US20170146517A1

US20170146517A1 - Compounds and methods used in assessing mono-parp activity

Info

Publication number: US20170146517A1
Application number: US15/356,040
Authority: US
Inventors: Michael Cohen; Ian Carter-O'Connell; Rory Morgan; Haihong Jin
Original assignee: Oregon Health and Science University
Current assignee: Oregon Health and Science University
Priority date: 2015-11-20
Filing date: 2016-11-18
Publication date: 2017-05-25
Also published as: US20200123192A1; US11530235B2

Abstract

Mutant mono ADP-ribose-polymerases (mono-PARP) proteins and small molecule compound substrates specific for the mutant mono-PARP proteins as well as methods of using these compositions to identify protein targets of the mono-PARPs and to screen for antagonists of the mono-PARPs are described.

Description

RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent Application 62/258,397, filed on 20 Nov. 2015 and entitled COMPOUNDS AND METHODS USED IN ASSESSING MONO-PARP ACTIVITY which is incorporated by reference herein in its entirety.

ACKNOWLEDGEMENT OF GOVERNMENT SUPPORT

The disclosed invention was made with the support of the United States government under grant number NS088629 awarded by the National Institute of Neurological Disorders and Stroke (NINDS). The United States government has certain rights to this invention.

FIELD

Generally, the field involves methods of testing the activity of human proteins, more specifically, the field involves identifying targets of and testing inhibitors of mono-PARP enzymes.

BACKGROUND

ADP-ribosylation—the transfer of the ADP-ribose (ADPr) moiety from nicotinamide adenine dinucleotide (NAD+) to amino acids in proteins—is a reversible posttranslational modification essential for cellular function in mammals (Hottiger et al, Trends Biochem Sci 35, 208-219 (2010); incorporated by reference herein). The enzymes that catalyze ADP ribosylation, known as poly-ADP-ribose-polymerases (PARPs, of which there are 15 active family members in humans) have been implicated in a number of physiological roles, including gene regulation (Zhang et al, J Biol Chem 287, 12405-12416 (2012); incorporated by reference herein), differentiation (Hu et al, Am J Pathol 182, 71-83 (2013); incorporated by reference herein), and signal transduction (Strosznajder et al, Mol Neurobiol 31, 149-167 (2005); incorporated by reference herein); as well as a number of diseases - notably neurodegeneration (Cosi and Marien, Ann NY Acad Sci 890, 227-239 (1999); incorporated by reference herein) and cancer (Masutani and Fujimori, Mol Asp Med 34, 1202-1216 (2013); incorporated by reference herein). As such, the cellular functions of each PARP family member and their downstream targets have generated significant biological interest. That said, the targets of most PARPs are unknown, which has hampered efforts to delineate their specific roles in cellular processes.
While PARPs were termed polymerases based on their homology to the catalytic domain of the founding member PARP1 (a verified polymerase), most PARP family members (PARPs 6-8, 10-12, and 14-16) catalyze mono-ADP-ribosylation (MARylation) and not poly-ADP-ribosylation (PARylation) as previously thought (Vyas et al, Nat Comm 5, 4426 (2014); incorporated by reference herein). The PARPs that catalyze MARylation, referred to herein as mono-PARPs, are not understood in nearly as much detail as the PARPs that catalyze PARylation, referred to herein as poly-PARPs. This is due, in part, to the lack of chemical tools to study MARylation in the cell. PARylated proteins can be detected using specific antibodies (e.g. 10H) (Affar et al, Anal Biochem 259, 280-283 (1998); incorporated by reference herein). No such antibodies exist for detecting MARylated proteins. Similarly, PARylated and MARylated proteins can be enriched using different protein domains (e.g. macro) (Jungmichel et al, Mol Cell 52, 272-285 (2013); incorporated by reference herein;) or the modification of the ADPr adduct with chemical tags (e.g. biotin, boronate resin) (Jiang et al, J Am Chem Soc 132, 9363-9372 (2010) and Zhang et al, Nat Methods 10, 981-984 (2013); both of which are incorporated by reference herein) followed by protein identification by liquid-chromatography and tandem mass spectrometry (LC-MS/MS). But, none of these methods are able to distinguish between MARylation and PARylation and, most importantly, they cannot determine which mono-PARP is responsible for a given modification. As a result, advances in mono-PARP biology have been painstaking, requiring the identification of targets through traditional molecular biology approaches (i.e. deletion and overexpression assays with an individual mono-PARP, in vitro MARylation assays with radioactive or biotinylated NAD+, etc.). Complicating matters further, the mono-PARP family members are known to form complexes with each other in the cell and could be playing semiredundant roles in signal transduction (Leung et al, Mol Cell 42, 489-499 (2011); incorporated by reference herein). To push this field forward, new strategies are needed to link a given mono-PARP to its direct protein targets as well as screens for inhibitors of mono-PARPs.

SUMMARY

Poly-ADP-ribose-polymerases (PARP1-16) have emerged as major downstream effectors of NAD+ signaling in the cell. Most PARPs (PARP6-8, 10-12, and 14-16) catalyze the transfer of a single unit of ADP-ribose from NAD+ to amino acids in target proteins, a process known as mono-ADP-ribosylation (MARylation). Progress in understanding the cellular functions of MARylation has been limited by the inability to identify the direct targets for individual mono-PARPs. Herein are disclosed engineered mono-PARPs to use an NAD+ analogue that is orthogonal to wild-type PARPs. The MARylomes of PARP10 and PARP11 were analyzed, identifying isoform-specific targets and revealing a potential role for PARP11 in nuclear pore complex biology. It is further disclosed that PARP11 targeting is dependent on both its regulatory and catalytic domains, which has important implications for how PARPs recognize their targets. The chemical genetic strategy disclosed herein will be generalizable to all mono-PARP family members based on the similarity of the mono-PARP catalytic domains.
Disclosed herein are small molecule compounds (SMCs) of formula:
wherein R is aryl or alkyl provided that R is not ethyl. Such SMCs can act as PARP substrates.
Further disclosed are recombinant proteins including a mutant catalytic domain of PARP6, PARP7, PARP8, PARP10, PARP11, PARP12, PARP14, PARP15, and PARP16, with a mutation from leucine, isoleucine or tyrosine in the position as indicated by Xaa in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8 to a glycine, alanine, serine, cysteine, valine, threonine, or proline, wherein the remainder of the polypeptide is at least 90% identical to SEQ ID NO: 1 SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, or SEQ ID NO: 8 and wherein the polypeptide catalyzes the addition of SMCs (e.g., 5-Bn-6-a-NAD+) to a PARP protein target. Further examples of these polypeptides include SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, and SEQ ID NO: 24.
Also disclosed is a method of identifying a protein target of a mono-PARP. This method involves contacting a SMC of formula:
wherein R is alkyl or aryl; with one or more of the disclosed recombinant proteins including a mutant catalytic domain of a mono-PARP. The contacting for this method occurs within a cell. The cell is subjected to conditions that result in the recombinant protein catalyzing a covalent attachment of the SMC with one or more cellular protein targets. The cellular protein to which the SMC is covalently attached is identified as a protein target of the mono-PARP.
Still further disclosed are screening methods that can be used to identify and select test compounds as inhibitors of a mono-PARP. Such methods involve contacting a SMC of formula:
wherein R is alkyl or aryl; with (i) one or more of the disclosed recombinant proteins including a mutant catalytic domain of a mono-PARP, (ii) one or more test compounds, and (iii) one or more known protein targets of the mono-PARP(s) from which the catalytic domain was derived. The contacting occurs within a mixture, the mixture is subjected to conditions that are known to result in the covalent attachment of the SMC to the known protein targets via mono-PARP activity, at least in the absence of the one or more test compounds. A test compound that inhibits the ability of the recombinant mono-PARP protein to catalyze the reaction that binds the SMC to the known protein target is identified as an inhibitor of the mono-PARP.
The disclosed methods can be used to identify direct targets of any member of the mono-PARP subclass.
The disclosed methods can be used to identify PARP complexes where multiple PARP family members are responsible for a given target modification (Leung et al, 2011 supra),
The disclosed methods can be used to decouple the role for a given PARP family member in signaling pathways, even when specific function is unknown.
The disclosed methods can be used to assign PARylated and MARylated protein targets to each individual PARP family-member with a specific ADP-ribose transfer.
The disclosed methods can be used to generate a database of mono-PARP MARylation targets that can be used immediately to examine the biological role of these mono-PARPs in the cell.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

Some of the drawings are best understood when shown in color. Although color drawings are not available in patent application publications, Applicants consider the drawings containing color as part of the original disclosure and reserve the right to submit color versions of the drawings in later proceedings.

FIGS. 1A-1E. FIG. 1A is a sequence alignment of the nicotinamide binding site of the poly-PARPs (above dashed line) and the mono-PARPs (below). FIG. 1B is an overlay of the crystal structures of PARP1cat (dark green) (PDB ID: 3PAX, Ruf et al, Biochemistry 37, 3893-3900 (1998); incorporated by reference herein) and PARP10cat (yellow) (PDB ID: 3HKV) showing the nicotinamide binding sites. The distance between the key amino acids identified in PARP10, L926 and I987, and the C-5 position of 3-methoxybenzamide are indicated. FIG. 1C is a schematic of one aspect of the disclosed methods: PARP10 variants were incubated with the PARP10 target, SRPK2, in the presence of each individual NAD+ analogue. Modified SRPK2 was subjected to “click” conjugation with a fluorogenic probe and total MARylation was observed using in-gel detection. FIG. 1D is an image of an immunoblot plus coomassie gel (load control) summarizing the results from an orthogonal SRPK2 MARylation screen. Engineered PARP10 variants are listed above the gels. C-5 substitutions on the nicotinamide ring are indicated. For each modified NAD+ analogue tested the same gel was first fluorescently imaged to detect SRPK2 MARylation (top gel, gray) and then stained to detect total SRPK2 (bottom gel, blue). FIG. 1E is a heat map depicting the normalized global MARylation efficiency for the engineered pairs tested in FIG. 1D.

FIGS. 2A-2D. FIG. 2A is an immunoblot of lysates labeled by I987G-PARP10 or I313G-PARP11 in the presence of 5-Bn-6-a-NAD+. HEK 293T cells were transfected with either WT- or IG-PARP10 or -PARP11 and the resulting lysate was incubated for 2 hours in the presence of 5-Bn-6-a-NAD+. MARylation of direct protein targets was observed using streptavidin-HRP (Biotin). The faint bands in the WT-PARP lanes correspond to endogenous biotinylated proteins. Expression of each PARP was confirmed via immunoblot detection of GFP. FIG. 2B is a Venn diagram comparing the I987G-PARP10 targets identified via LC-MS/MS in either HEK 293T or HeLa cells. FIG. 2C is a set of two plots showing the observed distribution functions for the I987G-PARP10 targets identified via LC-MS/MS in either HEK 293T (top) or HeLa (bottom) cells. The distributions for the total protein pool (total) as well as the subset of proteins that were identified in both HEK 293T and HeLa (shared) are indicated. The shared targets identified in HEK 293T cells display significantly elevated peptide counts per identified protein as compared to the total target pool (p<0.05, non-parametric Mann-Whitney U test). The shared targets identified in HeLa cells also display elevated peptide counts per protein, but the difference compared to the total target pool is not significant. FIG. 2D is an image of an immunoblot of the LC-MS/MS identified PARP10 targets (GFP-PARP10, XPO5, WRIP1) following NeutrAvidin enrichment. MARylation levels were determined using streptavidin-HRP (Biotin). Differences in labeling efficiency between HEK 293T and HeLa lysate required separate immunoblot exposures.

FIGS. 3A-3D. FIG. 3A is an image of an immunoblot of Lysate labeling by I987G-PARP10 or I313G-PARP11 in the presence of 5-Bn-6-a-NAD+. HEK 293T cells were transfected with either WT- or I987G-PARP10 or I313G-PARP11 and the resulting lysate was incubated for 2 hours in the presence of 5-Bn-6-a-NAD+. MARylation of direct protein targets was observed using streptavidin-HRP (Biotin). The faint bands in the WT-PARP lanes correspond to endogenous biotinylated proteins. Expression of each PARP was confirmed via immunoblot detection of GFP. FIG. 3B is a Venn diagram comparing the total I987G-PARP10 target pool with both the current I313G-PARP11 and the previously identified KA-PARP1 and KA-PARP2 (Carter-O'Connell et al., 2014) target pools. The protein counts in bold represent the protein targets identified in both LC-MS/MS I987G-PARP10 replicates while the counts in parentheses represent targets identified in at least one replicate. I987G-PARP10 specific targets are shown in the gray circle. FIG. 3C is a Venn diagram comparing the total I313G-PARP11 target pool with both the current I987G-PARP10 and the previously identified KA-PARP1 and KA-PARP2 (Carter-O'Connell et al., 2014) target pools. The protein counts in bold represent the protein targets identified in both LC-MS/MS I313G-PARP11 replicates while the counts in parentheses represent targets identified in at least one replicate. I313G-PARP11 specific targets are shown in the gray circle. FIG. 3D is a set of two circle plots depicting enriched GO terms attached to the I987G-PARP10 (left,) or I313G-PARP11 (right, yellow) specific LC-MS/MS identified targets. GO term enrichment was performed using the PANTHER toolkit. Significantly enriched GO terms (p<0.05) were condensed using Revigo and similar terms were plotted based on semantic similarity. Select groups of terms are indicated. Circle radii are scaled proportionally to the -log10(p-value). The I313G-PARP11 specific proteins associated with RNA transport are listed.

FIGS. 4A-4C. FIG. 4A is a schematic showing the domain architecture of PARP11, PARP10, and the chimeric protein (Chimera) created by fusing the PARP11 n-terminus to the PARP10cat domain. FIG. 4B is a pie chart representing the total MARylated protein targets identified via LC-MS/MS for the chimeric protein. Shared protein targets are indicated by the protein schematics depicted in FIG. 4A. Shared protein targets were identified based on their presence in at least one of the I987G-PARP10 or I313G-PARP11 LC-MS/MS replicates. FIG. 4C is an image of an immunoblot of selected LC-MS/MS identified PARP targets (GFP-PARP, UBE3C, XPO5, NXF1, NUP98, NAGK, WRIP1) following NeutrAvidin enrichment. Overall MARylation levels were determined using streptavidin-HRP (Biotin). PARP10-specific, PARP11-specific, PARP11-WWE dependent and shared chimera targets are indicated to the left.

FIG. 5 is a structure-based sequence alignment of the mono-PARPcat Domains: The aligned primary sequence of the catalytic domains for PARPs 6-8, 10-12, and 14-16 are presented. Secondary structural elements are designated above the alignments (spiral: α-helix, arrow: β-sheet) and the variable d-loop element is indicated. Red asterisks mark the H-Y-I/L/Y triad. The residues targeted for mutagenesis in the present study are highlighted and their position (PARP10 numbering) is noted.

FIGS. 6A and 6B. FIG. 6A is an image of results from orthogonal MARylation of SRPK2 by LG-PARP15 and 5-Bn-6-a-NAD+. WT- and SEQ ID NO: 23 (L659G-PARP15) are indicated above the gel and the non-substituted 6-a-NAD+ and 5-Bn-6-a-NAD+ probes are listed to the right of the gel. For each modified NAD+ analogue tested the same gel was first fluorescently imaged to detect SRPK2 MARylation (top gel, gray) and then stained to detect total SRPK2 (bottom gel, blue). FIG. 6B is a bar graph quantifying the results shown in FIG. 6A.

FIG. 7 is a set of four images of immunoblots of the indicated fractions from the NeutrAvidin enrichment protocol (Carter-O'Connell et al, 2015 infra) were imaged using streptavidin-HRP. 5-Bn-6-a-NAD+ was spiked into the appropriate lysate (expressing either WT- or IG-PARP), samples were labeled, conjugated to biotin-PEG3-azide, enriched, and submitted for LC-MS/MS analysis.

FIG. 8 is a set of two circle plots depicting enriched GO terms attached to the KA-PARP1 (left) or KA-PARP2 (right) specific LC-MS/MS identified targets. GO term enrichment was performed using the PANTHER toolkit. Significantly enriched GO terms (p<0.10, PARP1 or p<0.05, PARP2) were condensed using Revigo and similar terms were plotted based on semantic similarity. Select groups of terms are indicated. Circle radii are scaled proportionally to the −log 10 (p-value).

FIGS. 9A and 9B. FIG. 9A is an image of an Immunoblot detection of the input fractions prior to the enrichment shown in FIG. 2D. Overall MARylation levels were determined using streptavidin-HRP (Biotin). Differences in labeling efficiency between HEK 293T and HeLa lysate required separate immunoblot exposures. FIG. 9B is an image of an Immunoblot detection of the input fractions prior to the enrichment shown in FIG. 4C. Overall MARylation levels were determined using streptavidin-HRP (Biotin). Differences in labeling efficiency between HEK 293T and HeLa lysate required separate immunoblot exposures.

SEQUENCE LISTING

SEQ ID NO: 1 is an example of a Homo sapiens PARP6 catalytic domain with a mutation indicated by Xaa at position 113 of the sequence.
SEQ ID NO: 2 is an example of a Homo sapiens PARP7 catalytic domain with a mutation indicated by Xaa at position 166 of the sequence.
SEQ ID NO: 3 is an example of a Homo sapiens PARP8 catalytic domain with a mutation indicated by Xaa at position 168 of the sequence.
SEQ ID NO: 4 is an example of a Homo sapiens PARP10 catalytic domain with a mutation indicated by Xaa at position 120 of the sequence.
SEQ ID NO: 5 is an example of a Homo sapiens PARP11 catalytic domain with a mutation indicated by Xaa at position 164 of the sequence.
SEQ ID NO: 6 is an example of a Homo sapiens PARP12 catalytic domain with a mutation indicated by Xaa at position 165 of the sequence.
SEQ ID NO: 7 is an example of a Homo sapiens PARP14 catalytic domain with a mutation indicated by Xaa at position 161 of the sequence.
SEQ ID NO: 8 is an example of a Homo sapiens PARP15 catalytic domain with a mutation indicated by Xaa at position 160 of the sequence.
SEQ ID NO: 9 is an example of a Homo sapiens PARP6 catalytic domain with a G residue at position 113 of the sequence.
SEQ ID NO: 10 is an example of a Homo sapiens PARP6 catalytic domain with an A residue at position 113 of the sequence.
SEQ ID NO: 11 is an example of a Homo sapiens PARP7 catalytic domain with a G residue at position 166 of the sequence.
SEQ ID NO: 12 is an example of a Homo sapiens PARP7 catalytic domain with an A residue at position 166 of the sequence.
SEQ ID NO: 13 is an example of a Homo sapiens PARP8 catalytic domain with a G at position 168 of the sequence.
SEQ ID NO: 14 is an example of a Homo sapiens PARP8 catalytic domain with an A at position 168 of the sequence.
SEQ ID NO: 15 is an example of a Homo sapiens PARP10 catalytic domain with a G residue at position 120 of the sequence.
SEQ ID NO: 16 is an example of a Homo sapiens PARP10 catalytic domain with an A residue at position 120 of the sequence.
SEQ ID NO: 17 is an example of a Homo sapiens PARP11 catalytic domain with a G residue at position 164 of the sequence.
SEQ ID NO: 18 is an example of a Homo sapiens PARP11 catalytic domain with an A residue at position 164 of the sequence.
SEQ ID NO: 19 is an example of a Homo sapiens PARP12 catalytic domain with a G residue at position 165 of the sequence.
SEQ ID NO: 20 is an example of a Homo sapiens PARP12 catalytic domain with an A residue at position 165 of the sequence.
SEQ ID NO: 21 is an example of a Homo sapiens PARP14 catalytic domain with a G residue at position 161 of the sequence.
SEQ ID NO: 22 is an example of a Homo sapiens PARP14 catalytic domain with an A residue at position 161 of the sequence.
SEQ ID NO: 23 is an example of a Homo sapiens PARP15 catalytic domain with a G residue at position 160 of the sequence.
SEQ ID NO: 24 is an example of a Homo sapiens PARP15 catalytic domain with an A residue at position 160 of the sequence.

DETAILED DESCRIPTION

Disclosed herein is method of labeling specific targets of a single engineered mono-PARP with a clickable NAD+ analogue including a benzyl substituent at the C-5 position of the nicotinamide ring and an alkyne at the N-6 position of the adenosine ring (S-Bn-6-a-NAD+). When combined with LC-MS/MS analysis, a set of 140 preferred PARP10-specific targets involved in a wide-array of biological processes was identified. Also identified was a set of 21 preferred PARP11-specific targets that are primarily involved in nuclear pore complex biology (Natalizio B J and Wente S R, Trends Cell Biol 23, 365-373 (2013); incorporated by reference herein). This represents the first identification of cellular PARP11 targets and implicates PARP11 in a previously uncharacterized biological role. The disclosed methods were also used to explore the requirements for target recognition at both the NAD+ active site and the modular n-terminal regulatory domains of PARPs 10 and 11. Provided herein is the first evidence of the structurally conserved PARPcat domains and that the non-conserved modular n-terminal regulator domains in the mono-PARP family play specific, and necessary, roles in precise target recognition.
Terms:
Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCR Publishers, Inc., 1995 (ISBN 1-56081-569-8).
Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. It is further to be understood that all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for description. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below.
As will be understood by one of ordinary skill in the art, each embodiment disclosed herein can comprise, consist essentially of, or consist of its particular stated element, step, ingredient or component. Thus, the terms “include” or “including” should be interpreted to recite: “comprise, consist essentially of, or consist of.” The transition term “comprise” or “comprises” means includes, but is not limited to, and allows for the inclusion of unspecified elements, steps, ingredients, or components, even in major amounts. The transitional phrase “consisting essentially of” limits the scope of the embodiment to the specified elements, steps, ingredients or components and to those that do not materially affect the embodiment. As used herein, a material effect would cause a statistically-significant reduction in an embodiment's ability to identify (i) a mono-PARP protein target; or (ii) a test compound that is a mono-PARP inhibitor. The transitional phrase “consisting of” excludes any element, step, ingredient or component not specified.
In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. In order to facilitate review of the various embodiments of the disclosure, the following explanations of specific terms are provided:
Alkyl: a branched or unbranched saturated hydrocarbon group, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, t-butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, tetradecyl, hexadecyl, eicosyl, tetracosyl and the like. A lower alkyl group is a saturated branched or unbranched hydrocarbon having from 1 to 6 carbon atoms (C1-6 alkyl). The term alkyl also includes cycloalkyls. Alkyl also includes substituted alkyls which are alkyl groups wherein one or more hydrogen atoms are replaced with a substituent such as alkyl, alkynyl, alkenyl, aryl, halide, nitro, amino, ester, ether, ketone, aldehyde, hydroxyl, carboxyl, cyano, amido, haloalkyl, haloalkoxy, or alkoxy. The term alkyl also includes heteroalkyls. A heteroalkyl contains at least one heteroatom such as nitrogen, oxygen, sulfur, or phosphorus replacing one or more of the carbons. Substituted heteroalkyls are also encompassed by the term alkyl.
Antagonist: An antagonist is an agent, such as a small molecule or protein that binds to a protein and prevents, stops, or reduces (to a statistically significant degree) the protein from producing a particular biological effect. An antagonist can be a naturally occurring or artificially synthesized compound. For example, a mono-PARP antagonist is a compound that inhibits natural activity of a mono-PARP. An antagonist can also be called an inhibitor and the terms can be used interchangeably.
Aryl: any carbon-based aromatic group including benzene, naphthalene, and phenyl. The term aryl also includes substituted aryls in which one or more of the hydrogens is substituted with one or more groups including alkyl, alkynyl, alkenyl, aryl, halide, nitro, amino, ester, ether, ketone, aldehyde, hydroxy, carboxylic acid, cyano, amido, haloalkyl, haloalkoxy, or alkoxy. The term aryl also includes heteroaryls in which one or more of the carbons is replaced by a heteroatom. Examples of heteroatoms include nitrogen, oxygen, sulfur, and phosphorous. Substituted heteroaryls are also encompassed by the term aryl.
Contacting: Placement under conditions in which direct physical association occurs, including contacting of a solid with a solid, a liquid with a liquid, a liquid with a solid, or either a liquid or a solid with a cell or tissue, whether in vitro or in vivo. Contacting can occur in vitro with isolated cells or tissue or in vivo by administering to a subject.
Conservative amino acid substitution: A substitution of an amino acid residue for another amino acid residue having similar biochemical properties. “Conservative” amino acid substitutions are those substitutions that do not substantially affect or decrease an activity of a polypeptide such as a mono-PARP catalytic domain, WWE domain, or zinc finger domain. A polypeptide can include one or more conservative substitutions up to and including 1-10 total conservative substitutions, 1% conservative substitutions, 5% conservative substitutions, 10% conservative substitutions, 15% conservative substitutions, 20% conservative substitutions, 25% conservative substitutions, 30% or more conservative substitutions, or any intervening value. Specific examples of conservative substitutions include the following:


	Original Amino Acid	Conservative Substitutions

	Ala	Ser
	Arg	Lys
	Asn	Gln, His
	Asp	Glu
	Gln	Asn
	Cys	Ser
	Glu	Asp
	His	Asn; Gln
	Ile	Leu, Val
	Leu	Ile; Val
	Lys	Arg; Gln; Glu
	Met	Leu; Ile
	Phe	Met; Leu; Tyr
	Ser	Thr
	Thr	Ser
	Trp	Tyr
	Tyr	Trp; Phe
	Val	Ile; Leu

While examples of polypeptide sequences are provided in the amino acid sequences filed with this application, not all variants of polypeptide sequences with all possible combinations of conservative amino acid substitutions encompassed by the disclosure are provided in the sequence listing. This table can be used in combination with the sequence listing to provide explicit examples of polypeptide sequences encompassed by the disclosure.
Control: A reference standard. A control can be a test compound that is known to be an antagonist of a mono-PARP (positive control). A control can also be a test compound known not to act as an antagonist of a mono-PARP, such as the vehicle in which the test compound is provided, otherwise lacking the test compound (negative control).
Cycloalkyl: a non-aromatic carbon-based ring composed of at least three carbon atoms. Examples of cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Cycloalkyls also encompass substituted cycloalkyls and heterocycloalkyls where at least one of the carbon atoms is replaced with a heteroatom such as nitrogen, sulfur or phosphorus. A heterocycloalkyl wherein one or more of the carbons is replaced with nitrogen is also termed a cycloalkylamino herein. The term also includes substituted heterocycloalkyls.
Derivative: a compound or portion of a compound that is derived from or is theoretically derivable from a parent compound. Within the current disclosure, a derivative exhibits a substantially similar biological effect in the methods disclosed and claimed herein.
Domain: A domain of a polypeptide or protein may be any part of a protein that exhibits a particular defined structure and/or mediates a particular protein function. An example of a domain is the catalytic domain of a mono-PARP.
Heterocycle: A chemical group that includes both heteroaryls and heterocycloalkyls. Heterocycles may be monocyclic or polycyclic rings. Exemplary heterocycles include azepinyl, aziridinyl, azetyl, azetidinyl, diazepinyl, dithiadiazinyl, dioxazepinyl, dioxolanyl, dithiazolyl, furanyl, isooxazolyl, isothiazolyl, imidazolyl, morpholinyl, oxetanyl, oxadiazolyl, oxiranyl, oxazinyl, oxazolyl, piperazinyl, pyrazinyl, pyridazinyl, pyrimidinyl, piperidyl, piperidino, pyridyl, pyranyl, pyrazolyl, pyrrolyl, pyrrolidinyl, thiatriazolyl, tetrazolyl, thiadiazolyl, triazolyl, thiazolyl, thienyl, tetrazinyl, thiadiazinyl, triazinyl, thiazinyl, thiopyranyl, furoisoxazolyl, imidazothiazolyl, thienoisothiazolyl, thienothiazolyl, imidazopyrazolyl, cyclopentapyrazolyl, pyrrolopyrrolyl, thienothienyl, thiadiazolopyrimidinyl, thiazolothiazinyl, thiazolopyrimidinyl, thiazolopyridinyl, oxazolopyrimidinyl, oxazolopyridyl, benzoxazolyl, benzisothiazolyl, benzothiazolyl, imidazopyrazinyl, purinyl, pyrazolopyrimidinyl, imidazopyridinyl, benzimidazolyl, indazolyl, benzoxathiolyl, benzodioxolyl, benzodithiolyl, indolizinyl, indolinyl, isoindolinyl, furopyrimidinyl, furopyridyl, benzofuranyl, isobenzofuranyl, thienopyrimidinyl, thienopyridyl, benzothienyl, cyclopentaoxazinyl, cyclopentafuranyl, benzoxazinyl, benzothiazinyl, quinazolinyl, naphthyridinyl, quinolinyl, isoquinolinyl, benzopyranyl, pyridopyridazinyl and pyridopyrimidinyl groups. The term also includes substituted heterocycles, including substituted forms of all the species above.
Label: A label may be any substance capable of aiding a machine, detector, sensor, device, column, or enhanced or unenhanced human eye in differentiating a labeled composition from an unlabeled composition. Labels may be used for any of a number of purposes and one skilled in the art will understand how to match the proper label with the proper purpose. Examples of uses of labels include purification of biomolecules, identification of biomolecules, detection of the presence of biomolecules, detection of protein folding, and localization of biomolecules within a cell, tissue, or organism. Examples of labels include: radioactive isotopes or chelates thereof; dyes (fluorescent or nonfluorescent), stains, enzymes, nonradioactive metals, magnets, protein tags, any antibody epitope, any specific example of any of these; any combination between any of these, or any label now known or yet to be disclosed. A label may be covalently attached to a biomolecule or bound through hydrogen bonding, Van Der Waals or other forces. A label may be covalently or otherwise bound to the N-terminus, the C-terminus or any amino acid of a polypeptide or the 5′ end, the 3′ end or any nucleic acid residue in the case of a polynucleotide.
One particular example of a label is a protein tag. A protein tag includes a sequence of one or more amino acids that may be used as a label as discussed above, particularly for use in protein purification. In some examples, the protein tag is covalently bound to the polypeptide. It may be covalently bound to the N-terminal amino acid of a polypeptide, the C-terminal amino acid of a polypeptide or any other amino acid of the polypeptide. Often, the protein tag is encoded by a polynucleotide sequence that is immediately 5′ of a nucleic acid sequence coding for the polypeptide such that the protein tag is in the same reading frame as the nucleic acid sequence encoding the polypeptide. Protein tags may be used for all of the same purposes as labels listed above and are well known in the art. Examples of protein tags include chitin binding protein (CBP), maltose binding protein (MBP), glutathione-S-transferase (GST), poly-histidine (His), thioredoxin (TRX), FLAG®, V5, c-Myc, HA-tag, and so forth.
A His-tag facilitates purification and binding to on metal matrices, including nickel matrices, including nickel matrices bound to solid substrates such as agarose plates or beads, glass plates or beads, or polystyrene or other plastic plates or beads. Other protein tags include BCCP, calmodulin, Nus, Thioredoxin, Streptavidin, SBP, and Ty, or any other combination of one or more amino acids that can work as a label described above.
Another particular example of a label is biotin. Biotin is a natural compound that tightly binds proteins such as avidin or streptavidin. A compound labeled with biotin is said to be ‘biotinylated’. Biotinylated compounds can be detected with avidin or streptavidin when that avidin or streptavidin is conjugated another label such as a fluorescent, enzymatic, radioactive or other label.
Mass spectrometry: A method wherein, a sample is analyzed by generating gas phase ions from the sample, which are then separated according to their mass-to-charge ratio (m/z) and detected. Methods of generating gas phase ions from a sample include electrospray ionization (ESI), laserspray ionization (LSI), matrix-assisted laser desorption-ionization (MALDI), surface-enhanced laser desorption-ionization (SELDI), chemical ionization, and electron-impact ionization (El). Separation of ions according to their m/z ratio can be accomplished with any type of mass analyzer, including quadrupole mass analyzers (Q), time-of-flight (TOF) mass analyzers, magnetic sector mass analyzers, 3D and linear ion traps (IT), Fourier-transform ion cyclotron resonance (FT-ICR) analyzers, and combinations thereof (for example, a quadrupole-time-of-flight analyzer, or Q-TOF analyzer). Prior to separation, the sample may be subjected to one or more dimensions of chromatographic separation, for example, one or more dimensions of liquid or size exclusion chromatography or gel-electrophoretic separation.
Mutation: A mutation can be any difference in the sequence of a biomolecule relative to a reference or consensus sequence of that biomolecule. A mutation can be observed in a nucleic acid sequence or a protein sequence. Such a reference or consensus sequence may be referred to as “wild type”. For example, a mutation such as a mutation from isoleucine at position 987 to a glycine in the catalytic domain of PARP10 is a mutation relative to the PARP10 consensus sequence. Other mutations can result in conservative amino acid substitutions.
NAD: An abbreviation of nicotinamide adenine dinucleotide. The oxidized form is referred to as NAD+. The reduced form is referred to as NADH. NAD has a number of physiological roles including as an enzyme cofactor, as an oxidizing (NAD+) or reducing (NADH) agent, and as a signaling molecule. NAD (without a plus-sign) is a common term that includes both the oxidized and reduced forms of the NAD molecule. NAD has important roles in transcription, DNA repair, cellular metabolism, and apoptosis and both NAD levels and oxidation state are considered to be important mechanisms in cancer growth and development (Chiarugi et al, Nat Rev Cancer 12, 741-752 (2012); incorporated by reference herein).
Nucleic acid or nucleic acid sequence: a polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA). The term can be used interchangeably with the term ‘polynucleotide.’ A nucleic acid is made up of four bases; adenine, cytosine, guanine, and thymine/uracil (uracil is used in RNA). A coding sequence from a nucleic acid is indicative of the sequence of the protein encoded by the nucleic acid.
Operably Linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in such a way that it has an effect upon the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operably linked DNA sequences may be contiguous, or they may operate at a distance.
Polypeptide: Any chain of amino acids, regardless of length or posttranslational modification (such as glycosylation, methylation, ubiquitination, phosphorylation, or the like). Herein as well as in the art, the term ‘polypeptide’ is used interchangeably with peptide or protein, and is used to refer to a polymer of amino acid residues. The term ‘residue’ can be used to refer to an amino acid or amino acid mimetic incorporated in a polypeptide by an amide bond or amide bond mimetic. Polypeptide sequences are generally written with the N-terminal amino acid on the left and the C-terminal amino acid to the right of the sequence.
Promoter: A promoter may be any of a number of nucleic acid control sequences that directs transcription of a nucleic acid. Typically, a eukaryotic promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element or any other specific DNA sequence that is recognized by one or more transcription factors. Expression by a promoter may be further modulated by enhancer or repressor elements. Numerous examples of promoters are available and well known to those of skill in the art. A nucleic acid including a promoter operably linked to a nucleic acid sequence that codes for a particular polypeptide can be termed an expression vector.
Purification: Purification of a polypeptide or molecular complex may be achieved by any method now known or yet to be disclosed. In some examples, purification is achieved by contacting the complex with a reagent that binds to a component of the complex to the exclusion of other components.
Recombinant: A recombinant nucleic acid or polypeptide has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more naturally occurring sequences. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. A recombinant polypeptide can refer to a polypeptide that has been made using recombinant nucleic acids, including recombinant nucleic acids transferred to a host organism that is not the natural source of the polypeptide.
Sequence homology: Sequence homology between two or more nucleic acid sequences or two or more amino acid sequences, may be expressed in terms of the identity or similarity between the sequences. Sequence identity can be measured in terms of percentage identity; the higher the percentage, the more identical the sequences are. Sequence similarity can be measured in terms of percentage similarity (which takes into account conservative amino acid substitutions); the higher the percentage, the more similar the sequences are. Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith & Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol. Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp, CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988; Huang et al. Computer Appls in the Biosciences 8, 155-65, 1992; and Pearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J. Mol. Biol. 215:403-10, 1990, presents a detailed consideration of sequence alignment methods and homology calculations.
The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., J. Mol. Biol. 215:403-10, 1990) is available from several sources, including the National Center for Biological Information (NCBI, National Library of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. Additional information can be found at the NCBI web site. BLASTN is used to compare nucleic acid sequences, while BLASTP is used to compare amino acid sequences. If the two compared sequences share homology, then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology, then the designated output file will not present aligned sequences.
Once aligned, the number of matches is determined by counting the number of positions where an identical nucleotide or amino acid residue is presented in both sequences. The percent sequence identity is determined by dividing the number of matches either by the length of the sequence set forth in the identified sequence, or by an articulated length (such as 100 consecutive nucleotides or amino acid residues from a sequence set forth in an identified sequence), followed by multiplying the resulting value by 100. For example, a nucleic acid sequence that has 1166 matches when aligned with a test sequence having 1154 nucleotides is 75.0 percent identical to the test sequence (1166÷1554*100=75.0). The percent sequence identity value is rounded to the nearest tenth. For example, 75.11, 75.12, 75.13, and 75.14 are rounded down to 75.1, while 75.15, 75.16, 75.17, 75.18, and 75.19 are rounded up to 75.2. The length value will always be an integer. In another example, a target sequence containing a 20-nucleotide region that aligns with 20 consecutive nucleotides from an identified sequence as follows contains a region that shares 75 percent sequence identity to that identified sequence (that is, 15÷20*100=75). For comparisons of amino acid sequences of greater than 30 amino acids, the Blast 2 sequences function is employed using the default BLOSUM62 matrix set to default parameters, (gap existence cost of 11, and a per residue gap cost of 1). Homologs are typically characterized by possession of at least 70% sequence identity counted over the full-length alignment with an amino acid sequence using the NCBI Basic Blast 2.0, gapped blastp with databases such as the nr or swissprot database. Queries searched with the blastn program are filtered with DUST (Hancock and Armstrong, 1994, Comput. Appl. Biosci. 10:67-70). In addition, a manual alignment can be performed. Proteins with even greater similarity will show increasing percentage identities when assessed by this method, such as at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 100% sequence identity.
When aligning short peptides (fewer than around 30 amino acids), the alignment is to be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties). Proteins with even greater similarity to the reference sequence will show increasing percentage identities when assessed by this method, such as at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity to a protein. When less than the entire sequence is being compared for sequence identity, including a comparison of, for example, a mono-PARP catalytic domain, homologs will typically possess at least 75% sequence identity over short windows of 10-20 amino acids, and can possess sequence identities of at least 85%, 90%, 95% or 98% depending on their identity to the reference sequence. Methods for determining sequence identity over such short windows are described at the NCBI web site.
A pair of proteins or nucleic acids with 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity to one another can be termed ‘homologs,’ particularly if they perform the same function as one another, even more particularly if they perform the same function to substantially the same degree, and still more particularly if they perform the same function substantially equivalently. One of skill in the art in light of this disclosure, particularly in light of the Examples below, would be able to determine without undue experimentation whether or not a given protein or nucleic acid sequence with 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identity to the sequences listed herein is a homolog to the sequences listed herein. Homologs need not be the same length as the biological molecules listed herein and may include truncations (fewer amino acids or nucleotides) or extensions (more amino acids or nucleotides) than the biological molecules listed herein.
Test Compound: A test compound can be any compound that is suspected of or might effect mono-PARP activity. Examples of test compounds include small molecules, proteins, peptides, or other potential therapeutic compounds. A test compound can also be a compound known to inhibit mono-PARP activity that is used as a positive control. A test compound can also be a compound known not to affect mono-PARP activity that is used as a negative control.
Small Molecule Compounds (SMCs): Disclosed herein are SMCs of formula:
wherein R is selected from alkyl and aryl. In some examples, this is provided that R is not ethyl. Aside from that provision, R can be any alkyl including any straight chain alkyl (such as methyl and propyl) any branched alkyl (such is isobutyl), or cycloalkyl. R can also be any aryl including benzyl, any substituted aryl, or any heteroaryl. Such SMCs can be provided in a vehicle such as a buffer or other appropriate solution.
The disclosed SMCs can be used as substrates of mutant mono-PARP catalytic domains as described below. The SMCs will not work as substrates of wild-type mono-PARP catalytic domains. In addition, a label such as a fluorescent compound, biotin, protein tag, or other label can be conjugated to the SMCs.
Polypeptide Compositions: Further disclosed are recombinant polypeptides that include a mono-PARP catalytic domain. The mono-PARP catalytic domain can be selected from that of PARP6, PARP7, PARP8, PARP10, PARP11, PARP12, PARP14, PARP15, and PARP16. In particular embodiments, the mono-PARP catalytic domain is further characterized as having a mutation in a particular position in the catalytic domain. The particular positions are described in the sequence listing section of the specification above and as Xaa in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8 in the disclosed sequences. The wild type version of the PARP catalytic domain has an isoleucine residue (for PARP6, PARP7, PARP8, PARP10, PARP11, and PARP 12), a leucine residue (PARP14, PARP15), or a tyrosine residue (PARP16) in the indicated position. In the disclosed polypeptides, an amino acid substitution mutation is introduced that results in a residue smaller than an isoleucine or leucine residue (for example, a glycine, alanine, serine, cysteine, valine, threonine, or proline residue). In further examples of the disclosed polypeptide, the amino acid is mutated to an alanine or guanine as exemplified by SEQ ID NO: 9-SEQ ID NO: 24.
The disclosed polypeptides can further include mono-PARP domains other than the catalytic domain. Such domains include a WWE domain, one or more Zn finger domains, one or more macro domains, or one or more N-terminal domains. Such domains can be derived from the same mono-PARP as the mono-PARP from which the catalytic domain was derived or from a different mono-PARP as contemplated by the Examples below.
The amino acid substitutions described herein allow the mono-PARP catalytic domain to use one of the disclosed SMCs (such as 5-Bn-6-a-NAD+), as a substrate. The substrate can thereby be covalently attached to a target protein as described in the example below. The disclosed polypeptide compositions have the further characteristic that they do not catalyze the reaction with natural NAD+.
The disclosed polypeptides can include additional mutations (outside of the mutations indicated in the sequence listing) that result in amino acid substitutions—including conservative amino acid substitutions—that can result in a mono-PARP catalytic domain that has substantially the same catalytic specificity and substantially the same catalytic activity as the polypeptides described as SEQ ID NO: 1 to SEQ ID NO: 24. Substantially the same means not statistically significantly different when measured according to a method disclosed herein. Such mutations can have other improved characteristics such as more efficient expression in a recombinant expression system, particular antibody specificity, or improved stability or other characteristics.
The disclosed polypeptides can further include a label or protein tag as described above to facilitate purification, identification, or other activities.
Methods of identifying targets of a mono-PARP. Disclosed are methods of identifying a protein target of a mono-PARP. These methods involve contacting one of the disclosed SMCs (for example 5-Bn-6-a-NAD+), with one of the disclosed polypeptides (said polypeptide including, for example, SEQ ID NO: 15). Any one or more of the disclosed SMCs and any one or more of the disclosed polypeptides can be used in any combination. For the purposes of this method, in particular embodiments, the contacting occurs within a cell, such as a living cell. The cell can be any cell such as a human cell line, a cell collected from a biopsy (including a blood cell), a tumor cell, or any other living human cell for which the user of the method wishes to identify a mono-PARP target. The contacting can occur by any method known in the art. For example, the polypeptide can be expressed within the cell via an expression vector that is transfected into the cell by any method known in the art and the SMC can be added to the media.
In the specific example described above, the cell is subjected to conditions that result in the polypeptide including SEQ ID NO: 15 catalyzing a reaction that results in the covalent attachment of 5-Bn-6-a-NAD+ to its protein targets within the cell. The 5-Bn-6-a-NAD+ conjugated protein targets can then be identified by any method known in the art, including those methods described below. For example, a label such as biotin can be conjugated to the 5-Bn-6-a-NAD+, the protein targets purified using avidin or streptavidin, and the protein targets identified by mass spectrometry. Alternatively, the 5-Bn-6-a-NAD+ on the protein targets can be labeled with a fluorescent protein, a tag, or other label.
Methods of selecting mono-PARP antagonists. Also disclosed are methods of selecting a test compound as an antagonist of a mono-PARP. The methods involve contacting one of the disclosed SMCs (for example, 5-Bn-6-a-NAD+) with one of the disclosed polypeptides (for example, a polypeptide including SEQ ID NO: 15.) Any one or more of the disclosed SMCs and any one or more of the disclosed polypeptides can be used in any combination. These are further contacted with a known protein target of the mono-PARP (in this particular example, the target can be SRPK2 or any fragment thereof that is MARylated by PARP10 or another PARP, but any protein target of the selected PARP can be used including a protein target determined by the method above) under conditions that are known to result in the covalent attachment of the SMC to the known protein target via mono-PARP activity, at least in the absence of the one or more test compounds These are further contacted with a test compound. The contacting occurs within a mixture. If a reliable reduction in covalent attachment of the SMC to the known protein target is observed, the test compound is a mono-PARP antagonist. As is understood by one of ordinary skill in the art, a reliable reduction is one that is statistically significant and reproducible. The various components can be added to the mixture in any order. The mixture can be any mixture including a cell-free mixture. Alternatively, the mixture can include a cell, including a living cell, including a living cell that expresses the disclosed polypeptide as described above.
In the specific example described above, the mixture is subjected to conditions that result in the polypeptide including SEQ ID NO: 15 catalyzing a reaction that results in the covalent attachment of 5-Bn-6-a-NAD+ to the protein target. If a test compound causes less covalent attachment of the 5-Bn-6-a-NAD+ to the protein target relative to a negative control (such as a vehicle only control including the buffer in which the test compound was originally provided), then that test compound is selected as an antagonist of (in the specific example here) PARP10.
The methods herein can be used to screen a plurality of test compounds, also described as a library of test compounds. The methods herein can be further adapted to high throughput screening of a set of test compounds in batches of 96, 384, 1048, or more on assay plates adapted for such screening.

EXAMPLES

The following examples are illustrative of disclosed compositions and methods.

Example 1

Identification of Engineered mono-PARP—Modified NAD+ Analogue Pairs. A sensitized enzyme-modified substrate (“bump-hole”) method was used in identifying the direct protein targets of poly-PARPs (Carter-O'Connell and Cohen, Curr Prot Chem Biol 7, 121-139 (2015) and Carter-O'Connell et al, J Am Chem Soc 136, 5201-5204 (2014); both of which are incorporated by reference herein. This method involved mutating an active site lysine residue (Lys903 in human PARP1, referred to here as the “ceiling” position) to an alanine to create a unique pocket for accommodating a C-5 ethyl group on the nicotinamide ring of the NAD+ analogue, 5-Et-6-a-NAD+. This NAD+ analogue contains an alkyne at the N-6 position of the adenine ring to aid in target identification using click conjugation to a rhodamine-azide or biotin-azide. It was shown that 5-Et-6-a-NAD+ can be used as a selective substrate for K903A (KA), but not wild-type (WT) PARP1, and mutation of the ceiling lysine to an alanine in the other poly-PARPs yielded similar results (Carter-O'Connell and Cohen, 2015 supra, Carter-O'Connell et al, 2014 supra).
Unlike the poly-PARPs, the mono-PARPs do not have a lysine at the ceiling position; rather, they contain a leucine (PARP10, 15), an isoleucine (PARP16, 17), or a tyrosine (PARP7, 8, 11, 12, and 14) as demonstrated by a structure-based sequence alignment (FIGS. 1A and 5). Overlay of the crystal structures of 3-aminobenzamide-bound PARP10 and PARP1 (Ruf et al, 1998 supra) reveals that Leu926 in PARP10 occupies a similar space as Lys903 in PARP1 (FIG. 1B), suggesting that mutation of the ceiling position in mono-PARPs to a smaller amino acid (e.g. alanine, glycine, serine, cysteine, valine, threonine, or proline) would accommodate 6-a-NAD+ analogues containing a substitution at the C-5 position of the nicotinamide ring.
It was first tested whether or not mutation of the leucine at position 120 of the wild type PARP10 catalytic domain (corresponding to SEQ ID NO: 4 herein with an L residue at position 120, also called WT-PARP10cat herein) to an alanine or glycine (corresponding to SEQ ID NO: 18 and SEQ ID NO: 17, respectively) would confer sensitivity to C-5 substituted 6-a-NAD+ analogues. In addition to the 6-a-NAD+ analogue—5-Et-6-a-NAD+—a panel of analogues containing either a methyl, propyl, isobutyl, or benzyl group at the C-5 position (5-Me-6-a-NAD+, 5-Pr-6-a-NAD+, 5-iBu-6-a-NAD+, and 5-Bn-6-a-NAD+, respectively) was synthesized to further probe the unique binding pockets in engineered mono-PARPs (See Example 8 below). To test the reaction of these mutants C-5 substituted 6-a-NAD+ analogue pairs, wild type PARP10 catalytic domain (PARP10cat)-mediated MARylation of the known substrate SRSF protein kinase 2 (SRPK2) (Haikarainen et al, PLoS One 8, e65404 (2013) and Morgan and Cohen, ACS Chem Biol (2015); both of which are incorporated by reference herein) was monitored by click conjugation to a rhodamine-azide probe and a subsequent in-gel fluorescence detection (FIG. 1C). 6-a-NAD+ was used as a substrate to mediate SRPK2 MARylation by WT-PARP10cat, and to a lesser extent by L926A- and L296G-PARP10cat (FIGS. 1D, 1E). Importantly, none of the C-5 substituted 6-a-NAD+ analogues were used by WT-PARP10cat (FIGS. 1D, 1E). 5-Me-6-a-NAD+ and 5-Et-6-a-NAD+ were used by L296G-PARP10cat, but were very poor substrates (5% MARylation activity compared to WTPARP10cat with 6-a-NAD+, FIGS. 1D, 1E).
Based on these results, an alternative amino acid within the nicotinamide binding site of mono-PARPs was sought such that when mutated to a smaller amino acid, the site might confer sensitivity to the orthogonal NAD+ analogues. Amino acid 120 of SEQ ID NO: 4 herein (which is isoleucine in wild type PARP10 and also called IIe987 herein) is located in the “floor” position of PARP10. This amino acid was selected for two reasons: (1) it makes van der Waals contacts with the C-5 position of the benzamidine ring of 3-aminobenzamide (FIG. 1B); and (2) it is well-conserved across the mono-ARTD subfamily (FIG. 1A). This amino acid was then mutated in PARP10cat to either an alanine or glycine (corresponding to SEQ ID NO: 16 and SEQ ID NO: 15 respectively) and it was then determined if these engineered mutants could use C-5 substituted 6-a-NAD+ analogues as substrates. It was found that 5-Bn-6-a-NAD+ was used efficiently by a polypeptide including SEQ ID NO: 15 (also called I987G-PARP10 herein). The polypeptide including SEQ ID NO: 15 showed 140% MARylation activity compared to WT-PARP1Ocat with 6-a-NAD+, FIGS. 1D, 1E); by contrast, 6-a-NAD+ was a poor substrate the construct including SEQ ID NO: 15 (5% MARylation activity compared to WT-PARP10cat with 6-a-NAD+, FIGS. 1D, 1E). Taken together, these results demonstrate that mutation of the isoleucine at position 120 of SEQ ID NO: 4 herein in the floor position of PARP10 results in an orthogonal switch in substrate specificity from 6-a-NAD+ to 5-Bn-6-a-NAD+.
It was next tested whether mutating the floor position in another mono-PARP would confer sensitivity to 5-Bn-6-a-NAD+. A construct including a wild type PARP15 catalytic domain, which corresponds to a leucine at position 160 of SEQ ID NO: 8 (also called WT-PARP15cat) and a construct including SEQ ID NO: 23 (also called L659G-PARP15cat herein) were expressed and their in vitro MARylation activity tested with both 6-a-NAD+ and 5-Bn-6-a-NAD+. Similar to SEQ ID NO: 15, SEQ ID NO: 23 used 5-Bn-6-a-NAD+ selectively to MARylate SRPK2 (FIGS. 6A and 6B). Importantly, WT-PARP15cat did not use 5-Bn-6-a-NAD+ (FIGS. 6A and 6B). All of the mono-PARPs contain a leucine or isoleucine at corresponding positions in the catalytic domain (with the exception of PARP16 which has a tyrosine, see sequence listing and FIG. 1A). This result suggests that this residue may be mutated to a smaller amino acid to generate a 5-Bn-6-a-NAD+ sensitive catalytic domain throughout the mono-PARP subclass. Examples of such mutants are listed in detail as SEQ ID NO: 9-SEQ ID NO: 24 herein.

Example 2

SEQ ID NO: 15—5-Bn-6-a-NAD+ Pair Specifically Labels Direct Protein Targets in Multiple Cell Lines. It was next determined if a polypeptide including SEQ ID NO: 15 could be used to label direct protein targets in a cellular context. GFP-SEQ ID NO: 15 (1G-PARP10) or GFP-WT-PARP10 —GFP linked to SEQ ID NO: 4 with an isoleucine at position 120—WT-PARP10) were expressed in human embryonic kidney (HEK) 293T cells. Lysates were prepared and incubated with 5-Bn-6-a-NAD+ (100 μM), followed by click conjugation with biotin-azide. Treatment of lysates from SEQ ID NO: 15 transfected cells with 5-Bn-6-a-NAD+ resulted in labeling of several bands, the predominant band corresponding to the size of auto-MARylated SEQ ID NO: 15 (FIG. 2A). By contrast, treatment of lysates from WT-PARP10 transfected cells with 5-Bn-6-a-NAD+ resulted in a low-level of background labeling—most likely due to endogenously biotinylated proteins (FIG. 2A). These result demonstrate that the SEQ ID NO: 15—5-Bn-6-a-NAD+ pair can be used to label direct MARylation targets of PARP10.
Next, the disclosed labeling method was used to identify direct MARylation targets of PARP10 using LC-MS/MS. HEK 293T lysates generated from cells expressing WT-PARP10 or SEQ ID NO: 15 were treated with 5-Bn-6-a-NAD+ (100 μM). MARylated proteins were conjugated to biotin-azide, enriched using NeutrAvidin agarose, digested with trypsin, and subjected to LC-MS/MS (FIG. 7). A total of 803 PARP10-specific protein targets were found. This represents a much broader target set than that found for either PARP1 or PARP2 (42 and 339 proteins, respectively), (Carter-O'Connell et al, 2014 supra). There was no overlap between the targets determined using the disclosed method and previously published PARP10 targets identified using protein microarrays (Feijs et al, Cell Comm Sig 11, 5 (2013); incorporated by reference herein). This could be due to differences in the context in which the labeling reactions are performed in that the disclosed methods identify PARP10 targets in a complex cellular context in that other PAR and MAR detection methods rely on non-family member specific labeling methods.
Given the scarcity of data regarding the physiological role of PARP10, including its basal activity in different cell types, it was possible that the choice of cell type could be inflating the actual target list of PARP10 targets. To address this possibility, the labeling experiment was repeated in HeLa cells (FIG. 7). In HeLa cells 256 direct PARP10 targets were identified. A comparison with the list of PARP10 targets identified in HEK 293T cells revealed that a majority of the targets found in HeLa cells (69%) were also identified in the HEK 293T samples (FIG. 2B). The smaller number of targets identified in HeLa cells compared to HEK 293T cells is likely due to the decreased expression levels or activity of PARP10 in HeLa cells compared to HEK 293T cells.
To identify the most relevant cellular targets of PARP10, each of the PARP10 direct protein targets found using the disclosed methods were ranked based on the number of peptide counts per protein identified in the LC-MS/MS analysis. Preferred PARP10 targets would be labeled more efficiently and would thus be enriched relative to less relevant targets. Preferred PARP10 target peptide fragments would also appear more frequently in the LC-MS/MS run.
Importantly, the control sample generated from lysates expressing WT-PARP10 allowed the removal of any proteins that would be enriched for non-enzymatic reasons (e.g. higher abundance proteins that bind non-specifically to NeutrAvidin agarose or proteins that are labeled non-enzymatically by 5-Bn-6-a-NAD+) from this analysis. The bulk of I987G-PARP10 targets identified in HEK 293T cells were identified based on a median of 2 peptides. Selecting for proteins that were also identified in HeLa cells causes a shift in median peptide counts from 2 to 6 peptides per protein. The cumulative distribution frequency of peptide counts per identified protein target for the shared protein pool (HEK 293T and HeLa targets) is elevated significantly above the cumulative distribution generated from the total pool of HEK 293T protein targets (p<0.0001, Mann-Whitney test, FIG. 2C). As the majority of HeLa targets are shared with HEK 293T there was not a significant difference in the cumulative distribution frequencies between the shared and total HeLa target pools (FIG. 2C). While it is acknowledged that some of the targets identified with lower peptide counts in the LC-MS/MS analysis might still represent relevant cellular targets of PARP10, the ranking of proteins based on peptide frequency counts—as well as their likelihood to be found in multiple cell lines—provides a starting point for linking PARP10-specific MARylation to cellular processes.
To confirm the LC-MS/MS results, two protein targets shared by HeLa and HEK 293T-XPO5 and WRIP1 were identified by Western blot with target-specific antibodies after NeutrAvidin enrichment. Both XPO5 and WRIP1, as well as auto-MARylated IG-PARP10, were selectively enriched from lysates generated from either HEK 293T or HeLa cells expressing SEQ ID NO: 15 and treated with the 5-Bn-6-a-NAD+ (FIG. 2D). Taken together, the results demonstrate that the disclosed methods can be used for the identification of direct MARylation targets of PARP10 in a complex mixture.

Example 3

PARP11 and PARP10 MARylate Separate Target Pools Involved in Distinct Cellular Processes. The generalizability of the disclosed methods was determined by identifying the direct MARylation targets of another mono-PARP. The target profile of PARP11 is interesting for a number of reasons: first, PARP11 includes a fairly simple modular structure as compared to the other mono-PARPs. Second, wild type PARP11 has an isoleucine at position 164 of SEQ ID NO: 5, corresponding to the isoleucine at position 120 of SEQ ID NO: 4 of wild type PARP10, but a tyrosine at the PARP10-L926 ‘ceiling’ position (See FIG. 1A), allowing confirmation that the disclosed methods will work with mono-PARPs with different amino acids at the L926-I987 interface. Furthermore, the comparison of two separate mono-PARP target profiles would allow an examination of the level of redundant target selection in the mono-PARP family. Finally, recent work has implicated PARP11 in nuclear membrane maintenance (Meyer-Ficca et al, Biol Reprod 92, 80 (2015); incorporated by reference herein) providing a potential biological pathway to probe the target list resulting from the disclosed methods against.
The MARylation activity of polypeptides including GFP-SEQ ID NO: 17 (also called I313G-PARP11 herein) was compared to that of SEQ ID NO: 15 in HEK 293T lysates. Treatment of lysates from SEQ ID NO: 17 transfected cells with 5-Bn-6-a-NAD+ resulted in labeling of several bands (FIG. 3A). Minimal background labeling was detected in lysates expressing WT-PARP11, further demonstrating the inability of non-engineered mono-PARPs to use 5-Bn-6-a-NAD+ as a substrate for MARylation. The banding pattern for SEQ ID NO: 17 is different from that produced by PARP10, indicating that PARP11 and PARP10 are indeed targeting distinct and family-member specific proteins (FIG. 3A).
Next, direct targets of PARP11 were identified using LC-MS/MS. HEK 293T lysates generated from cells expressing WT-PARP11 or SEQ ID NO: 17 were treated with 5-Bn-6-a-NAD+ (100 μM). MARylated proteins were conjugated to biotin-azide, enriched using NeutrAvidin agarose, digested with trypsin, and subjected to LC-MS/MS (FIG. 7). A total of 260 direct SEQ ID NO: 17 targets were identified (thresholds discussed in methods). Of the 803 and 260 protein targets identified for PARP10 and PARP11, respectively, a total of 140 and 21 proteins (respectively) were identified in duplicate biological replicates (Table 1). For the subsequent analysis comparing PARP10 and PARP11 MARylation, targets that were present in both replicates were selected because the selection of protein targets identified in two separate LC-MS/MS experiments would limit the amount of non-specific target enrichment. It is possible that proteins identified in a single replicate could still represent true cellular PARP10/PARP11 targets, so full data sets for the combined protein pools were generated. Based on previous observations with KA-PARP1 and KA-PARP2, as well as the current study, it is apparent that the PARP family displays a spectrum of target specificity. In the case of both PARP2 and PARP10, a broad range of cellular targets was observed, while PARP1 and PARP11 have a much narrower target profile (Table 1). The disclosed methods have yielded the first data set capable of distinguishing the PAR and MAR targeting preferences for multiple PARP family members. Further the disclosed methods are generalizable through the mono-PARP subclass and should aid in future investigations with the other family-members.

TABLE 1

Comparing the protein target lists for KA-P
Table 1. Direct Protein Targets Identified by LC-MS/MS

	KA-PARP1^a	KA-PARP2^a	IG-PARP10	IG-PARP11

Total Proteins Identified	123	488	961	479
Proteins with ≧ 2 Unique Peptides	91	428	848	294
Proteins Enriched Above Background^b	38	279	803	260
Proteins Identified in Duplicate	15	N.D.^d	140	21
PARP Family-Member Specific	13/14	117/N.D.^d	534/90	43/13
Proteins^c

^aKA-PARP1 and KA-PARP2 targets were identified as previously described (Carter-O'Connell et al., 2014)
^bDefined as ≧ 2-fold enrichment in the IG-PARP sample versus the WT-PARP sample
^cTargets that were identified for a single PARP family-member from the collected datasets from either at least a single replicate (left) or in duplicate (right)
^dKA-PARP2 identification was completed for a single replicate and is not included in the duplicate analysis

ARP1, KA-PARP2, SEQ ID NO: 15, and SEQ ID NO: 17 allowed the identification of the extent of overlap between these PARP family-members. Interestingly, the PARP10 target list overlaps to a greater degree with each of the other tested PARP family members than it does with PARP11 (FIGS. 3B, 3C). PARP10 and PARP2 in particular share 37 (26% of the total PARP10 target pool) protein targets (FIG. 3B) while PARP11 shares only 2 targets with PARP2 and no targets with PARP1 (FIG. 3C). Comparing the combined target pools also allows isolation of the protein targets that are specific for a given PARP family-member. The bulk of the identified protein targets are actually unique to either PARP10 (64%) or PARP11 (62%).

Using the target datasets for each of the PARPs detailed above, potential cellular roles for PARP10- and PARP11-mediated MARylation were determined. Using the set of PARP10- and PARP11-specific target proteins, gene ontology (GO) terms were searched that were significantly enriched (p<0.05, Bonferoni correction) within either the PARP10 or PARP11 target list. Enriched GO terms were compressed using Revigo (Supek et al, PLoS One 6, e21800 (2011); incorporated by reference herein) and semantic similarities between unique terms were plotted against the significance of the GO term enrichment (FIG. 3D). The GO term enrichment profile for PARP10 displayed a wide spectrum of biological processes, with enriched terms such as cellular metabolism (p=1.73e-12), intracellular protein transport (p=2.26e-10), protein targeting to the ER (p=1.75e-07), and mRNA metabolism (p=6.68e-05) (FIG. 3D). In contrast, the PARP11 GO term profile was highly enriched for a closely clustered set of biological processes (FIG. 3D). For PARP11, it was noted that the proteins identified in duplicate were primarily nuclear pore proteins or proteins involved in nuclear membrane organization (13 of 21 proteins). The enrichment of nuclear pore proteins led to enrichment of processes related to nuclear envelope organization (p=7.27e-24) and RNA transport (p=2.62e-24).
To compare the mono-PARP GO term profiles to the poly-PARP target lists, this analysis was performed using previously obtained PARP1 and PARP2 target datasets (FIG. 8). Interestingly, the PARP1 GO term profile was fairly limited in scope with only 8 GO terms identified (p<0.10, Bonferroni correction). The PARP1 GO terms were related to demonstrated PARP1 functions—including gene regulation (p=2.47e-02) (Ji and Tulin, Curr Opin Genetics Dev 20, 512-518 (2010) and Wacker et al, Sub Cell Biochem 41, 45-69 (2007); both of which are incorporated by reference herein) and response to osmotic stress (p=7.95e-02) (Chen et al, Am J Phys Ren Phys 292, F981-992 (2007) and Morales et al, Biochem Biophys Res Comm 270, 1029-1035 (2000); both of which are incorporated by reference herein)—though no enrichment was found for terms associated specifically with DNA double-stranded break repair. Given that the number of unique PARP1 targets identified did contain a number of DNA repair targets (notably XRCCS/6) the lack of enrichment could be due to the fact that target identification was performed under basal and not DNA damage conditions. The PARP2 GO term profile was broader than PARP1 (FIG. 8) with a clear enrichment of terms related to translation (p=1.55e-43), protein localization (p=1.70e-25), and mRNA metabolic processes (p=1.89e-33). Comparing the GO term profiles between the multiple PARP family members results in the observation that PARP2 and PARP10 label a broad target pool, but clearly are involved in distinct roles in the cell. PARP10 MARylates a set of targets lacking a clear connection between highly distinct biological functions, while the PARP2 targets are clustered tightly around mRNA regulation. In contrast, PARP1 and PARP11 have very narrow GO term profiles and are involved in very specific biological roles. Taken together, the GO term profiles for each of the PARP enzymes are distinct, with the PARP11 profile implicating a specific and novel biological role for PARP11 MARylation in nuclear pore complex regulation.

Example 4

Both the mono-PARPcat and the Modular N-Terminal Domains are Necessary for Accurate PARP11-mediated MARylation. The PARP family is defined by the presence of a conserved PARPcat domain (Ame et al, BioEsssays 26, 882-893 (2004); incorporated by reference herein). Each of the mono-PARPs is then differentiated by the presence of at least one separate modular domain (e.g., WWE, Zn fingers, macro, etc.) found on the n-terminus of the mono-PARP protein (Schreiber et al, Nat Rev Mol Cell Biol 7, 517-528 (2006); incorporated by reference herein). A major unanswered question in the PARP field is whether the n-terminal regulatory domain alone, the PARP_catdomain alone, or both together mediate substrate targeting. One of the unique advantages of the disclosed mono-PARP—modified NAD+ analogue pairs is the ability to decouple proximal (i.e. PARP_cat) and distal (i.e. N-terminal domain) elements of mono-PARP protein targeting and address this question on a proteome-wide scale.
The PARPcat domain from PARP10 is attached to a number of Zn fingers, a nuclear export sequence, and a set of ubiquitin-interaction motifs (UIMs) whereas the PARP11_catdomain is attached only to a WWE domain (FIG. 4A). To address the differential protein target selection requirements for each of these domains, the SEQ ID NO: 15 domain was fused to the WWE domain from PARP11 (FIG. 4A). The resulting chimeric protein (SEQ ID NO: 15-PARP11 chimera) now possesses the distal targeting features of PARP11 and the proximal targeting features of PARP10. By comparing the direct protein targets of the SEQ ID NO: 15-PARP11 chimera with the targets of SEQ ID NO: 15 and SEQ ID NO: 17 it can be determined whether or not the targets can be selected based on proximal and/or distal interactions.
LC-MS/MS analysis was performed on an HEK 293T lysate from cells expressing I987G-chimera that were treated with the 5-Bn-6-a-NAD+ (FIG. 7). A total of 85 SEQ ID NO: 15-PARP11 chimera-specific protein targets were identified. A total of 60% of the SEQ ID NO: 15-PARP11-chimera targets are shared with both SEQ ID NO: 15 and SEQ ID NO: 17 (FIG. 4B). When the shared targets of PARP10, PARP11, and the chimera are compared to the SEQ ID NO: 15-PARP11 chimera targets that are only shared with PARP10 (85% of the SEQ ID NO: 15-PARP11 chimera targets), it is clear that the PARP10_catdomain plays an important role in target selection (FIG. 4B). However, it is also apparent that the loss of the PARP10 n-terminus has drastically reduced the number of proteins that can be targeted by the PARP10cat domain. Interestingly, there are two targets where the n-terminus of PARP11 appears to be required for target selection by the SEQ ID NO: 15-PARP11 chimera (FIG. 4B). It was also noted that of the proteins identified in duplicate PARP11 LC-MS/MS runs, only 2 were shared with the SEQ ID NO: 15-PARP11 chimera protein (NAGK and WRIP1). All of the nuclear pore proteins require both the n-terminus and the PARP11cat domain for MARylation. Finally, there was a subset of 12 proteins that are unique to the SEQ ID NO: 15-PARP11 chimera. Taken together, these results suggest that both proximal and distal substrate interactions are necessary for proper target selection. This result also suggests that the structurally similar PARP_catdomains are playing distinct roles in target selection.
To confirm all of the LC-MS/MS results with SEQ ID NO: 15, SEQ ID NO: 17, and the SEQ ID NO: 15-PARP11 chimera, a set of PARP10-specific (UBE3C and XPO5), PARP11-specific (NXF1 and NUP98), PARP11-WWE-dependent (NAGK), and shared targets (WRIP1) were selected for identification by Western blot with target specific antibodies after NeutrAvidin enrichment. For all of the IG constructs examined, robust enrichment of the auto-MARylated proteins were observed using the GFP antibody (FIG. 4C). Enrichment of UBE3C and XPO5 was observed only in the PARP10 lane and NXF1 and NUP98 in the PARP11 lane (FIG. 4C). This result confirms that the disclosed methods are capable of distinguishing between the specific targets of multiple mono-PARP family members from a complex mixture. The PARP11-specific target, NAGK, is enriched in both the PARP11 and chimera lane and is therefore dependent primarily on PARP11 n-terminal recognition for labeling (FIG. 4C). Finally, the mono-PARP pan-selective target, WRIP1, is enriched in all three IG variant lanes (FIG. 4C). In each case, none of the selected targets are enriched from HEK 293T lysates expressing the WT constructs, confirming the necessity of the IG mutation for mono-PARP family-member specific MARylation using 5-Bn-6-a-NAD+ (FIG. 4C). Taken together, the disclosed methods are able to identify direct family-member specific mono-PARP targets in complex lysates.

Example 5

PARP10 Targets. The PARP10 targets identified using the disclosed methods share notable overlap with previously reported cellular functions of PARP10. In particular, the presence of a number of ubiquitin ligases (e.g. UBE3C) was noted. PARP10 contains two UIMs that were shown to interact with ubiquitinylated tumor-necrosis factor-receptor associated factor (TRAF) to aid PARP10 in targeting the NF-KB essential modulator (NEMO) for MARylation (Verheugd et al, Nature Comm 4, 1683 (2013); incorporated by reference herein). One possibility is that PARP10 regulates the ubiquitin signal cascade through MARylation of ubiquitin ligases. Additionally, PARP10 has been implicated in the coordination of cellular trafficking (Kleine et al, CCS 10, 28 (2012); incorporated by reference herein) and a number of cellular trafficking proteins were found in the target dataset. However, while the target list for PARP10 most likely contains a number of targets that are involved in specific signaling events mediated by PARP10, there is still a broad array of cellular targets that are MARylated by PARP10 that have no clear functional relationship to each other. Potentially, the broad promiscuity evidenced by PARP10 might actually play a role in the function of PARP10 in the cell. PARP10 has been shown to interact with p62, a ubiquitin receptor associated with autophagy (Kleine et al, 2012 supra). In certain conditions, PARP10 forms cytosolic clusters that bind p62, which implicates PARP10 in trafficking targets to the autophagosome. It is therefore possible that in this role, PARP10 is modifying a broad array of targets that are being sent to the autophagosome for degradation. If PARP10 MARylation were key to autophagosomal trafficking, then its potential targets would by definition not be highly specific. Further exploration of the role for PARP10 in autophagy will be required to determine if the broad targeting of PARP10 is important for its function in this pathway.

Example 6

PARP 11 targets. Compared to PARP10, relatively little is known regarding the function of PARP11 in the cell. Recent work has linked PARP11 to nuclear shaping in spermatids undergoing nuclear condensation and differentiation (Meyer-Ficca et al, 2015 supra), yet the PARP11-specific targets responsible for this process are unknown. The PARP11 targets identified using the disclosed methods appear to be directly related to the coordination of the nuclear envelope and the organization of nuclear pores. One of the PARP11-specific targets identified using the disclosed methods—the nuclear pore complex protein Nup98-Nup96 (NUP98)—was previously disclosed elsewhere as interacting with PARP11. The target list for PARP11 derived from the disclosed methods provides a clear point of entry for exploring in molecular detail how PARP11 MARylation regulates nuclear pore complex biology.

Example 7

Other examples of the mono-PARP subclass. A PARP1 homolog can be found in all five of the eukaryotic supergroups for which sequencing data is available (Citarelli et al, BMC Evolut Biol 10, 308 (2010). In contrast, homologs to the mono-PARPs are not conserved throughout eukaryotes; yet, there was a last common eukaryotic ancestor that expressed a PARP-like protein with mono-transferase activity that evolved separately from the poly-PARPs (Citarelli et al, 2010 supra); incorporated by reference herein). Two related mono-PARP clades apparently underwent parallel evolution to develop similar catalytic domains, suggesting that the mono-PARP_catdomains are tightly constrained to maintain key structural features. The constrained mono-PARP_catdomain was attached to a diverse array of modular regulatory domains during evolution. Some of these domains—notably the macro domains found on PARP9, PARP14, and PARP15—are under positive selection and changing rapidly (Daugherty et al, PLoS Genetics 10, e1004403 (2014); incorporated by reference herein). Therefore it seemed possible that the constrained mono-PARP_catdomains played a minor role in target selection while the rapidly evolving modular regulatory domains directed the target selection for the mono-PARPs. For PARP10 and PARP11 at least this is not the case as the SEQ ID NO: 15-PARP11 chimera construct demonstrated that both the catalytic domain and the modular n-termini are necessary but insufficient to drive precise MARylation. It will be important determine which motifs in the catalytic domain are driving proximal target selection and how changes in both the regulatory and catalytic domains have cooperated to drive the diversity of mono-PARP target selection.
One of the remaining challenges in understanding the relationship between PARP family member specific targeting and cellular function is the identification of the specific amino acids targeted by a given mono-PARP. It appears that while PARylation primarily targets acidic amino acids (i.e. glutamate and aspartate), MARylation may be more promiscuous in its site selection. Indeed, a recent study demonstrated that mono-PARPs could be auto-MARylated not only on glutamate and aspartate acids, but also on lysine and cysteine (Vyas et al, 2014 supra). The identity of the MARylated amino acids will be essential for more complete understating of mono-PARPs functions in cells. The disclosed methods can be combined with a recently described method to globally identify PARylated and MARylated sites in protein targets (Daniels et al, J Proteome Res 13, 3510-3522 (2014); incorporated by reference herein). In this fashion the disclosed methods can be used to map PARP targeting to a specific site on a protein substrate and delve deeper into the functional role of MARylation in the cell.

Example 8

Procedures. Cell Culture: HEK 293T and HeLa cells were grown in DMEM (Gibco) supplemented with 10% fetal bovine serum (FBS, HyClone), penicillin/streptomycin (Invitrogen), and 1× glutamax (Gibco) at 37° C. and 5% CO₂. Transient transfections of HEK 293T cells with 20 μg of GFP-tagged expression vectors per 10 cm dish (70% confluency) were performed using the CalPhos system (Clontech) according to manufacturer's instructions. Transient transfections of HeLa cells were performed with 15 μg GFP tagged expression vectors and 30 μg lipofection reagent per 10 cm dish using Lipofectamine 2000 (Invitrogen). Cells were lysed in HEPES buffer supplemented with cOmplete EDTA-free protease inhibitor (Roche) and cell debris was cleared by centrifugation at 14,000 g for 5 min at 4° C.
SRPK2 MARylation Assay: 1 μM of each PARP10cat variant was incubated with 3 μM SRPK2 and 100 μM of each modified NAD+ analogue for 2 hours at 30° C. in a 20 μL reaction volume including 50 mM HEPES, pH 7.5, 100 mM NaCl, 10 mM MgCl2, and 0.5 mM TCEP. Click conjugation was performed with 1.5 mM THPTA, 750 μM CuSO4, 300 μM sulforhodamine B-PEG3-azide, and 7.5 mM sodium ascorbate in 1× PBS for 1 hour at room temperature (rt). SRPK2 labeling was quantified using Image Lab v5.2 (Bio-Rad).
NeutrAvidin Enrichment and LC-MS/MS Analysis: 1 mg of total protein from either HEK 293T or HeLa lysate from cells expressing WT- or IG-tagged PARP variants was incubated with 100 μM 5-Bn-6-a-NAD+ for 2 hours at 30° C., click conjugated to biotin-PEG3-azide, subjected to enrichment using NeutrAvidin agarose (Pierce), and proteolysis as previously described (Carter-O'Connell and Cohen, 2015 supra; Carter-O'Connell et al, 2014 supra). MS experiments were performed using an Orbitrap Fusion (Thermo) equipped with a capillary HPLC system. Raw MS/MS scans were interpreted by SEQUEST using a UniProtKB/Swiss-Prot human database amended with sequences for the GFP-tagged PARP variants and common contaminants as previously described (Yan et al, Mol Biol Cell 21, 1945-1954 (2010); incorporated by reference herein). MARylated PARP10, PARP11, and chimeric targets were identified based on the following: (1) at least two unique peptide identifications; (2) total peptide counts enriched 2-fold above GFP-WT-PARP controls; (3) and appearance in half the total background datasets analyzed to date using modified 6-a-NAD+ probes. GO enrichment was performed using Amigo (Ashburner et al, Nat Genetics 25, 25-29 (2000); Mi et al, Nucl Acids Res 38, D204-D210 (2010); Thomas et al, Genome Res 13, 2129-2141 (2003); all of which are incorporated by reference herein)—selecting for GO terms enriched with a p-value 0.05 (unless stated otherwise)—and compression was performed using Revigo (Supek et al, 2011 supra). Confirmation of select MS targets was performed via immunoblot analysis of NeutrAvidin enriched lysate as previously described (Carter-O'Connell et al, 2014 supra). Input controls are shown in FIGS. 9A and 9B.

Example 9

Chemistry. Chemical Synthesis: Synthesis of 6-a-NAD+ and 5-Et-6-a-NAD+ was completed as previously described (Carter-O'Connell et al, 2014 supra). C-5 substituted 6-a-NAD+ analogs were synthesized according to Scheme 1 below:
Reagents and conditions: (a) HBr (33 wt % in acetic acid), toluene, 0° C.; (b) C-5 substituted nicotinamide, MeCN; (c) 7N NH3 in MeOH, −10° C.; (d) POCl3, trimethyl phosphate, H2O, rt; (e) 6-allkyne-AMP-morpholidate, MnCl₂, MgSO4, formamide, rt.
General: ¹H and ¹³NMR were recorded on a Bruker DPX spectrometer at 400 MHz and 100 MHz, respectively. Chemical shifts are reported as parts per million (ppm) downfield from an internal tetramethylsilane standard or solvent references. For air- and water-sensitive reactions, glassware was oven-dried prior to use and reactions were performed under argon. Dichloromethane, dimethylformamide, and tetrahydrofuran were dried using the solvent purification system manufactured by Glass Contour, Inc. (Laguna Beach, Calif.). All other solvents were of ACS chemical grade (Fisher Scientific) and used without further purification unless otherwise indicated. Commercially available starting reagents were used without further purification. Nicotinamide (Sigma-Aldrich, >99.5%), and 5-methylnicotinamide (Alfa Aesar, 97%) were used without further purification. Analytical thin-layer chromatography was performed with silica gel 60 F254 glass plates (SiliCycle). Flash column chromatography was conducted with either prepacked Redisep Rf normal/reverse phase columns (Teledyne ISCO) or self-packed columns containing 200-400 mesh silica gel (SiliCycle) on a Combiflash Companion purification system (Teledyne ISCO). High performance liquid chromatography (HPLC) was performed on a Varian Prostar 210 (Agilent) with a flow rate of 20 ml/min using Polaris 5 C18-A columns (150×4.6 mm, 3 mm -analytical, 150×21.2 mm, 5 mm preparative) (Agilent). UV-Vis detection: λ1=254 nm, λ2=280 nm.
General procedure for the synthesis of N′-(2,3,5-Tri-O-Benzoyl-β-D-ribofuranosyl)-3-aminocarbonyl-5-R-pyridinium bromide A. μ-D-ribofuranose-acetate-2,3,5-tribenzoate (504 mg, 1 mmol) was dissolved in toluene (15 ml) and cooled to 0° C. HBr (33 wt % in acetic acid) (368 mg, 1.5 mmol) was added dropwise and the reaction was stirred at 0° C. for 2 h. 0.5 ml of the solution mixture was taken and evaporated to dryness for ¹H NMR analysis [chemical shifts for the anomeric protons: β isomer=6.6 ppm (s, ¹H); α isomer=6.9 ppm (d, ¹H)]. After the starting material was consumed and 1H NMR confirmed the formation of the β isomer, the reaction was concentrated in vacuo. The crude μ-D-ribofuranose-bromo-2,3,5-tribenzoate was azeotroped with toluene (3×20 ml) to remove remaining acetic acid and dried in vacuo for 2 h. Crude μ-D-ribofuranosebromo-2,3,5-tribenzoate and appropriate C-5-substituted nicotinamide (90 mg, 0.55 mmol) (prepared as described previously: Carter-O'Connell et al., 2014 supra) was dissolved in ACN (40 ml). The reaction was stirred under Ar gas at rt for 2 days. The reaction was concentrated in vacuo (temperature kept below 35° C.). The crude product was dissolved in CHCl₃(2 ml) and ppt by adding ethyl ether (10 ml). The entire procedure was repeated three times to yield the desired product, which was used in subsequent reactions without further purification. Yields: 1A: yield, 260 mg (58%), 2A: yield, 350 mg (92%), 3A: yield, 230 mg (60%), 4A: yield, 282 mg (77%).
General procedure for the synthesis of N′-(μ-D-ribofuranosyl)-3-aminocarbonyl-5-R-pyridinium bromide B. A was dissolved in ammonia (25 ml, 7 N in MeOH) and the reaction was stirred at −10° C. for 36 h. The reaction was concentrated in vacuo and the crude product was dissolved in MeOH (1 ml). Addition of ethyl ether 10 ml) resulted in ppt of the desired product. The procedure was repeated three times to yield the desired product as an off white powder (90 mg, 66% yield), which was used in subsequent reactions without further purification. Some epimerization was observed (5-10% α isomer was present as determined by 1H NMR analysis).
1B: amount of 1A: 100 mg, 0.14 mmol; yield, 35 mg (60%). 1H NMR (400 MHz, D2O) δ 9.42 (s, 1H), 9.08 (s, 1H), 8.78 (d, J=1.7 Hz, 1H), 7.49-7.25 (m, 5H), 6.16 (d, J=4.1 Hz, 1H), 4.42 (dd, J=6.0, 3.4 Hz, 2H), 4.36-4.22 (m, 3H), 3.98 (dd, J=13.0, 2.9 Hz, 1H), 3.81 (dd, J=13.0, 3.5 Hz, 1H).
2B: amount of 2A: 250 mg, 0.36 mmol; yield, 90 mg (66%). 1H NMR (400 MHz, D2O) δ 9.40 (s, 1H), 9.13 (s, 1H), 8.81 (s, 1H), 6.19 (d, J=4.2, 1H), 4.45 (m, 2H), 4.33 (m, 1H), 4.05 (ddd, J=13.0, 2.8, 1.7 Hz, 1H), 3.88 (ddd, J=12.9, 3.3, 1.7 Hz, 1H), 2.97 (t, J=7.5 Hz, 2H), 1.73 (q, J=7.5 Hz, 2H), 0.92 (t, J=7.5, 3H).
3B: amount of 3A: 140 mg, 0.20 mmol; yield, 62 mg (79%). 1H NMR (400 MHz, D2O) δ 9.41 (s, 1H), 9.14 (s, 1H), 8.79 (s, 1H), 6.19 (d, J=4.2 Hz, 1H), 4.45 (t, J=4.3 Hz, 2H), 4.33 (d, J=5.1 Hz, 1H), 4.05 (d, J=13.2 Hz, 1H), 3.89 (d, J=12.9 Hz, 1H), 2.81 (d, J=7.2 Hz, 2H), 2.07-1.90 (m, 1H), 0.91 (d, J=6.6 Hz, 6H).
4B: amount of 4A: 140 mg, 0.20 mmol; yield, 71 mg (56%).
General procedure for the synthesis of 5-R-nicotinamide mononucleotide C. B was dissolved in trimethyl phosphate (0.18 ml) and the reaction was cooled to 0° C. POCl₃(10 eq.) was added and the reaction was stirred at 0° C. for 4 h. A few drops H₂O was then added to quench the reaction. Trimethyl phosphate was removed by extraction with ethyl ether (20 ml). The remaining trimethyl phosphate was removed by a second extraction with THF (5 ml). The aqueous layer was concentrated in vacuo. The crude product was dissolved in H₂O (0.5 ml) and purified via two-step ion exchange chromatography (Dowex resin 1×2, formate resin, eluted with water; H⁺ resin, eluted with water). Fractions containing the desired product were pooled and concentrated in vacuo to yield the desired product (54 mg, 60% yield).
1C: amount of 1B: 30 mg (0.07 mmol); yield, 24 mg (80%). ¹H NMR (400 MHz, D₂O) δ 9.28 (s, 1H), 9.03 (s, 1H), 8.70 (s, 1H), 7.30 (d, J=7.6 Hz, 5H), 6.13-6.03 (m, 1H), 4.57 (s, 1H), 4.48 (d, J=4.4 Hz, 1H), 4.42-4.34 (m, 1H), 4.31 (s, 2H), 4.29-4.15 (m, 1H), 4.08 (d, J=11.6 Hz, 1H).
2C: amount of 2B: 90 mg, 0.24 mmol; yield, 54 mg (60%).1H NMR (400 MHz, D₂O) δ 9.40 (s, 1H), 9.13 (s, 1H), 8.81 (s, 1H), 6.19 (d, J=4.2, 1H), 4.45 (m, 2H), 4.33 (m, 1H), 4.05 (ddd, J=13.0, 2.8, 1.7 Hz, 1H), 3.88 (ddd, J=12.9, 3.3, 1.7 Hz, 1H), 2.97 (t, J=7.5 Hz, 2H), 1.73 (q, J=7.5 Hz, 2H), 0.92 (t, J=7.5, 3H).
3C: amount of 3B: 100 mg, 0.3 mmol; yield, 74 mg (74%). 1H NMR (400 MHz, D2O) δ 9.35 (s, 1H), 9.01 (s, 1H), 8.80 (d, J=1.7 Hz, 1H), 6.13 (d, J=5.8 Hz, 1H), 4.61 (d, J=2.4 Hz, 1H), 4.52 (t, J=5.4 Hz, 1H), 4.43 (dd, J=5.0, 2.2 Hz, 1H), 4.34-4.19 (m, 1H), 4.18-4.05 (m, 1H), 2.83 (d, J=7.2 Hz, 2H), 2.00 (m, 1H), 0.91 (dd, J=6.6, 4.9 Hz 6H).
4C: amount of 4B: 60 mg, 0.17 mmol; yield, 22 mg (37%). 1H NMR (400 MHz, D₂O) δ 9.23 (s, 1H), 9.07 (s, 1H), 8.76 (s, 1H), 6.11 (dd, J=5.6, 2.4 Hz, 1H), 4.58 (p, J=2.5 Hz, 1H), 4.50 (td, J=5.2, 2.5 Hz, 1H), 4.40 (dt, J=5.3, 2.7 Hz, 1H), 4.27 (ddd, J=11.8, 4.5, 2.5 Hz, 1H), 4.16-3.99 (m, 1H), 2.60 (s, 3H).
General procedure for the synthesis of 5-R-6-a-NAD+analogues: the appropriate C-5-substituted nicotinamide mononucleotide C, 6-alkyne-AMP-morpholidate (1 eq.) (prepared as described previously: Carter-O'Connell et al, 2014 supra), and MgSO₄(16 mg) were dissolved in a solution of MnCl2 (0.5 ml, 0.2 M in formamide) and stirred at rt for 48 h. The reaction was concentrated in vacuo and the crude product was purified via preparative HPLC (MP A: 0.1% formic acid (aq), MP B: 0.1% formic acid in ACN; 0-5 min: 0-10% B, 5-8 min: 10-15% B, 8-10 min: 15-20% B, 10-12 min: 20-50% B). Fractions containing the desired product were pooled and concentrated in vacuo to yield the desired product.
5-benzyl-6-a-NAD+: amount of 1C: 11 mg (0.02 mmol); yield, 5 mg (32%). 1H NMR (400 MHz, D2O) δ 9.11 (s, 1H), 8.98 (s, 1H), 8.55 (s, 1H), 8.37 (s, 1H), 8.14 (s, 1H), 7.41-7.09 (m, 5H), 5.96 (t, J=5.0 Hz, 2H), 4.74-4.57 (m, 7H), 4.55-4.35 (m, 3H), 4.35-4.08 (m, 5H), 2.58 (s, 1H).
5-propyl-6-a-NAD+: amount of 2C: 24 mg (0.05 mmol); yield, 10 mg (27%). 1H NMR (400 MHz, D2O) δ 9.18 (s, 1H), 8.94 (s, 1H), 8.74 (s, 1H), 8.51 (s, 1H), 8.31 (s, 1H), 6.04 (dd, J=17.2, 5.6 Hz, 2H), 4.72 (m, 1H), 4.60-4.28 (m, 6H), 4.29-4.09 (m, 3H), 2.86 (t, J=7.6 Hz, 2H), 2.70(s, 1H) 1.68 (dt, J=14.5, 7.2 Hz, 2H), 0.91 (t, J=7.3 Hz, 3H).
5-isobutyl-6-a-NAD+: amount of 3C: 10 mg (0.02 mmol); yield, 8.9 mg (56%). 1H NMR (400 MHz, D2O) δ 9.24 (s, 1H), 8.94 (s, 1H), 8.80-8.69 (m, 1H), 8.61-8.49 (m, 1H), 8.34 (s, 1H), 6.07 (dd, J=16.4, 5.4 Hz, 2H), 4.72 (dd, J=6.6, 4.1 Hz, 1H), 4.65-4.30 (m, 4H), 4.24 (d, J=14.9 Hz, 3H), 2.78 (d, J=6.9 Hz, 2H), 2.71(s, 1H), 1.96 (dd, J=13.6, 6.8 Hz, 1H), 0.88 (dd, J=6.5, 4.3 Hz, 6H).
5-methyl-6-a-NAD+: amount of 4C: 26 mg (0.05 mmol); yield, 9 mg (25%). 1H NMR (400 MHz, D2O) δ 9.08 (s, 1H), 8.91 (s, 1H), 8.65 (s, 1H), 8.44 (s, 1H), 8.17 (s, 1H), 5.97 (dd, J=18.7, 5.6 Hz, 2H), 4.70-4.56 (m, 1H), 4.53-4.24 (m, 5H), 4.24-4.00 (m, 4H), 2.55 (s, 3H).

Claims

1. A small molecule compound (SMC) of formula:

wherein R is selected from aryl and alkyl, provided that R is not ethyl.

2. The compound of claim 1 wherein R is selected from benzyl, propyl, isobutyl, and methyl.

3. A recombinant polypeptide comprising a mono-poly-ADP-ribose-polymerases (PARP) catalytic domain selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7 or SEQ ID NO: 8 or a polypeptide with 90% identity thereto provided that the amino acid indicated by Xaa is glycine, alanine, serine, cysteine, valine, threonine, or proline and wherein the polypeptide catalyzes the addition of the SMC of claim 1 to a PARP protein target.

4. The recombinant polypeptide of claim 3 comprising a sequence selected from SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, or a polypeptide with 90% identity thereto provided that the polypeptide catalyzes the addition of the SMC of claim 1 to a PARP protein target.

5. The recombinant polypeptide of claim 3 comprising no more than 10% conservative amino acid substitutions.

6. A method of identifying a protein target of a mono-PARP, the method comprising:

contacting a SMC of formula:

wherein R is alkyl or aryl with a protein, said protein comprising a polypeptide of claim 3, wherein said contacting occurs within a living cell; and

subjecting the cell to conditions that result in the protein catalyzing the reaction by which the SMC is covalently attached to one or more cellular proteins;

identifying the one or more cellular proteins to which the SMC is covalently attached as protein target(s) of the mono-PARP.

7. The method of claim 6 wherein the SMC comprises 5-Bn-6-a-NAD⁺.

8. The method of claims 6 further comprising conjugating a label to the SMC.

9. The method of claim 8 wherein the label comprises biotin or a fluorescent molecule.

10. The method of claims 6 further comprising detecting the one or more cellular proteins to which the SMC is covalently attached via a method that comprises mass spectrometry.

11. A method of determining if a test compound is an antagonist of a mono-PARP, the method comprising:

contacting a SMC of formula:

wherein R is alkyl or aryl;

with (i) a polypeptide of claims 3-6, said polypeptide corresponding to the mono-PARP;

(ii) a test compound; and

(iii) a mono-PARP protein target;

said contacting occurring within a mixture;

subjecting the mixture to conditions that result in the polypeptide catalyzing the reaction by which the SMC is covalently attached to the mono-PARP protein target;

wherein a test compound that results in a reliable reduction of covalent attachment of the SMC to the mono-PARP protein target relative to the covalent attachment of the SMC to the mono-PARP protein target in the presence of a negative control is selected as an antagonist of the mono-PARP.

12. The method of claim 11 wherein the SMC comprises 5-Bn-6-a-NAD⁺.

13. The method of claim 11 wherein the mono-PARP protein target was selected using the method of claim 7.

14. The method of claim 11 wherein the polypeptide comprises SEQ ID NO: 15, SEQ ID NO: 17, or SEQ ID NO: 23.

15. The method of claim 14 wherein the mono-PARP protein target comprises at least a fragment of SRPK2 that is mono-ADP-ribosylated by PARP10.

16. The method of claim 11 further comprising conjugating a label to the SMC.

17. The method of claim 11 wherein the contacting occurs within a cell.