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WO2025226057A1 - Composé ligand d'ubiquitine ligase et molécule protac le comprenant - Google Patents

Composé ligand d'ubiquitine ligase et molécule protac le comprenant

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Publication number
WO2025226057A1
WO2025226057A1 PCT/KR2025/005561 KR2025005561W WO2025226057A1 WO 2025226057 A1 WO2025226057 A1 WO 2025226057A1 KR 2025005561 W KR2025005561 W KR 2025005561W WO 2025226057 A1 WO2025226057 A1 WO 2025226057A1
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Prior art keywords
amino
alkyl
oxopropan
guanidinophenyl
propanamido
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PCT/KR2025/005561
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English (en)
Korean (ko)
Inventor
임현석
왕희명
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Camel Bioscience Inc
POSTECH Research and Business Development Foundation
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Camel Bioscience Inc
POSTECH Research and Business Development Foundation
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Publication of WO2025226057A1 publication Critical patent/WO2025226057A1/fr
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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07CACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C279/00Derivatives of guanidine, i.e. compounds containing the group, the singly-bound nitrogen atoms not being part of nitro or nitroso groups
    • C07C279/04Derivatives of guanidine, i.e. compounds containing the group, the singly-bound nitrogen atoms not being part of nitro or nitroso groups having nitrogen atoms of guanidine groups bound to acyclic carbon atoms of a carbon skeleton
    • C07C279/12Derivatives of guanidine, i.e. compounds containing the group, the singly-bound nitrogen atoms not being part of nitro or nitroso groups having nitrogen atoms of guanidine groups bound to acyclic carbon atoms of a carbon skeleton being further substituted by nitrogen atoms not being part of nitro or nitroso groups
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07CACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C279/00Derivatives of guanidine, i.e. compounds containing the group, the singly-bound nitrogen atoms not being part of nitro or nitroso groups
    • C07C279/18Derivatives of guanidine, i.e. compounds containing the group, the singly-bound nitrogen atoms not being part of nitro or nitroso groups having nitrogen atoms of guanidine groups bound to carbon atoms of six-membered aromatic rings
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    • C07DHETEROCYCLIC COMPOUNDS
    • C07D207/00Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom
    • C07D207/02Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D207/18Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having one double bond between ring members or between a ring member and a non-ring member
    • C07D207/22Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having one double bond between ring members or between a ring member and a non-ring member with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D207/24Oxygen or sulfur atoms
    • C07D207/262-Pyrrolidones
    • C07D207/2632-Pyrrolidones with only hydrogen atoms or radicals containing only hydrogen and carbon atoms directly attached to other ring carbon atoms
    • C07D207/272-Pyrrolidones with only hydrogen atoms or radicals containing only hydrogen and carbon atoms directly attached to other ring carbon atoms with substituted hydrocarbon radicals directly attached to the ring nitrogen atom
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    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D211/00Heterocyclic compounds containing hydrogenated pyridine rings, not condensed with other rings
    • C07D211/04Heterocyclic compounds containing hydrogenated pyridine rings, not condensed with other rings with only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D211/06Heterocyclic compounds containing hydrogenated pyridine rings, not condensed with other rings with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members
    • C07D211/08Heterocyclic compounds containing hydrogenated pyridine rings, not condensed with other rings with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members with hydrocarbon or substituted hydrocarbon radicals directly attached to ring carbon atoms
    • C07D211/18Heterocyclic compounds containing hydrogenated pyridine rings, not condensed with other rings with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members with hydrocarbon or substituted hydrocarbon radicals directly attached to ring carbon atoms with substituted hydrocarbon radicals attached to ring carbon atoms
    • C07D211/26Heterocyclic compounds containing hydrogenated pyridine rings, not condensed with other rings with only hydrogen or carbon atoms directly attached to the ring nitrogen atom having no double bonds between ring members or between ring members and non-ring members with hydrocarbon or substituted hydrocarbon radicals directly attached to ring carbon atoms with substituted hydrocarbon radicals attached to ring carbon atoms with hydrocarbon radicals, substituted by nitrogen atoms
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D213/00Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members
    • C07D213/02Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members
    • C07D213/04Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom
    • C07D213/24Heterocyclic compounds containing six-membered rings, not condensed with other rings, with one nitrogen atom as the only ring hetero atom and three or more double bonds between ring members or between ring members and non-ring members having three double bonds between ring members or between ring members and non-ring members having no bond between the ring nitrogen atom and a non-ring member or having only hydrogen or carbon atoms directly attached to the ring nitrogen atom with substituted hydrocarbon radicals attached to ring carbon atoms
    • C07D213/54Radicals substituted by carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals
    • C07D213/56Amides
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D295/00Heterocyclic compounds containing polymethylene-imine rings with at least five ring members, 3-azabicyclo [3.2.2] nonane, piperazine, morpholine or thiomorpholine rings, having only hydrogen atoms directly attached to the ring carbon atoms
    • C07D295/04Heterocyclic compounds containing polymethylene-imine rings with at least five ring members, 3-azabicyclo [3.2.2] nonane, piperazine, morpholine or thiomorpholine rings, having only hydrogen atoms directly attached to the ring carbon atoms with substituted hydrocarbon radicals attached to ring nitrogen atoms
    • C07D295/12Heterocyclic compounds containing polymethylene-imine rings with at least five ring members, 3-azabicyclo [3.2.2] nonane, piperazine, morpholine or thiomorpholine rings, having only hydrogen atoms directly attached to the ring carbon atoms with substituted hydrocarbon radicals attached to ring nitrogen atoms substituted by singly or doubly bound nitrogen atoms
    • C07D295/125Heterocyclic compounds containing polymethylene-imine rings with at least five ring members, 3-azabicyclo [3.2.2] nonane, piperazine, morpholine or thiomorpholine rings, having only hydrogen atoms directly attached to the ring carbon atoms with substituted hydrocarbon radicals attached to ring nitrogen atoms substituted by singly or doubly bound nitrogen atoms with the ring nitrogen atoms and the substituent nitrogen atoms attached to the same carbon chain, which is not interrupted by carbocyclic rings
    • C07D295/13Heterocyclic compounds containing polymethylene-imine rings with at least five ring members, 3-azabicyclo [3.2.2] nonane, piperazine, morpholine or thiomorpholine rings, having only hydrogen atoms directly attached to the ring carbon atoms with substituted hydrocarbon radicals attached to ring nitrogen atoms substituted by singly or doubly bound nitrogen atoms with the ring nitrogen atoms and the substituent nitrogen atoms attached to the same carbon chain, which is not interrupted by carbocyclic rings to an acyclic saturated chain
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D307/00Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom
    • C07D307/02Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom not condensed with other rings
    • C07D307/04Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom not condensed with other rings having no double bonds between ring members or between ring members and non-ring members
    • C07D307/10Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom not condensed with other rings having no double bonds between ring members or between ring members and non-ring members with substituted hydrocarbon radicals attached to ring carbon atoms
    • C07D307/14Radicals substituted by nitrogen atoms not forming part of a nitro radical
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D307/00Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom
    • C07D307/02Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom not condensed with other rings
    • C07D307/34Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members
    • C07D307/38Heterocyclic compounds containing five-membered rings having one oxygen atom as the only ring hetero atom not condensed with other rings having two or three double bonds between ring members or between ring members and non-ring members with substituted hydrocarbon radicals attached to ring carbon atoms
    • C07D307/52Radicals substituted by nitrogen atoms not forming part of a nitro radical
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D309/00Heterocyclic compounds containing six-membered rings having one oxygen atom as the only ring hetero atom, not condensed with other rings
    • C07D309/02Heterocyclic compounds containing six-membered rings having one oxygen atom as the only ring hetero atom, not condensed with other rings having no double bonds between ring members or between ring members and non-ring members
    • C07D309/08Heterocyclic compounds containing six-membered rings having one oxygen atom as the only ring hetero atom, not condensed with other rings having no double bonds between ring members or between ring members and non-ring members with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to ring carbon atoms
    • C07D309/14Nitrogen atoms not forming part of a nitro radical
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D317/00Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms
    • C07D317/08Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3
    • C07D317/44Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 ortho- or peri-condensed with carbocyclic rings or ring systems
    • C07D317/46Heterocyclic compounds containing five-membered rings having two oxygen atoms as the only ring hetero atoms having the hetero atoms in positions 1 and 3 ortho- or peri-condensed with carbocyclic rings or ring systems condensed with one six-membered ring
    • C07D317/48Methylenedioxybenzenes or hydrogenated methylenedioxybenzenes, unsubstituted on the hetero ring
    • C07D317/50Methylenedioxybenzenes or hydrogenated methylenedioxybenzenes, unsubstituted on the hetero ring with only hydrogen atoms, hydrocarbon or substituted hydrocarbon radicals, directly attached to atoms of the carbocyclic ring
    • C07D317/58Radicals substituted by nitrogen atoms

Definitions

  • the present invention relates to a ligand compound of ubiquitin ligase and a PROTAC (proteolysis targeting chimera) molecule comprising the same, and more particularly, to a compound acting as a ligand of E3 ubiquitin ligase or a prodrug thereof, and a PROTAC heterobifunctional molecule comprising the same.
  • the N-end rule states that the lifetime of a protein depends on the characteristics of its N-terminal residue.
  • the N-terminal residue that destabilizes the protein is called an N-degron, and is divided into type 1 and type 2.
  • Type 1 N-degrons contain basic amino acid residues that can be positively charged, such as arginine (Arg), lysine (Lys), and histidine (His), while type 2 N-degrons contain hydrophobic amino acid residues, such as phenylalanine (Phe), tryptophan (Trp), tyrosine (Tyr), leucine (Leu), or isoleucine (Ile) (Varshavsky, A. et al. Protein Science 2011, 20, 1298-1345).
  • UBR ubiquitin protein ligase E3 component n-recognin
  • the protein crystal structures of the UBR box of human UBR1, UBR2, and yeast UBR1 are known, and the UBR box contains three Zn cations and two zinc finger motifs that can coordinate Zn 2+ ions, and two binding pockets that can recognize the first and second amino acid residues of the N-degron (Choi, W. S. et al. Nat. Struct. Mol. Biol. 2010, 17, 1175-1181; Matta-Camacho, E. et al. Nat. Struct. Mol. Biol. 2010, 17, 1182-1187; Munoz-Escobar, J. Structure 2017, 25, 719-729).
  • the first binding pocket is composed of aspartic acid (Asp), threonine (Thr), and phenylalanine (Phe) residues, which form a negatively charged protein surface and allow strong interactions with type 1 N-degrons, which have positively charged basic residues, through hydrogen bonding and charge-charge interactions.
  • the second binding pocket also allows selective recognition of N-degrons through interactions with specific residues, such as serine (Ser), valine (Val), phenylalanine (Phe), and threonine (Thr).
  • the UBR box of the UBR protein recognizes N-degrons and plays a crucial role in cellular protein degradation.
  • Ligand compounds that bind to the UBR box can participate in protein degradation pathways.
  • UBR proteins are known to play essential regulatory roles in numerous signaling pathways, including G-protein signaling, apoptosis, and inflammation. Dysregulation in these signaling pathways can lead to disease states such as cancer and neurodegeneration.
  • GPCRs G-protein-coupled receptors
  • GPCRs G-protein-coupled receptors
  • GPCRs G-protein-coupled receptors
  • RGS Regulator of G-protein signaling (RGS) proteins, which play a key role in this signaling cascade, undergo arginylation of their N-terminal residues through metabolism, followed by ubiquitination by UBR1 and UBR2, leading to protein degradation (Lee, M. J. et al. Proc. Natl. Acad. Sci. USA 2005, 102, 15030-15035).
  • Inflammation is a protective response induced by the well-conserved innate immune system to protect against pathogens, damaged cells, or harmful stimuli.
  • Some inflammatory fragments contain unstable N-terminal residues, leading to their degradation via the N-degron pathway, such as UBR1, UBR2, UBR4, and UBR5.
  • UBR1, UBR2, UBR4, and UBR5 exhibit unstable N-terminal residues, leading to their degradation via the N-degron pathway, such as UBR1, UBR2, UBR4, and UBR5.
  • knockdown of UBR1, UBR2, UBR4, and UBR5 via siRNA significantly increased IL-1 ⁇ secretion (Leboeuf, D. Biomolecules 2020, 10, 903), suggesting that UBR E3 ligases are also involved in inflammatory responses.
  • a proteolysis targeting chimera is a heterobifunctional molecule consisting of a ligand for a target protein and a ligand that binds to an E3 ubiquitin ligase, linked via a linker.
  • PROTACs simultaneously bind to both proteins, bringing the target protein into close proximity to the E3 ubiquitin ligase. This allows the E3 ubiquitin ligase to recognize the target protein as a substrate, triggering polyubiquitination and subsequent proteasomal degradation. This principle allows for the effective removal of specific proteins from cells. Therefore, PROTACs can be used as chemical probes for studying the function of target proteins and, furthermore, hold great potential as therapeutic agents for diseases.
  • E3 ubiquitin ligases In the human body, only a few, such as cereblon (CRBN) and Von Hippel-Lindau tumor suppressor (VHL), are currently used as E3 ubiquitin ligases in the PROTAC design.
  • CBN cereblon
  • VHL Von Hippel-Lindau tumor suppressor
  • the present invention has as a technical problem a compound or a prodrug thereof that can efficiently act as a ligand of an E3 ubiquitin ligase by binding to the UBR box of a UBR protein.
  • the present invention has as another technical object to provide a PROTAC (proteolysis targeting chimera) heterobifunctional molecule comprising a ligand compound of the E3 ubiquitin ligase or a prodrug thereof.
  • PROTAC proteolysis targeting chimera
  • the present invention provides a compound of the following chemical formula 1 or a prodrug thereof:
  • R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , L, m and n are as defined herein.
  • the present invention provides a chimeric compound of the following chemical formula 2:
  • a and B are as defined herein, and A and B are chemically linked by a linker.
  • the compound according to the present invention or a prodrug thereof can act as a ligand for an efficient E3 ubiquitin ligase, thereby efficiently degrading a target protein by the ubiquitin-proteasome system of a cell in a PROTAC (proteolysis targeting chimera) technology utilizing the compound.
  • Figure 1 shows the seven isoforms of ubiquitin protein ligase E3 component n-recognin (UBR) proteins.
  • Figure 2 shows the LC and Mass analysis data of PROTAC of Example 164.
  • Figure 3 is a graph showing the results of measuring the binding affinity of the compound of Example 31 and the PROTAC of Example 164 to the UBR1 protein in Experimental Example 2.
  • Figure 4 shows the results of evaluating the BRD4 protein decomposition ability of PROTAC of Example 164 in Experimental Example 3 (BRD4: bromodomain-containing protein 4, GAPDH: glyceraldehyde-3-phosphate dehydrogenase).
  • Figure 5 shows the results of evaluating the decomposition ability of BRD4 protein in Experimental Example 4 (JQ1: BET bromodomain inhibitor, MG132: proteasome inhibitor, BRD4: bromodomain-containing protein 4, GAPDH: glyceraldehyde-3-phosphate dehydrogenase).
  • Figure 6 shows the LC and Mass analysis data of the prodrug of Example 165.
  • Figure 7 shows the results of evaluating the decomposition ability of BRD4 protein of PROTAC of Example 164 and prodrug of Example 165 in Experimental Example 5 (BRD4: bromodomain-containing protein 4, GAPDH: glyceraldehyde-3-phosphate dehydrogenase).
  • a compound of the following chemical formula 1 or a prodrug thereof is provided:
  • R 1 and R 2 are each independently -H, -D, alkyl, deuterated alkyl or haloalkyl;
  • R 3 is -DEG; wherein D is a direct bond or alkylene; E is alkylene, alkenylene, alkynylene, cycloalkylene, cycloalkenylene, heterocycloalkylene, heterocycloalkenylene, arylene, or heteroarylene; wherein the alkylene, alkenylene, alkynylene, cycloalkylene, cycloalkenylene, heterocycloalkylene, heterocycloalkenylene, arylene or heteroarylene is optionally -D, halo, hydroxy, thiol (-SH), amino, nitro, cyano, alkyl, haloalkyl, deuterated alkyl, hydroxyalkyl, alkoxy, haloalkoxy, alkoxyalkyl, alkylthio, alkylamino, dialkylamino, aminoalkyl, alkylaminoalkyl, dialkylaminoalkyl, aminocarbonyl, alkyla
  • R 4 is -H, -D, alkyl, deuterated alkyl or haloalkyl
  • L is -C-, -CH-, or and wherein R 10 and R 11 are each independently -H, -D, halo, alkyl, deuterated alkyl or haloalkyl;
  • R 5 is -JM; wherein J is a direct bond, alkylene, alkenylene, alkynylene, alkylene-O- or alkylene-NH-; M is -H, halo, hydroxy, amino, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkenyl, aryl or heteroaryl; wherein said alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkenyl, aryl or heteroaryl is optionally -D, hydroxy, thiol, amino, halo, nitro, cyano, alkyl, haloalkyl, deuterated alkyl, hydroxyalkyl, alkoxy, haloalkoxy, cycloalkyl-oxy, heterocycloalkyl-oxy, aryl-
  • R 6 is -H, , , , , , , , or and wherein R 12 to R 27 are each independently -H, nitro, cyano, azido, halo, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkenyl, aryl, heteroaryl, cycloalkyl-alkyl, cycloalkenyl-alkyl, alkoxy-alkyl, alkylthio-alkyl, dialkylaminoalkyl, heterocycloalkyl-alkyl, heterocycloalkenyl-alkyl, aryl-alkyl, alkyl-aryl-alkyl, alkoxy-aryl-alkyl, heteroaryl-alkyl, partially unsaturated heterocyclyl-alkyl, alkyl-heterocycloalkyl, aryl-alkyl-he
  • n 1, 2 or 3; when n is 2 and 3, the repeating units may be the same or different;
  • n 1 or 2;
  • heterocycloalkylene, heterocycloalkenylene, heteroarylene, heterocycloalkyl, heterocycloalkenyl, partially unsaturated heterocyclyl and heteroaryl have one or more heteroatoms selected from N, O and S.
  • halo or “halogen”, when used alone or in combination with other additional terms (e.g., haloalkyl), means fluorine (F), chlorine (Cl), bromine (Br), or iodine (I).
  • hydroxy means -OH.
  • nitro group means -NO 2 .
  • cyano means -CN
  • thiol means -SH.
  • oxy means -O-.
  • amino in the present invention may refer to a primary, secondary, or tertiary amino group, alone or in combination, bonded via a nitrogen atom.
  • the secondary amino group may refer to one having an alkyl substituent
  • the tertiary amino group may refer to one having two similar or different alkyl substituents.
  • the term “azido” means -N 3 .
  • alkyl when used alone or in combination with other additional terms (e.g., haloalkyl), means a radical of a straight or branched saturated aliphatic hydrocarbon group having, for example, 1 to 7 carbon atoms or 1 to 5 carbon atoms.
  • alkyl groups include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, isopentyl, neopentyl, tert-pentyl, 1-methylbutyl, 2-methylbutyl, 1-ethylpropyl, and 1,2-dimethylpropyl.
  • deuterated alkyl means an alkyl group having one or more deuterium atoms.
  • alkenyl means a radical of an aliphatic hydrocarbon group containing at least one carbon-carbon double bond, for example, having 2 to 7 carbon atoms or 2 to 5 carbon atoms.
  • alkynyl means a radical of an aliphatic hydrocarbon group containing at least one carbon-carbon triple bond, for example, having 2 to 7 carbon atoms or 2 to 5 carbon atoms.
  • alkoxy means an alkyloxy (-O-alkyl group), for example, an alkyloxy having 1 to 7 carbon atoms or 1 to 5 carbon atoms.
  • alkylthio means an -S-alkyl group, for example, an -S-alkyl group having 1 to 7 or 1 to 5 carbon atoms.
  • alkylene means a radical of a divalent straight-chain or branched-chain saturated aliphatic hydrocarbon group having, for example, 1 to 7 carbon atoms or 1 to 5 carbon atoms.
  • alkynylene means a radical of an aliphatic hydrocarbon group containing at least one carbon-carbon double bond of two valences, for example, having 2 to 7 carbon atoms or 2 to 5 carbon atoms.
  • alkynylene means a radical of an aliphatic hydrocarbon group containing at least one carbon-carbon triple bond of two valences, for example, having 2 to 7 carbon atoms or 2 to 5 carbon atoms.
  • hydroxyalkyl means an alkyl group substituted with hydroxy.
  • cycloalkyl refers to a saturated aliphatic hydrocarbon radical having, for example, 3 to 10 carbon atoms or 3 to 8 carbon atoms in a ring shape.
  • Typical examples of cycloalkyl groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and the like.
  • the cycloalkyl may include a bridged structure, a fused structure, or a spiro structure.
  • heterocycloalkyl in the present invention means a radical of a saturated aliphatic hydrocarbon group containing one or more heteroatoms selected from N, O and S as a reducing group, for example, a 4 to 12 membered or a 4 to 10 membered group.
  • the heterocycloalkyl may include a bridged structure, a fused structure or a spiro structure.
  • partially unsaturated heterocyclyl as used herein means a cyclic, for example, 4 to 12-membered or 4 to 10-membered, partially unsaturated hydrocarbon group containing one or more heteroatoms selected from N, O and S as a reducing group.
  • the partially unsaturated heterocyclyl may include a bridged structure, a fused structure or a spiro structure.
  • aryl means an aromatic hydrocarbon having, for example, 6 to 12 or 6 to 10 carbon atoms, and specific examples include, but are not limited to, phenyl and naphthyl.
  • heteroaryl means, for example, a 5- to 12-membered or 5- to 10-membered aromatic hydrocarbon containing one or more heteroatoms selected from N, O and S as a reducing group and forming a single or fused ring that can be fused with benzo or cycloalkyl.
  • the term “prodrug” includes a form in which the compound of the above chemical formula 1 is converted in vivo to exhibit the same effect, and can be prepared according to a method known in the art, and there are no particular limitations thereto.
  • the prodrug can be provided in the form of, but is not limited to, carbamates, esters, N-Mannich adducts, phosphates, phosphonooxymethylethers, phosphoramidates, acylsulfonamides, amides, sulfenamides, imines, azo conjugates, N-acyloxyalkylamines, etc.
  • R 1 and R 2 are each independently -H, -D, C 1 -C 7 alkyl, deuterated C 1 -C 7 alkyl or halo-C 1 -C 7 alkyl;
  • R 3 is -DEG; wherein D is a direct bond or C 1 -C 7 alkylene; E is C 1 -C 7 alkylene, C 2 -C 7 alkenylene, C 2 -C 7 alkynylene, C 3 -C 10 cycloalkylene , C 3 -C 10 cycloalkenylene, C 6 -C 12 arylene, 4 to 12 membered heterocycloalkylene, 4 to 12 membered heterocycloalkenylene, or 5 to 12 membered heteroarylene; wherein said alkylene, alkenylene, alkynylene, cycloalkylene.
  • Cycloalkenylene, heterocycloalkylene, heterocycloalkenylene, arylene or heteroarylene is optionally -D, halo, hydroxy, thiol, amino, nitro, cyano, C 1 -C 7 alkyl, halo-C 1 -C 7 alkyl, deuterated C 1 -C 7 alkyl, hydroxy-C 1 -C 7 alkyl, C 1 -C 7 alkoxy, halo-C 1 -C 7 alkoxy, C 1 -C 7 alkoxy-C 1 -C 7 alkyl, C 1 -C 7 alkylthio, C 1 -C 7 alkylamino, di(C 1 -C 7 alkyl)amino, amino-C 1 -C 7 alkyl , C 1 -C 7 alkylamino-C 1 -C 7 alkyl, di(C 1 -C 7 Alkyl)amino-C 1 -C 7 alkyl, aminocarbon
  • R 4 is -H, -D, C 1 -C 7 alkyl, deuterated C 1 -C 7 alkyl or halo-C 1 -C 7 alkyl;
  • L is -C-, -CH-, or and wherein R 10 and R 11 are each independently -H, -D, halo, C 1 -C 7 alkyl, deuterated C 1 -C 7 alkyl or halo-C 1 -C 7 alkyl;
  • R 5 is -JM; wherein J is a direct bond, C 1 -C 7 alkylene, C 2 -C 7 alkenylene, C 2 -C 7 alkynylene, C 1 -C 7 alkylene-O- or C 1 -C 7 alkylene-NH-; M is -H, halo, hydroxy, amino, C 1 -C 7 alkyl, C 2 -C 7 alkenyl, C 2 -C 7 alkynyl, C 3 -C 10 cycloalkyl, C 3 -C 10 cycloalkenyl, 4 to 12 membered heterocycloalkyl, 4 to 12 membered heterocycloalkenyl, C 6 -C 12 aryl or 5 to 12 membered heteroaryl; wherein said alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, heterocycloalkyl, heterocycloalkenyl, aryl or heteroaryl is
  • R 6 is -H, , , , , , , , or and;
  • R 12 to R 27 are each independently -H, nitro, cyano, azido, halo, C 1 -C 7 alkyl, C 2 -C 7 alkenyl, C 2 -C 7 alkynyl, C 3 -C 10 cycloalkyl, C 3 -C 10 cycloalkenyl, 4 to 12 membered heterocycloalkyl, 4 to 12 membered heterocycloalkenyl, C 6 -C 12 aryl, 5 to 12 membered heteroaryl, C 3 -C 10 cycloalkyl-C 1 -C 7 alkyl, C 3 -C 10 cycloalkenyl-C 1 -C 7 alkyl, C 1 -C 7 alkoxy-C 1 -C 7 alkyl, C 1 -C 7 alkylthio-C 1 -C 7 alkyl, amino-
  • n 1, 2 or 3; when n is 2 and 3, the repeating units may be the same or different;
  • n 1 or 2;
  • heterocycloalkylene, heterocycloalkenylene, heteroarylene, heterocycloalkyl, heterocycloalkenyl, partially unsaturated heterocyclyl and heteroaryl have 1 to 4 heteroatoms selected from N, O and S.
  • R 1 and R 2 are each independently -H or C 1 -C 5 alkyl.
  • R 3 is -DEG; wherein D is C 1 -C 5 alkylene; E is C 1 -C 5 alkylene, C 6 -C 10 arylene or 5 to 10 membered heterocycloalkylene having 1 to 3 N atoms; G is amino, 5 to 10 membered heteroaryl, , or and wherein R 7 , R 8 and R 9 is each independently -H, C 1 -C 5 alkyl or halo-C 1 -C 5 alkyl.
  • R 4 is -H or C 1 -C 5 alkyl.
  • L is -C-, -CH-, or -CH-CH 2 -;
  • R 5 is -JM; wherein J is a direct bond, C 1 -C 5 alkylene, or C 2 -C 5 alkenylene;
  • M is -H, hydroxy, C 1 -C 5 alkyl, C 3 -C 8 cycloalkyl, C 6 -C 10 aryl, or 5 to 10 membered heteroaryl; wherein the cycloalkyl, aryl, or heteroaryl may be optionally substituted with 1 to 3 substituents selected from hydroxy, halo, cyano, C 1 -C 5 alkyl, halo-C 1 -C 5 alkyl, C 1 -C 5 alkoxy, and C 6 -C 10 aryl;
  • L may be linked to R 5 to form a C 3 -C 8 cycloalky
  • R 6 is , or and;
  • R 16 to R 19 are each independently -H, C 1 -C 5 alkyl, C 2 -C 5 alkenyl, C 3 -C 8 cycloalkyl, 4 to 10 membered heterocycloalkyl, C 1 -C 5 alkoxy-C 1 -C 5 alkyl, C 3 -C 8 cycloalkyl-C 1 -C 5 alkyl, C 3 -C 8 cycloalkenyl-C 1 -C 5 alkyl, 4 to 10 membered heterocycloalkyl-C 1 -C 5 alkyl, partially unsaturated 4 to 10 membered heterocyclyl-C 1 -C 5 alkyl, amino-C 1 -C 5 alkyl, di(C 1 -C 5 alkyl)amino-C 1 -C 5 alkyl, C 1 -C 5 alkylthio-C 1 -C 5
  • Representative compounds of the chemical formula 1 according to the present invention may include, but are not limited to, the following compounds:
  • a chimeric compound of the following chemical formula 2 is provided:
  • A is a ubiquitin ligase binding moiety (ULM) and is a compound of the above chemical formula 1 or a prodrug thereof;
  • B is a protein target moiety (PTM);
  • a and B are chemically linked by a linker.
  • any linker used in the production of PROTAC in the relevant field can be used, and there are no special limitations thereto.
  • the linker can be a compound having the structure of the following chemical formula 3,
  • Y 1 does not exist, or , , , , , , , , , , , , , , , , , cycloalkylene, cycloalkenylene, heterocycloalkylene, heterocycloalkenylene, arylene, heteroarylene, bridged cyclclylene, fused cyclylene, spiro-cyclylene, poly-cyclylene, bridged heterocyclclylene, fused heterocyclylene, spiro-heterocyclylene and poly-heterocyclylene; wherein R'" and R" are each independently -H, -D, halo, hydroxy, amino, cyano, alkyl, haloalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxyalkyl, aminoalkyl, alkoxyalkyl, alkylthio, alkylamino, dialkylamino, alkylaminoalky
  • Y 2 is -not present, or , , , , , , , , , , , , , , , , , cycloalkylene, cycloalkenylene, heterocycloalkylene, heterocycloalkenylene, arylene, heteroarylene, bridged cyclclylene, fused cyclylene, spiro-cyclylene, poly-cyclylene, bridged heterocyclclylene, fused heterocyclylene, spiro-heterocyclylene and poly-heterocyclylene; wherein R'" and R" are each independently -H, -D, halo, hydroxy, amino, cyano, alkyl, haloalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxyalkyl, aminoalkyl, alkoxyalkyl, alkylthio, alkylamino, dialkylamino, alkylamino
  • Y 3 does not exist, or , , , , , , , , , , , , , , , , , cycloalkylene, cycloalkenylene, heterocycloalkylene, heterocycloalkenylene, arylene, heteroarylene, bridged cyclclylene, fused cyclylene, spiro-cyclylene, poly-cyclylene, bridged heterocyclclylene, fused heterocyclylene, spiro-heterocyclylene and poly-heterocyclylene; wherein R'" and R" are each independently -H, -D, halo, hydroxy, amino, cyano, alkyl, haloalkyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, hydroxyalkyl, aminoalkyl, alkoxyalkyl, alkylthio, alkylamino, dialkylamino, alkylaminoalky
  • a linker having the structure shown below may be used, and as another specific example, the linker is as described and defined in International Publication Nos. WO 2016/149668 A1, WO 2020/051564 A1 and WO 2023/076161 A1, which are incorporated herein by reference, but are not limited thereto.
  • B which is a protein target moiety (PTM)
  • PTM protein target moiety
  • compounds targeting BET bromodomain-containing proteins such as those shown in Table 1 below may be used, but are not limited thereto.
  • kinase and phosphatase inhibitor compounds such as those shown in Table 2 below may be used, but are not limited thereto.
  • JAK Janus kinase family proteins
  • compounds targeting PARP-1 poly [ADP-ribose] polymerase 1
  • compounds targeting PARP-1 poly [ADP-ribose] polymerase 1) such as those shown in Table 4 below may be used, but are not limited thereto.
  • FAM focal adhesion kinase
  • RAF rapidly accelerated fibrosarcoma receptor
  • kinase kinase
  • compounds targeting the androgen receptor (AR) such as those shown in Table 7 below may be used, but are not limited thereto.
  • compounds targeting the estrogen receptor (ER) such as those shown in Table 8 below may be used, but are not limited thereto.
  • BTK Brunauer tyrosine kinase
  • HSP90 heat shock protein 90 inhibitors
  • Table 10 compounds targeting heat shock protein 90 (HSP90) inhibitors
  • HDM2/MDM2 human double minute 2/mouse double minute 2 inhibitors
  • Table 11 compounds targeting HDM2/MDM2 (human double minute 2/mouse double minute 2) inhibitors such as those shown in Table 11 below may be used, but are not limited thereto.
  • immunosuppressive compounds such as those shown in Table 12 below may be used, but are not limited thereto.
  • the UBR1 ligand was prepared through the following solid phase synthesis.
  • Rink amide MBHA resin 50 mg, 0.52 mmol/g loading, 0.026 mmol, 1.0 equiv.
  • a 5.0 mL fritted syringe was placed in a 5.0 mL fritted syringe and incubated with DMF for 2 h at room temperature.
  • the resin was treated with HATU (0.078 mmol, 3 equiv.), HOAt (0.078 mmol, 3 equiv.), DIPEA (0.156 mmol, 6 equiv.), and the Fmoc-protected amino acid (0.078 mmol, 3 equiv.).
  • the reaction mixture was discarded, and the resin was washed with DMF (3 ⁇ ), MeOH (3 ⁇ ), CH 2 Cl 2 (3 ⁇ ), and DMF (3 ⁇ ). This process was repeated to obtain the desired compound (Method AB).
  • the compound on the resin was cleaved by treating with 1.0 mL of a cleavage cocktail (95% TFA, 2.5% TIPS, and 2.5% DDW) at room temperature for 3 h, and the compound was purified using reverse-phase column chromatography (C18 Silica Kelp, YL9100 GPC system) (solvent A: DDW with 0.1% TFA added, solvent B: ACN with 0.1% TFA added; gradient).
  • the compound was analyzed by LC (Agilent 1220 LC system Ontario, CA, USA) and MALDI-TOF MS (Autoflex Speed LRF, Bruker, Billerica, MA, USA).
  • the purified compound was lyophilized to obtain a white solid, and Examples 1 to 95, Examples 97 to 110, and Examples 112 to 118 were synthesized using the above synthetic method.
  • the Fmoc protecting group on the piperidine ring was removed by treatment with 20% piperidine (v/v) in DMF (0.50 mL), and then the guanidination reaction was carried out by treating with 1-aminopyrazole hydrochloride (0.26 mmol, 10 equiv.), DMAP (0.52 mmol, 20 equiv.), and DMF (0.50 mL) at room temperature for 24 hours.
  • the purification and analysis methods of the compounds were the same as in the above examples, and the purified compounds were freeze-dried to obtain a white solid, and Examples 96, 111, and 119 were synthesized.
  • PAL resin 50 mg, 0.92 mmol/g loading, 0.046 mmol, 1.0 equiv.
  • THF 4.0 mL vial using Method E
  • THF was added and left for 2 h.
  • the resin was treated with the primary amine (0.23 mmol, 5.0 equiv.) together with 1.0 mL of THF at room temperature for 2 h.
  • the solution was then treated with NaBH(OAc) 3 (0.32 mmol, 7.0 equiv.) and AcOH (0.46 mmol, 10 equiv.) at room temperature for 12 h.
  • the reaction mixture was transferred to a 5.0 mL fritted syringe, and the resin was washed with THF (3 ⁇ ), MeOH (3 ⁇ ), CH 2 Cl 2 (3 ⁇ ), and DMF (3 ⁇ ).
  • the Fmoc-protected amino acid (0.23 mmol, 5.0 equiv.) was then treated on the resin.
  • the reaction mixture was discarded, and the resin was washed with DMF (3x), MeOH (3x), CH 2 Cl 2 (3x), and DMF (3x). This process was repeated to obtain the desired compound.
  • the compound on the resin was cleaved by treating with 1.0 mL of a cleavage cocktail (95% TFA, 2.5% TIPS, and 2.5% DDW) for 3 h at room temperature, and the compound was purified using reversed-phase column chromatography (C18 Silica Kelp, YL9100 GPC system) (Solvent A: DDW with 0.1% TFA, Solvent B: ACN with 0.1% TFA; Gradient).
  • the compounds were analyzed by LC (Agilent 1220 LC system Ontario, CA, USA) and MALDI-TOF MS (Autoflex Speed LRF, Bruker, Billerica, MA, USA).
  • the purified compounds were freeze-dried to obtain white solids, and Examples 120 to 163 were synthesized using the above synthetic method.
  • Example 164 Synthesis of PROTAC in which the compound of Example 31 and a bromodomain-containing protein 4 (BRD4) ligand are linked via a linker
  • the beads were treated with HBTU (0.675 mmol, 5 equiv.), HOBt (0.675 mmol, 5 equiv.), DIPEA (1.35 mmol, 10 equiv.), Fmoc-1-Nal-OH (0.675 mmol, 5 equiv.) at room temperature for 2 h to initiate the amide coupling reaction, and then the resin was washed with DMF (3x), MeOH (3x), DCM (3x), and DMF (3x). Next, the Fmoc protecting group was removed by treating with a 20% piperidine in DMF (1 mL) solution.
  • the obtained compound was treated with a solution of HATU (0.27 mmol, 2.0 equiv.), HOAt (0.27 mmol, 2.0 equiv.), DIPEA (0.54 mmol, 4.0 equiv.), JQ1 carboxylic acid (0.135 mmol, 1.0 equiv.) in DMF at room temperature for 2 hours, and then piperidine was added to obtain a final 20% piperidine in DMF solution. After reacting at room temperature for 30 minutes, purification was performed by reverse-phase HPLC.
  • MDA-MB-231 cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with penicillin-streptomycin with 10% fetal bovine serum (FBS) and 5% CO 2 at 37°C.
  • DMEM Dulbecco's modified Eagle's medium
  • FBS fetal bovine serum
  • TNBC human triple-negative breast cancer
  • lysis buffer 50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Triton X, 0.1% SDS, 0.5% Sodium deoxycholate, 1x protease inhibitor cocktail
  • lysis buffer 50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Triton X, 0.1% SDS, 0.5% Sodium deoxycholate, 1x protease inhibitor cocktail
  • the cell lysate was centrifuged at 13,000 rpm for 15 minutes at 4°C. The supernatant was collected, and the protein concentration was measured using Pierce TM 660 nm Assay Reagent.
  • 6x SDS loading buffer was added to the cell lysate and heated at 95°C for 5 minutes. Equal amounts of protein were loaded onto SDS-PAGE and transferred to PVDF membranes.
  • PVDF membranes were blocked with 5% skim milk in TBST (Tris-buffered saline containing 0.01% Tween-20) and treated with primary antibodies for 15 hours at 4°C. After incubation with HRP-conjugated secondary antibodies for 1 hour at room temperature, Western blot images were obtained with ECL solution.
  • PROTAC of Example 164 reduced the intracellular BRD4 protein expression level by more than 50% at a concentration of about 0.5 ⁇ M, and exhibited stronger BRD4 protein decomposition activity as the concentration increased (Fig. 4).
  • Example 164 To determine whether the PROTAC of Example 164 induces BRD4 protein degradation via the proteasome-mediated pathway, the PROTAC of Example 164 (1 ⁇ M) was treated alone or in combination with the proteasome inhibitor MG-132 (5 ⁇ M). MDA-MB-231 cells were seeded in 6-well plates and cultured at 37°C for 24 hours, followed by compound treatment in Opti-MEM medium. Cells were then washed twice with cold DPBS to lyse the cells, and lysis buffer was added to the cells, which were then placed on ice. The cell lysate was centrifuged at 13,000 rpm for 15 minutes at 4°C, the supernatant was collected, and the protein concentration was measured using Pierce TM 660 nm Assay Reagent.
  • MDA-MB-231 cells were treated with the PROTAC of Example 164 (1 ⁇ M) and JQ1 (10 ⁇ M) or the compound of Example 31 (10 ⁇ M), and then the amount of intracellular BRD4 was measured by Western blot.
  • JQ1 (10 ⁇ M) or the compound of Example 31 (10 ⁇ M) no BRD4 degradation effect was observed, thereby proving that the degradation of BRD4 by the PROTAC of Example 164 was due to the formation of a ternary complex with the BRD4 protein and UBR1 protein (Fig. 5).
  • Example 165 Prodrug synthesis of PROTAC in which the compound of Example 31 and a bromodomain-containing protein 4 (BRD4) ligand are linked via a linker
  • the beads were treated with HBTU (0.68 mmol, 5.0 equiv.), HOBt (0.68 mmol, 5.0 equiv.), DIPEA (1.4 mmol, 10 equiv.), Fmoc-1-Nal-OH (0.68 mmol, 5.0 equiv.) at room temperature for 2 h to initiate the amide coupling reaction, and then the resin was washed with DMF (3x), MeOH (3x), DCM (3x), and DMF (3x). Next, the Fmoc protecting group was removed by treating with a 20% piperidine in DMF (1.0 mL) solution.
  • the obtained compound was treated with a solution of HATU (0.27 mmol, 2.0 equiv.), HOAt (0.27 mmol, 2.0 equiv.), DIPEA (0.54 mmol, 4.0 equiv.), JQ1 carboxylic acid (0.14 mmol, 1.0 equiv.) in DMF at room temperature for 2 hours, and then piperidine was added to obtain a final 20% piperidine in DMF solution. After reacting at room temperature for 30 minutes, purification was performed by reverse-phase HPLC. The purified compound was lyophilized to obtain an off-white solid.
  • the obtained compound (10 mg, 0.01 mmol, 1.0 equiv.) was treated with 1-((2,5-dioxopyrrolidin-1-yloxy)carbonyloxy)ethyl isobutyrate (1-((2,5-dioxopyrrolidin-1-yloxy)carbonyloxy)ethyl isobutyrate) (0.01 mmol, 1.0 equiv.) and DIPEA (0.04 mmol, 4.0 equiv.) in dry DMF solution, reacted at room temperature for 2 hours, and then purified using reverse phase HPLC.
  • the purification and analysis methods of the synthesized compound were the same as in the above examples, and the purified compound (6 S ,9 S ,12 S )-23-(( S )-4-(4-chlorophenyl)-2,3,9-trimethyl-6 H -thieno[3,2- f ][1,2,4]triazolo[4,3- a ][1,4]diazepin-6-yl)-6-(4-guanidinobutyl)-9-isobutyl-12-(naphthalen-1-ylmethyl)-4,7,10,13,22-pentaoxo-3-oxa-5,8,11,14,21-pentaazatricosan-2-ylisobutyrate was freeze-dried to obtain an off-white solid (Fig. 6).
  • PC-3 cells were treated with DMSO or various concentrations of protac compounds.
  • PC-3 cells were seeded in 6-well plates and cultured at 37°C for 24 hours, and then treated with DMSO or protac compounds in Opti-MEM medium for 48 hours. Before cell lysis, cells were washed twice with cold Dulbecco's phosphate-buffered saline (DPBS).
  • DPBS cold Dulbecco's phosphate-buffered saline
  • lysis buffer 50 mM Tris ⁇ HCl pH 7.4, 150 mM NaCl, 1% Triton X, 0.1% SDS, 0.5% Sodium deoxycholate, 1x protease inhibitor cocktail
  • the cell lysate was then centrifuged at 13,000 rpm for 15 minutes at 4°C. The supernatant was collected, and the protein concentration was measured using Pierce TM 660 nm Assay Reagent.
  • 6x SDS loading buffer was added to the cell lysate and heated at 95°C for 5 minutes. Equal amounts of protein were loaded onto SDS-PAGE and transferred to PVDF membranes.
  • PVDF membranes were blocked with 5% skim milk in TBST (Tris-buffered saline containing 0.01% Tween-20) and treated with primary antibodies for 15 hours at 4°C. After incubation with HRP-conjugated secondary antibodies for 1 hour at room temperature, Western blot images were obtained with ECL solution ( Figure 7).

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Abstract

La présente invention concerne un composé ligand ubiquitine ligase et une molécule chimère ciblant la protéolyse (PROTAC) le comprenant et, plus particulièrement, un composé agissant en tant que ligand de l'ubiquitine ligase E3 ou un promédicament de celui-ci, et une molécule hétérobifonctionnelle PROTAC le comprenant.
PCT/KR2025/005561 2024-04-25 2025-04-24 Composé ligand d'ubiquitine ligase et molécule protac le comprenant Pending WO2025226057A1 (fr)

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