toxic due to their unique potency at targeting active-site serines. In particular, fluorophosphonates can inhibit AChE, resulting in cholinergic stress. ACHe is expressed in the soluble fraction of mouse brain proteome and can be liganded by FP-Rh. Results of a study to determine the ability of PhAzE compounds to compete for FP-Rh binding are shown in Figure 3. It is possible that RJG-2-259A and RJG-2-259B competed for AChE labeling by FP-Rh), as indicated 30 by the inhibition of probe labeling of the band at about 75 kilodalton (kDa). The labeling profile of exemplary PhAzE compounds (see Figure 4A) was performed in live cells and in vitro. Live cell treatment with RGJ-2-259A labels comparable tyrosine and lysine sites as RGJ-2276. See Figure 4B. Changes to the leaving group or adduct portion of the probe can modify the reactivity of the PhAzE compound. In some cases, changes can lead to reduced reactivity in live cells, 35 which can potentially be due to insolubility or poor membrane permeability. Reactivity of the PhAzE compounds in vitro was generally similar to the reactivity in vivo. See Figure 4C. However, while RJG- - 86 - Attorney Docket No.: 3436/2 PCT 2-259B performs well in vitro, there is negligible labeling with RJG2-259B in vivo. Steric bulk near the phosphorous atom or an electron donating group on the adduct portion of the compound can reduce labeling activity. The use of a non-substituted 1,2,4-triazole leaving group improves reactivity. There were a significant number of unique proteins and protein sites labeled by PhAzE compounds in live 5 HEK293T cells compared to SuTEx probe HHS-475. See Figures 5A and 5B. Fluorophosphonates undergo phosphorous-fluoride exchange with active-site serine residues and are toxic due to their inhibition of AChE in the brain. Accordingly, the development of a covalent ligand for serine esterases that has reduced reactivity with AChE would be very beneficial. The inhibition of AChE with PhAzE compounds was compared to the inhibition of AChE with other AChE 10 inhibitors using Ellman’s assay. See Ellman et al., 1961; and Hammond & Forster, 1989. For instance, inhibition of AChE inhibits the production of thiocholine. Thiols like thiocholine can be detected with a colorogenic chemical, 5,5’dithiobis-(2-nitrobenzoic acid) (DTNB, also known as Ellman’s reagent). More particularly, when a thiol reacts with DTNB, it cleaves a disulfide bond in DTNB, releasing 2- nitro-5-thiobenzoate (TNB-), which oxidizes to a dianion (TNB^2-) at neural and alkaline pH. The dianion 15 can be detected via its yellow colored fluorescence. Therefore, when ACHe is inhibited, resulting in less production of thiocholine, less fluorescence is detected via Ellman’s assay. Results are shown in Figure 6B. FP-Biotin and Donezepil (see Figure 6A) are potent inhibitors of AChE, with 50% inhibitory concentrations (IC₅₀s) of about 12 nM. Fluorophosphonate electrophile RJG-2273 was also a potent inhibitor (IC₅₀ = 140 nM). All the PhAzE compounds were significantly less potent AChE inhibitors 20 (IC₅₀ > 1 ^M), indicating an improved safety profile. Additional studies to demonstrate serine hydrolase labeling were performed using tandem-mass tag (TMT) to demonstrate inhibition of FP-biotin labeling with PhAzE probes in N2a soluble lysate. More particularly, N2a soluble lysate was treated with 5 ^M inhibitor (e.g., PhAzE compound) for four hours at 37 °C and then with 5 ^M FP-biotin for one hour at room temperature. Samples were processed 25 via LC-MS and labeled with TMT6plex reagents. The results showed that several serine hydrolases were inhibited by PhAzE compounds, such as ACPH and DPP9, and a few compounds increased FP- biotin labeling of PA1B2 (Q61206), suggesting modification at a different site. See Table 1, below. Although AChE was not significantly labeled, the inhibition of FP-biotin labeling corroborates the AChE biochemical assay with N2a soluble lysate. PFEx compound RJG-2273 was the best inhibitor of 30 AChE probe labeling followed by RJG-2-259A and RJG-2-2279. See Figure 7. A few serine hydrolases were selectively labeled by PhAzE compounds. See Figure 8. These included acylamino-acid releasing enzyme (ACPH; Q8R146), which hydrolyses the N-terminal peptide bond of an N-acylated peptide; dipeptidyl peptidase 9 (DPP9; Q8BVG4), which cleaves off N-terminal dipeptides from proteins having a proline (Pro) or alanine (Ala) residue at position 2; and platelet-activating factor acetylhydrolase IB35 subunit alpha 2 (PA1B2; Q61206), which hydrolyzes the acetyl group at the sn-2 position of platelet- - 87 - Attorney Docket No.: 3436/2 PCT activating factor (PAF) and it analogs and modulates the action of PAF. While PFEx also labeled PA1B2, only the PhAzE compounds selectively labeled ACPH and DPP9. Table 1 TMT Ratio for Serine Hydrolase Labeling 5 compounds 2279, 2292, 3025, and 3026 at serine 730. The ability to selectively target DPP9 could be therapeutically useful, as DPP9 is known to promote tumorigenesis in clear cell renal cell carcinoma (ccRCC) by binding KEAP1, thereby stabilizing Nrf2 and stimulating the pro-inflammatory response. Although LC-MS/MS that utilizes HCD cell for fragmentation historically prevents identification of 10 PFEx-labeled serines and threonines, PhAzE-labeled serine 48 or threonine 8 were observed for PA1B2 and macrophage migration inhibitory factor (MIF), respectively. PA1B2 (also known as PAFAH1B2) is a heterotrimeric enzyme composed of catalytic 1b2 and 1b3 subunits that associate with non-catalytic 1b1. 1B2 and 1B3 are known to be modified by PFEx at serine 48. 1B3 is an enzyme important in maintaining breast cancer cell aggressiveness and tumor growth through regulating tumor-suppressing 15 lipids. That only two PhAzE compounds, e.g., RJG-2275 and RJG-2276 bind serine 48, supports the ability to tailor covalent modification by PhAzE by modification of the PhAzE compound leaving group. Additional studies using electron-transfer dissociation (ETD) mass spectrometry can be conducted to further evaluate the labeling of serine and threonine residues with PhAzE compounds. 20 Table 2 (below) provides a list of proteins covalently modified by PhAzE compounds in situ and in vitro and the amino acid residues modified. The Table lists the protein modified, its UniProt Accession number, and the tyrosine, lysine, arginine, serine, or threonine residue site modified. - 88 - Attorney Docket No.: 3436/2 PCT Table 2 PhAzE Modified Proteins - 89 - Attorney Docket No.: 3436/2 PCT - 90 - Attorney Docket No.: 3436/2 PCT - 91 - Attorney Docket No.: 3436/2 PCT - 92 - Attorney Docket No.: 3436/2 PCT - 93 - Attorney Docket No.: 3436/2 PCT - 94 - Attorney Docket No.: 3436/2 PCT - 95 - Attorney Docket No.: 3436/2 PCT - 96 - Attorney Docket No.: 3436/2 PCT - 97 - Attorney Docket No.: 3436/2 PCT - 98 - Attorney Docket No.: 3436/2 PCT - 99 - Attorney Docket No.: 3436/2 PCT - 100 - Attorney Docket No.: 3436/2 PCT - 101 - Attorney Docket No.: 3436/2 PCT - 102 - Attorney Docket No.: 3436/2 PCT - 103 - Attorney Docket No.: 3436/2 PCT - 104 - Attorney Docket No.: 3436/2 PCT - 105 - Attorney Docket No.: 3436/2 PCT - 106 - Attorney Docket No.: 3436/2 PCT - 107 - Attorney Docket No.: 3436/2 PCT - 108 - Attorney Docket No.: 3436/2 PCT - 109 - Attorney Docket No.: 3436/2 PCT - 110 - Attorney Docket No.: 3436/2 PCT - 111 - Attorney Docket No.: 3436/2 PCT - 112 - Attorney Docket No.: 3436/2 PCT - 113 - Attorney Docket No.: 3436/2 PCT - 114 - Attorney Docket No.: 3436/2 PCT - 115 - Attorney Docket No.: 3436/2 PCT - 116 - Attorney Docket No.: 3436/2 PCT - 117 - Attorney Docket No.: 3436/2 PCT - 118 - Attorney Docket No.: 3436/2 PCT - 119 - Attorney Docket No.: 3436/2 PCT - 120 - Attorney Docket No.: 3436/2 PCT - 121 - Attorney Docket No.: 3436/2 PCT - 122 - Attorney Docket No.: 3436/2 PCT - 123 - Attorney Docket No.: 3436/2 PCT - 124 - Attorney Docket No.: 3436/2 PCT - 125 - Attorney Docket No.: 3436/2 PCT - 126 - Attorney Docket No.: 3436/2 PCT * Amino acid residue(s) in corresponding UNIPROT ID NO. EXAMPLE 3 PhAzE In Situ: Non-Alkynyl PhAzE Ligands Four non-alkynyl PhAzE molecules synthesized towards TMT fragment screen. These included 5 RJG-3044, RJG-3045, RJG-3048, and RJG-3049, with the following structures: N2a cells were treated with vehicle or inhibitor for 4 hours at 37 °C followed by in vitro labeling competition with FP-Rh (1 µM) for 1 hour at room temperature. 10 REFERENCES All references listed in the instant disclosure, including but not limited to all patents, patent applications and publications thereof, scientific journal articles, and database entries (including but not limited to UniProt, EMBL, and GENBANK® biosequence database entries and including all annotations available therein) are incorporated herein by reference in their entireties to the extent that 15 they supplement, explain, provide a background for, and/or teach methodology, techniques, and/or compositions employed herein. The discussion of the references is intended merely to summarize the assertions made by their authors. No admission is made that any reference (or a portion of any reference) is relevant prior art. Applicants reserve the right to challenge the accuracy and pertinence of any cited reference. 20 Adibekian et al. (2011) Click-generated triazole ureas as ultrapotent in vivo-active serine hydrolase inhibitors. Nature Chemical Biology 7:469-478. Ausubel et al. (2002) Short Protocols in Molecular Biology, Fifth ed., John Wiley & Sons, New York, New York, United States of America. Ausubel et al. (2003) Current Protocols in Molecular Biology, John Wylie & Sons, Inc, New York, 25 New York, United States of America. Bern et al. (2012) Byonic: advanced peptide and protein identification software. Current Protocols in Bioinformatics. John Wiley & Sons, New York, New York, United States of America. Chapter 13:13.20.1-13.20.14. - 127 - Attorney Docket No.: 3436/2 PCT Chang et al. (2015) Selective inhibitor of platelet-activating factor acetylhydrolases 1b2 and 1b3 that impairs cancer cell survival. ACS Chemical Biology 10:925-932. Ellman et al. (1961) A new and rapid colorimetric determination of acetylcholinesterase activity. Biochemical Pharmacology 7(2):88-95. 5 Franks et al. (2017) The ligand binding landscape of diacylglycerol kinases. Cell Chemical Biology 24(7):870-880. Gait (1984) Oligonucleotide Synthesis: A Practical Approach, IRL Press, Oxford, England. Glover (1985) DNA Cloning: A Practical Approach. Oxford Press, Oxford, England. Grams & Hsu (2022) Reactive chemistry for covalent probe and therapeutic development. Trends in 10 Pharmacological Sciences 43:249-262. Hahm et al. (2020) Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. Nature Chemical Biology 16(2):150-159. Hammond & Forster (1989) A microassay-based procedure for measuring low levels of toxic organophosphorus compounds through acetylcholinesterase inhibition. Analytical 15 Biochemistry 180(2):380-383. Heberle et al. (2015) InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics 16(1):169. Hsu et al. (2012) DAGLβ inhibition perturbs a lipid network involved in macrophage inflammatory responses. Nature Chemical Biology 8:999-1007. 20 Ko et al. (2019) Macrophage Migration Inhibitory Factor Acts as the Potential Target of a Newly Synthesized Compound, 1-(9’-methyl-3’-carbazole)-3, 4-dihydro-β-carboline. Scientific Reports 9:2147. Liu et al. (1999) Activity-based protein profiling: the serine hydrolases. Proceedings of the National Academy of Sciences U S A 96:14694-14699. 25 Long & Cravatt. (2011) The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chemical Reviews 111:6022-6063. Moore et al. (2022) A phenotypic screen identifies potent DPP9 inhibitors capable of killing HIV-1 infected cells. ACS Chemical Biology 17:2595-2604. Mulvihill et al. (2014) Metabolic profiling reveals PAFAH1B3 as a critical driver of breast cancer 30 pathogenicity. Chemistry & Biology 21:831-840. PCT International Patent Application Publication No. WO 2020/214336. Roe et al. (1996) DNA Isolation and Sequencing: Essential Techniques. John Wiley, New York, New York, United States of America. Sambrook & Russell (2001) Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor 35 Laboratory Press, Cold Spring Harbor, New York, United States of America. - 128 - Attorney Docket No.: 3436/2 PCT Scaloni et al. (1992) Acylpeptide hydrolase: inhibitors and some active site residues of the human enzyme. Journal of Biological Chemistry 267:3811-3818. Sun et al. (2023) Phosphorus(V) Fluoride Exchange (PFEx): Multidimensional Click Chemistry from Phosphorus(V) Connective Hubs. Chem 9(8):2128-2143. 5 It will be understood that various details of the presently disclosed subject matter can be changed without departing from the scope of the presently disclosed subject matter. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation. - 129 -

Claims

Attorney Docket No.: 3436/2 PCT CLAIMS What is claimed is: 1. A compound having a structure of Formula (I): 5 wherein: each of Z₁, Z₂, and Z₃ is independently selected from CH and N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; X₁ is selected from -Oˉ, -OR₂, -NR₂R₃, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; 10 X₂ is selected from -O-, -OR₂ and -NR₂R₃; R₁ is selected from H, halo, alkyl, perhaloalkyl, aralkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; each R₂ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl, or wherein two R₂ groups together are a 15 bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus- containing ring, wherein said bivalent group is optionally substituted and/or fused to a substituted or unsubstituted aromatic ring; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, 20 aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. 25 2. The compound of claim 1, wherein two of Z₁, Z₂, and Z₃ are N, optionally wherein Z₁ and Z₃ are each N or wherein Z₁ and Z₂ are each N. 3. The compound of claim 1, wherein X₁ and/or X₂ comprise an alkyne moiety, optionally a terminal alkyne moiety, a fluorophore moiety, or a detectable labeling group, optionally wherein: 30 (i) X₁ or X₂ comprises an R₂ group wherein said R₂ group is an unsaturated alkyl group comprising an alkyne moiety, optionally wherein said R₂ is -CH₂-C^CH; - 130 - Attorney Docket No.: 3436/2 PCT (ii) X₁ or X₂ comprises an R₂ group wherein said R₂ group is selected from substituted alkyl, substituted aralkyl, or substituted aryl, wherein said substituted alkyl, substituted aralkyl, or substituted aryl is an alkyl, aralkyl, or aryl that is substituted with an alkyl or alkoxy group comprising an alkyne moiety, optionally where said alkyl or alkoxy 5 group is -CH₂-C^CH or -O-CH₂-C^CH; (iii) X₁ and X₂ each comprise an R₂ group that together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is substituted with an alkyl or alkoxy group comprising an alkyne10 moiety, optionally wherein said alkyl or alkoxy group is -CH₂-C^CH or -O-CH₂- C^CH; (iv) X₁ and X₂ each comprise an R₂ group that together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said 15 bivalent group is fused to a substituted aromatic ring, wherein said substituted aromatic ring is an aromatic ring substituted by an alkyl or alkoxy group comprising an alkyne moiety, optionally wherein said alkyl or alkoxy group is -CH_2-C^CH or -O-CH₂- C^CH; (v) R₁ is selected from H, phenyl, thiophenyl, furanyl, pyridinyl, and substituted phenyl, 20 wherein said substituted phenyl is phenyl substituted with one or more substituent selected from the group consisting of halo, alkoxy, and perhaloalkoxy, optionally wherein R₁ is phenyl substituted with fluoro or -OCF₃; or (vi) two R₂ together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered 25 phosphorus-containing ring, wherein said bivalent group is optionally substituted and/or fused to a substituted or unsubstituted aromatic ring; further optionally wherein the compound of Formula (I) has a structure of Formula (II) or Formula (III): - 131 - Attorney Docket No.: 3436/2 PCT wherein: each of Z₁, Z₂, and Z₃ is independently selected from the group consisting of CH and N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is 5 N; X₃ is selected from O and NH; X₄ is selected from O and NR₃; R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; 10 R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, 15 substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, - C(=O)R₄, -S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, 20 perfluoroalkoxy, aralkyl, substituted aralkyl, aryl and substituted aryl; R₁₁ is selected from H, -C(=O)R₄, -CH₂C(=O)R₄, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and R₁₂ and R₁₃ are independently selected from H, -C(=O)R₄, -CH₂C(=O)R₄, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. 25 4. The compound of claim 1, wherein the compound of Formula (I) comprises a chiral center and/or wherein X₁ and/or X₂ comprises an alkyne moiety, a fluorophore moiety, or a detectable labeling group. 5. The compound of claim 4, wherein the compound has a structure of Formula (II) wherein X₃ is O and X₄ is NR₃ and the compound has a structure of Formula (IIa): - 132 - Attorney Docket No.: 3436/2 PCT wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; 5 R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, optionally a linear or branched C1-C6 saturated alkyl group or a C1-C6 alkyl group comprising a terminal alkyne; substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, - 10 S(=O)₂R₄, and -C(=O)R₄, or is -CH₂-C^CH or -CH(CH₃)C(CH₃)₃; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl, optionally wherein R₄ is selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl, further optionally wherein R₄ is C1-C6 alkyl; 15 each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, - 20 S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, aryl and substituted aryl, optionally H, halo, alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, and aryl. 6. The compound of claim 5, wherein R₆ is H, wherein Z₁ and Z₃ are N and Z₂ is CH, and wherein the compound of Formula (IIa) has a structure of Formula (IIa1): - 133 - Attorney Docket No.: 3436/2 PCT wherein R₁, R₃, R₇, R₈, R₉, and R₁₀ are defined as for Formula (IIa), optionally wherein at least three of R₇, R₈, R₉, and R₁₀ are H, further optionally wherein at least R₇, R₈, and R₁₀ are H, Z₁ and Z₃ are N, and Z₂ is CH, and the compound of Formula (IIa1) has a structure of Formula 5 (IIa2): wherein R₁, R₃, and R₉ are defined as for Formula (IIa). 7. The compound of claim 1, wherein R₉ is alkoxy, optionally -O-CH₂-C^CH, and R₃ is a linear or branched C1-C6 alkyl group, optionally wherein R₃ comprises a chiral carbon atom and/or 10 is ethyl or -CH(CH₃)C(CH₃)₃. 8. The compound of claim 1, wherein R₉ is H and the compound of Formula (IIa2) has a structure of Formula (IIa3): , wherein R₁ is H, aryl, substituted aryl, heteroaryl, or substituted heteroaryl. 15 9. The compound of any one of claims 3-8, wherein R₁ is H, phenyl, furanyl, thiophenyl, pyridinyl, or substituted phenyl, optionally wherein substituted phenyl is phenyl substituted by one or more substituents selected from the group comprising halo, alkyl, alkoxy, perfluoroalkyl, and perfluoroalkoxy, and further optionally wherein R₁ is selected from phenyl, furanyl, fluoro- substituted phenyl, and trifluoromethoxy-substituted phenyl. 20 10. The compound of claim 1, wherein the compound is selected from the group consisting of 3- (prop-2-yn-1-yl)-2-(1H-1,2,4-triazol-1-yl)-3,4-dihydro-benzo-[e][1,3,2]oxazaphosphinine 2- - 134 - Attorney Docket No.: 3436/2 PCT oxide (RJG-2259A); 2-(3-phenyl-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4- dihydrobenzo[e][1,3,2]oxaza-phosphinine 2-oxide (RJG-2259B); 3-(prop-2-yn-1-yl)-2-(3-(4- (trifluoromethoxy)phenyl)-1H-1,2,4-triazol-1-yl)-3,4-dihydro- benzo[e][1,3,2]oxazaphosphinine 2-oxide (RJG-2275); 2-(3-(2-fluorophenyl)-1H-1,2,4- 5 triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4-dihydrobenzo[e][1,3,2]-oxazaphosphinine 2-oxide (RJG- 2276), 2-(3-(furan-2-yl)-1H-1,2,4-triazol-1-yl)-3-(prop-2-yn-1-yl)-3,4- dihydrobenzo[e][1,3,2]-oxazaphosphinine 2-oxide (RJG-2279); 3-((S)-3,3-dimethylbutan-2- yl)-2-(3-phenyl-1H-1,2,4-triazol-1-yl)-7-(prop-2-yn-1-yloxy)-3,4- dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (RJG-2284); 3-ethyl-7-(prop-2-yn-1-yloxy)- 10 2-(1H-1,2,4-triazol-1-yl)-3,4-dihydrobenzo[e][1,3,2]oxaza-phosphinine 2-oxide (RJG-2292), and 3-cyclopropyl-2-(9H-purin-9-yl)-3,4-dihydrobenzo[e][1,3,2]oxazaphosphinine 2-oxide (RJG-3130-9). 11. The compound of claim 1, wherein the compound has a structure of Formula (II) wherein X₃ is O and X₄ is O and the compound has a structure of Formula (IIb): 15 wherein Z₁, Z₂, Z₃, R₁, R₆, R₇, R₈, R₉, and R₁₀ are as defined for Formula (II); or wherein the compound has a structure of Formula (II) wherein X₃ is NH and X₄ is NR₃ and the compound has a structure of Formula (IIc): 20 wherein Z₁, Z₂, Z₃, R₁, R₃, R₆, R₇, R₈, R₉, and R₁₀ are as defined for Formula (II). 12. The compound of claim 1, wherein the compound has a structure of Formula (III) wherein X₃ is O and X₄ is NR₃ and the compound has a structure of Formula (IIIa): - 135 - Attorney Docket No.: 3436/2 PCT wherein Z₁, Z₂, Z₃, R₁, R₃, R₁₁, R₁₂, and R₁₃ are as defined for Formula (III), optionally wherein Z₁ and Z₃ are N and Z₂ is CH. 13. The compound of claim 12, wherein R₁₁ is selected from -C(=O)R₄ and -CH₂C(=O)R₄; R₄ is 5 selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; optionally wherein R₁₁ is selected from -C(=O)-OH and -CH₂C(=O)-OH. 14. The compound of claim 11 or claim 12, wherein R₁₂ and R₁₃ are independently selected from 10 H and C1-C6 alkyl, optionally wherein R₁₂ and R₁₃ are independently selected from H and methyl, and/or wherein R₃ is H. 15. The compound of any one of claims 12-14, wherein the compound has a structure of one of Formulas (IIIa1)-(IIIa4): - 136 - Attorney Docket No.: 3436/2 PCT 16. The compound of claim 1, wherein X₁ is selected from -Oˉ and -OR₂, and the compound has a structure of Formula (IVa), (IVb), or (IVc): 5 wherein: Z₁, Z₂, Z₃, and R₁ are as defined for Formula (I); each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; 10 R₃ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted 15 aralkyl, aryl, and substituted aryl; or wherein X₁ is selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and wherein the compound has a structure of Formula (IVd), (IVe), or (IVf): - 137 - Attorney Docket No.: 3436/2 PCT wherein: Z₁, Z₂, Z₃, and R₁ are as defined for Formula (I); each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, aralkyl, 5 substituted aralkyl, aryl, and substituted aryl; R₃ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and 10 each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl. A method for covalently modifying and/or modulating an activity of a protein, optionally a serine hydrolase, further optionally wherein the serine hydrolase is acetylcholinesterase (AChE), wherein the method comprises contacting a sample comprising a serine hydrolase with 15 a compound of any one of claims 1-16, optionally wherein the sample comprises a cell lysate or a live cell, optionally wherein modulating an activity of a serine hydrolase comprises inhibiting the serine hydrolase. 18. A method for identifying a reactive amino acid residue of a protein, wherein the reactive amino acid residue is a tyrosine residue, a lysine residue, a serine residue, or a threonine residue, the 20 method comprising: (a) providing a protein sample comprising isolated proteins, living cells, or a cell lysate; (b) contacting the protein sample with a compound of Formula (I) for a period of time sufficient for the compound to react with at least one reactive tyrosine, lysine, serine, or threonine in a protein in the protein sample, thereby forming at least one modified 25 reactive amino acid residue; and (c) analyzing proteins in the protein sample to identify at least one modified reactive amino acid residue, thereby identifying at least one reactive amino acid residue of a protein; wherein the probe compound has a structure of Formula (I): - 138 - Attorney Docket No.: 3436/2 PCT wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; 5 X₁ is selected from -Oˉ, -OR₂, -NR₂R₃, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; X₂ is selected from -O-, -OR₂ and -NR₂R₃; R₁ is selected from H, halo, alkyl, perhaloalkyl, aralkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; 10 each R₂ is selected from the group consisting of H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl, or wherein two R₂ groups together are a bivalent group that is covalently bonded to an oxygen or nitrogen atom in each of the X₁ and X₂ groups, thereby forming a five- or six-membered phosphorus-containing ring, wherein said bivalent group is optionally 15 substituted and/or fused to a substituted or unsubstituted aromatic ring; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, substituted aralkyl, aryl, and substituted aryl; and 20 each R₅ is independently selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; further wherein one of X₁ and X₂ comprises an alkyne moiety; and wherein the at least one modified reactive amino acid residue comprises a structure of Formula (V): 25 wherein X₁ and X₂ are as defined for formula (I) and X’ is O or NH. 19. The method of claim 18, wherein the probe compound is a compound of Formula (IIa): - 139 - Attorney Docket No.: 3436/2 PCT wherein: each of Z₁, Z₂, and Z₃ are independently selected from CH or N, subject to the proviso that at least one of Z₁, Z₂, and Z₃ is N; 5 R₁ is selected from H, halo, perhaloalkyl, aryl, substituted aryl, heteroaryl, and substituted heteroaryl; R₃ is selected from H, alkyl, substituted alkyl, cycloalkyl, aralkyl, substituted aralkyl, aryl, substituted aryl, -S(=O)R₄, -S(=O)₂R₄, and -C(=O)R₄; R₄ is selected from alkyl, substituted alkyl, -OH, -NH₂, -OR₅, -NHR₅, -N(R₅)₂, aralkyl, 10 substituted aralkyl, aryl, and substituted aryl; each R₅ is independently selected from alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; R₆ is selected from H, alkyl, substituted alkyl, aralkyl, substituted aralkyl, aryl, and substituted aryl; and 15 R₇, R₈, R₉, and R₁₀ are each independently selected from H, cyano, halo, -C(=O)R₄, - S(=O)₂R₄, alkyl, substituted alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, substituted aralkyl, aryl and substituted aryl, optionally H, halo, alkyl, alkoxy, perfluoroalkyl, perfluoroalkoxy, aralkyl, and aryl; wherein one of R₃, R₇, R₈, R₉, and R₁₀ comprises an alkyne moiety; and wherein the at 20 least one modified reactive amino acid residue comprises a structure of Formula (V-IIa): - 140 - Attorney Docket No.: 3436/2 PCT wherein R₃, R₆, R₇, R₈, R₉, and R₁₀ are as defined for formula (IIa) and X’ is O or NH. 20. The method of claim 18, wherein: the analyzing of step (c) comprises tagging the at least one modified reactive amino acid residue with a compound comprising a detectable labeling group, thereby forming at least one 5 tagged reactive amino acid residue, optionally wherein the detectable labeling group comprises biotin or a biotin derivative; further optionally wherein the tagging comprises reacting a terminal alkyne group in the at least one modified reactive amino acid residue with a compound comprising (i) an azide moiety and (ii) the detectable labeling group, optionally wherein the reacting comprises a copper-catalyzed azide- 10 alkyne cycloaddition (CuAAC) coupling reaction; and/or the analyzing further comprises digesting the protein sample with trypsin to provide a digested protein sample comprising a protein fragment comprising the at least one tagged reactive amino acid residue, optionally wherein the analyzing further comprises enriching the digested protein sample for the detectable labeling group, optionally 15 wherein the enriching comprises contacting the digested protein sample with a solid support comprising a binding partner of the detectable labeling group; and/or the analyzing further comprises analyzing the enriched the digested protein sample via liquid chromatography-mass spectrometry. 21. The method of claim 18, wherein: 20 providing the protein sample further comprises separating the protein sample into a first protein sample and a second protein sample; contacting the protein sample with a probe compound of Formula (I) comprises contacting the first protein sample with a first probe compound of Formula (I) at a first probe concentration for a first period of time and contacting the second protein sample with 25 one of the group consisting of: (b1) a second probe compound of Formula (I) at the first probe concentration for the first period of time, (b2) the first probe compound of Formula (I) at a second probe concentration for the first period of time, and (b3) the first probe compound of Formula (I) at the first probe concentration for a second period of time; thereby forming at least one modified reactive amino acid residue in said first 30 and/or said second protein sample; and analyzing proteins comprises analyzing the first and second protein samples to determine the presence and/or identity of a modified reactive amino acid residue in the first sample and the presence and/or identity of a modified reactive amino acid residue in the second sample. 35 22. The method of claim 18, wherein the protein sample comprises living cells and wherein providing the protein sample further comprises separating the protein sample into a first protein - 141 - Attorney Docket No.: 3436/2 PCT sample and a second protein sample and culturing the first protein sample in a first cell culture medium comprising heavy isotopes prior to the contacting of step (b), optionally wherein the first cell culture medium comprises ¹³C- and/or ¹⁵N-labeled amino acids, further optionally wherein the first cell culture medium comprises ¹³C-,¹⁵N-labeled lysine and arginine; and 5 culturing the second protein sample in a second cell culture medium, wherein said second cell culture medium comprises a naturally occurring isotope distribution, prior to the contacting of step (b). - 142 -