5vsb Citations

Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7.

Abstract

Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB⋅small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. Here, we report a small-molecule⋅ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.

Articles - 5vsb mentioned but not cited (1)

  1. Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7. Lamberto I, Liu X, Seo HS, Schauer NJ, Iacob RE, Hu W, Das D, Mikhailova T, Weisberg EL, Engen JR, Anderson KC, Chauhan D, Dhe-Paganon S, Buhrlage SJ. Cell Chem Biol 24 1490-1500.e11 (2017)


Reviews citing this publication (35)

  1. Breaking the chains: deubiquitylating enzyme specificity begets function. Clague MJ, Urbé S, Komander D. Nat Rev Mol Cell Biol 20 338-352 (2019)
  2. The role of ubiquitination in tumorigenesis and targeted drug discovery. Deng L, Meng T, Chen L, Wei W, Wang P. Signal Transduct Target Ther 5 11 (2020)
  3. USP7: Structure, substrate specificity, and inhibition. Pozhidaeva A, Bezsonova I. DNA Repair (Amst) 76 30-39 (2019)
  4. Dissenting degradation: Deubiquitinases in cell cycle and cancer. Bonacci T, Emanuele MJ. Semin Cancer Biol 67 145-158 (2020)
  5. Targeting USP7-Mediated Deubiquitination of MDM2/MDMX-p53 Pathway for Cancer Therapy: Are We There Yet? Qi SM, Cheng G, Cheng XD, Xu Z, Xu B, Zhang WD, Qin JJ. Front Cell Dev Biol 8 233 (2020)
  6. The Chemical Biology of Reversible Lysine Post-translational Modifications. Wang ZA, Cole PA. Cell Chem Biol 27 953-969 (2020)
  7. Proteasome Inhibitors: Harnessing Proteostasis to Combat Disease. Sherman DJ, Li J. Molecules 25 E671 (2020)
  8. Advances in the Development Ubiquitin-Specific Peptidase (USP) Inhibitors. Chen S, Liu Y, Zhou H. Int J Mol Sci 22 4546 (2021)
  9. USP7 Is a Master Regulator of Genome Stability. Valles GJ, Bezsonova I, Woodgate R, Ashton NW, Ashton NW. Front Cell Dev Biol 8 717 (2020)
  10. Chemically Induced Cellular Proteolysis: An Emerging Therapeutic Strategy for Undruggable Targets. Moon S, Lee BH. Mol Cells 41 933-942 (2018)
  11. Targeting the Ubiquitin-Proteasome System for Cancer Therapeutics by Small-Molecule Inhibitors. LaPlante G, Zhang W. Cancers (Basel) 13 3079 (2021)
  12. Ubiquitin-Specific Proteases: Players in Cancer Cellular Processes. Cruz L, Soares P, Correia M. Pharmaceuticals (Basel) 14 848 (2021)
  13. Molecular Mechanisms of DUBs Regulation in Signaling and Disease. Li Y, Reverter D. Int J Mol Sci 22 986 (2021)
  14. Small molecules that target the ubiquitin system. Wu HQ, Baker D, Ovaa H. Biochem Soc Trans 48 479-497 (2020)
  15. Modulating protein-protein interaction networks in protein homeostasis. Zhong M, Lee GM, Sijbesma E, Ottmann C, Arkin MR. Curr Opin Chem Biol 50 55-65 (2019)
  16. Regulation of Cancer Metabolism by Deubiquitinating Enzymes: The Warburg Effect. Kim SH, Baek KH. Int J Mol Sci 22 6173 (2021)
  17. Targeting Ubiquitin-Specific Protease 7 (USP7) in Cancer: A New Insight to Overcome Drug Resistance. Lu J, Zhao H, Yu C, Kang Y, Yang X. Front Pharmacol 12 648491 (2021)
  18. Targeting the MYC Ubiquitination-Proteasome Degradation Pathway for Cancer Therapy. Sun XX, Li Y, Sears RC, Dai MS. Front Oncol 11 679445 (2021)
  19. USP15: a review of its implication in immune and inflammatory processes and tumor progression. Georges A, Gros P, Fodil N. Genes Immun 22 12-23 (2021)
  20. Targeting ubiquitin specific protease 7 in cancer: A deubiquitinase with great prospects. Yeasmin Khusbu F, Chen FZ, Chen HC. Cell Biochem Funct 36 244-254 (2018)
  21. DUBs Activating the Hedgehog Signaling Pathway: A Promising Therapeutic Target in Cancer. Bufalieri F, Lospinoso Severini L, Caimano M, Infante P, Di Marcotullio L. Cancers (Basel) 12 E1518 (2020)
  22. Small-Molecule Inhibitors Targeting Proteasome-Associated Deubiquitinases. Moon S, Muniyappan S, Lee SB, Lee BH. Int J Mol Sci 22 6213 (2021)
  23. Deubiquitinases: Pro-oncogenic Activity and Therapeutic Targeting in Blood Malignancies. Gutierrez-Diaz BT, Gu W, Ntziachristos P. Trends Immunol 41 327-340 (2020)
  24. Highlights in USP7 inhibitors for cancer treatment. Oliveira RI, Guedes RA, Salvador JAR. Front Chem 10 1005727 (2022)
  25. Ubiquitination and Ubiquitin-Like Modifications in Multiple Myeloma: Biology and Therapy. Wirth M, Schick M, Keller U, Krönke J. Cancers (Basel) 12 E3764 (2020)
  26. Probing ubiquitin and SUMO conjugation and deconjugation. Ovaa H, Vertegaal ACO. Biochem Soc Trans 46 423-436 (2018)
  27. Deubiquitinases in hematological malignancies. Lei H, Wang J, Hu J, Zhu Q, Wu Y. Biomark Res 9 66 (2021)
  28. The chemical biology of IL-12 production via the non-canonical NFkB pathway. Koch PD, Pittet MJ, Weissleder R. RSC Chem Biol 1 166-176 (2020)
  29. Assay Systems for Profiling Deubiquitinating Activity. Cho J, Park J, Kim EE, Song EJ. Int J Mol Sci 21 E5638 (2020)
  30. Deubiquitinating Enzyme: A Potential Secondary Checkpoint of Cancer Immunity. Huang X, Zhang X, Xu J, Wang X, Zhang G, Tang T, Shen X, Liang T, Bai X. Front Oncol 10 1289 (2020)
  31. On the Study of Deubiquitinases: Using the Right Tools for the Job. Caba C, Mohammadzadeh A, Tong Y. Biomolecules 12 703 (2022)
  32. The emerging role of deubiquitylating enzymes as therapeutic targets in cancer metabolism. Tu R, Ma J, Zhang P, Kang Y, Xiong X, Zhu J, Li M, Zhang C. Cancer Cell Int 22 130 (2022)
  33. The equilibrium of tumor suppression: DUBs as active regulators of PTEN. Christine A, Park MK, Song SJ, Song MS. Exp Mol Med 54 1814-1821 (2022)
  34. Deubiquitylating Enzymes in Cancer and Immunity. Ren J, Yu P, Liu S, Li R, Niu X, Chen Y, Zhang Z, Zhou F, Zhang L. Adv Sci (Weinh) 10 e2303807 (2023)
  35. Function, mechanism and drug discovery of ubiquitin and ubiquitin-like modification with multiomics profiling for cancer therapy. Jiang Y, Ni S, Xiao B, Jia L. Acta Pharm Sin B 13 4341-4372 (2023)

Articles citing this publication (48)

  1. The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery. Fu Z, Huang B, Tang J, Liu S, Liu M, Ye Y, Liu Z, Xiong Y, Zhu W, Cao D, Li J, Niu X, Zhou H, Zhao YJ, Zhang G, Huang H. Nat Commun 12 488 (2021)
  2. Deubiquitinase Activity Profiling Identifies UCHL1 as a Candidate Oncoprotein That Promotes TGFβ-Induced Breast Cancer Metastasis. Liu S, González-Prieto R, Zhang M, Geurink PP, Kooij R, Iyengar PV, van Dinther M, Bos E, Zhang X, Le Dévédec SE, van de Water B, Koning RI, Zhu HJ, Mesker WE, Vertegaal ACO, Ovaa H, Zhang L, Martens JWM, Ten Dijke P. Clin Cancer Res 26 1460-1473 (2020)
  3. Small molecule inhibitors reveal allosteric regulation of USP14 via steric blockade. Wang Y, Jiang Y, Ding S, Li J, Song N, Ren Y, Hong D, Wu C, Li B, Wang F, He W, Wang J, Mei Z. Cell Res 28 1186-1194 (2018)
  4. USP30 sets a trigger threshold for PINK1-PARKIN amplification of mitochondrial ubiquitylation. Rusilowicz-Jones EV, Jardine J, Kallinos A, Pinto-Fernandez A, Guenther F, Giurrandino M, Barone FG, McCarron K, Burke CJ, Murad A, Martinez A, Marcassa E, Gersch M, Buckmelter AJ, Kayser-Bricker KJ, Lamoliatte F, Gajbhiye A, Davis S, Scott HC, Murphy E, England K, Mortiboys H, Komander D, Trost M, Kessler BM, Ioannidis S, Ahlijanian MK, Urbé S, Clague MJ. Life Sci Alliance 3 e202000768 (2020)
  5. Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism. Schauer NJ, Liu X, Magin RS, Doherty LM, Chan WC, Ficarro SB, Hu W, Roberts RM, Iacob RE, Stolte B, Giacomelli AO, Perera S, McKay K, Boswell SA, Weisberg EL, Ray A, Chauhan D, Dhe-Paganon S, Anderson KC, Griffin JD, Li J, Hahn WC, Sorger PK, Engen JR, Stegmaier K, Marto JA, Buhrlage SJ. Sci Rep 10 5324 (2020)
  6. Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in TP53 wild-type Ewing sarcoma. Stolte B, Iniguez AB, Dharia NV, Robichaud AL, Conway AS, Morgan AM, Alexe G, Schauer NJ, Liu X, Bird GH, Tsherniak A, Vazquez F, Buhrlage SJ, Walensky LD, Stegmaier K. J Exp Med 215 2137-2155 (2018)
  7. Maintaining protein stability of ∆Np63 via USP28 is required by squamous cancer cells. Prieto-Garcia C, Hartmann O, Reissland M, Braun F, Fischer T, Walz S, Schülein-Völk C, Eilers U, Ade CP, Calzado MA, Orian A, Maric HM, Münch C, Rosenfeldt M, Eilers M, Diefenbacher ME. EMBO Mol Med 12 e11101 (2020)
  8. Comprehensive Landscape of Active Deubiquitinating Enzymes Profiled by Advanced Chemoproteomics. Pinto-Fernández A, Davis S, Schofield AB, Scott HC, Zhang P, Salah E, Mathea S, Charles PD, Damianou A, Bond G, Fischer R, Kessler BM. Front Chem 7 592 (2019)
  9. Deubiquitinase USP20 promotes breast cancer metastasis by stabilizing SNAI2. Li W, Shen M, Jiang YZ, Zhang R, Zheng H, Wei Y, Shao ZM, Kang Y. Genes Dev 34 1310-1315 (2020)
  10. The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel. Ward SJ, Gratton HE, Indrayudha P, Michavila C, Mukhopadhyay R, Maurer SK, Caulton SG, Emsley J, Dreveny I. J Biol Chem 293 17362-17374 (2018)
  11. Identification and Characterization of USP7 Targets in Cancer Cells. Georges A, Marcon E, Greenblatt J, Frappier L. Sci Rep 8 15833 (2018)
  12. Small-Molecule Activity-Based Probe for Monitoring Ubiquitin C-Terminal Hydrolase L1 (UCHL1) Activity in Live Cells and Zebrafish Embryos. Kooij R, Liu S, Sapmaz A, Xin BT, Janssen GMC, van Veelen PA, Ovaa H, Dijke PT, Geurink PP. J Am Chem Soc 142 16825-16841 (2020)
  13. Re-Evaluating the Mechanism of Action of α,β-Unsaturated Carbonyl DUB Inhibitors b-AP15 and VLX1570: A Paradigmatic Example of Unspecific Protein Cross-linking with Michael Acceptor Motif-Containing Drugs. Ward JA, Pinto-Fernandez A, Cornelissen L, Bonham S, Díaz-Sáez L, Riant O, Huber KVM, Kessler BM, Feron O, Tate EW. J Med Chem 63 3756-3762 (2020)
  14. Discovery of peptide ligands targeting a specific ubiquitin-like domain-binding site in the deubiquitinase USP11. Spiliotopoulos A, Blokpoel Ferreras L, Densham RM, Caulton SG, Maddison BC, Morris JR, Dixon JE, Gough KC, Dreveny I. J Biol Chem 294 424-436 (2019)
  15. Inhibition of ubiquitin-specific protease 7 sensitizes acute myeloid leukemia to chemotherapy. Cartel M, Mouchel PL, Gotanègre M, David L, Bertoli S, Mansat-De Mas V, Besson A, Sarry JE, Manenti S, Didier C. Leukemia 35 417-432 (2021)
  16. USP7 Regulates Cytokinesis through FBXO38 and KIF20B. Georges A, Coyaud E, Marcon E, Greenblatt J, Raught B, Frappier L. Sci Rep 9 2724 (2019)
  17. Identification and Structure-Guided Development of Pyrimidinone Based USP7 Inhibitors. O'Dowd CR, Helm MD, Rountree JSS, Flasz JT, Arkoudis E, Miel H, Hewitt PR, Jordan L, Barker O, Hughes C, Rozycka E, Cassidy E, McClelland K, Odrzywol E, Page N, Feutren-Burton S, Dvorkin S, Gavory G, Harrison T. ACS Med Chem Lett 9 238-243 (2018)
  18. MYC multimers shield stalled replication forks from RNA polymerase. Solvie D, Baluapuri A, Uhl L, Fleischhauer D, Endres T, Papadopoulos D, Aziba A, Gaballa A, Mikicic I, Isaakova E, Giansanti C, Jansen J, Jungblut M, Klein T, Schülein-Völk C, Maric H, Doose S, Sauer M, Beli P, Rosenwald A, Dobbelstein M, Wolf E, Eilers M. Nature 612 148-155 (2022)
  19. A High-Throughput Assay for Monitoring Ubiquitination in Real Time. Franklin TG, Pruneda JN. Front Chem 7 816 (2019)
  20. USP47 Promotes Tumorigenesis by Negative Regulation of p53 through Deubiquitinating Ribosomal Protein S2. Cho J, Park J, Shin SC, Jang M, Kim JH, Kim EE, Song EJ. Cancers (Basel) 12 E1137 (2020)
  21. Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori B, Buhrlage SJ, Sorger PK. Elife 11 e72879 (2022)
  22. The deubiquitylase USP9X controls ribosomal stalling. Clancy A, Heride C, Pinto-Fernández A, Elcocks H, Kallinos A, Kayser-Bricker KJ, Wang W, Smith V, Davis S, Fessler S, McKinnon C, Katz M, Hammonds T, Jones NP, O'Connell J, Follows B, Mischke S, Caravella JA, Ioannidis S, Dinsmore C, Kim S, Behrens A, Komander D, Kessler BM, Urbé S, Clague MJ. J Cell Biol 220 e202004211 (2021)
  23. Kinetic analysis of multistep USP7 mechanism shows critical role for target protein in activity. Kim RQ, Geurink PP, Mulder MPC, Fish A, Ekkebus R, El Oualid F, van Dijk WJ, van Dalen D, Ovaa H, van Ingen H, Sixma TK. Nat Commun 10 231 (2019)
  24. Proteomics-Based Identification of DUB Substrates Using Selective Inhibitors. Bushman JW, Donovan KA, Schauer NJ, Liu X, Hu W, Varca AC, Buhrlage SJ, Fischer ES. Cell Chem Biol 28 78-87.e3 (2021)
  25. Neuroinflammation inhibition by small-molecule targeting USP7 noncatalytic domain for neurodegenerative disease therapy. Zhang XW, Feng N, Liu YC, Guo Q, Wang JK, Bai YZ, Ye XM, Yang Z, Yang H, Liu Y, Yang MM, Wang YH, Shi XM, Liu D, Tu PF, Zeng KW. Sci Adv 8 eabo0789 (2022)
  26. Evaluating enzyme activities and structures of DUBs. Pruneda JN, Komander D. Methods Enzymol 618 321-341 (2019)
  27. Small molecule inhibition of deubiquitinating enzyme JOSD1 as a novel targeted therapy for leukemias with mutant JAK2. Yang J, Weisberg EL, Liu X, Magin RS, Chan WC, Hu B, Schauer NJ, Zhang S, Lamberto I, Doherty L, Meng C, Sattler M, Cabal-Hierro L, Winer E, Stone R, Marto JA, Griffin JD, Buhrlage SJ. Leukemia 36 210-220 (2022)
  28. Targeting the deubiquitinase USP7 for degradation with PROTACs. Murgai A, Sosič I, Gobec M, Lemnitzer P, Proj M, Wittenburg S, Voget R, Gütschow M, Krönke J, Steinebach C. Chem Commun (Camb) 58 8858-8861 (2022)
  29. Targeting ubiquitin-specific protease 8 sensitizes anti-programmed death-ligand 1 immunotherapy of pancreatic cancer. Yang H, Zhang X, Lao M, Sun K, He L, Xu J, Duan Y, Chen Y, Ying H, Li M, Guo C, Lu Q, Wang S, Su W, Liang T, Bai X. Cell Death Differ 30 560-575 (2023)
  30. The ubiquitin interacting motifs of USP37 act on the proximal Ub of a di-Ub chain to enhance catalytic efficiency. Manczyk N, Veggiani G, Teyra J, Strilchuk AW, Sidhu SS, Sicheri F. Sci Rep 9 4119 (2019)
  31. Identification and validation of selective deubiquitinase inhibitors. Varca AC, Casalena D, Chan WC, Hu B, Magin RS, Roberts RM, Liu X, Zhu H, Seo HS, Dhe-Paganon S, Marto JA, Auld D, Buhrlage SJ. Cell Chem Biol 28 1758-1771.e13 (2021)
  32. Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis. Ramirez YA, Adler TB, Altmann E, Klemm T, Tiesmeyer C, Sauer F, Kathman SG, Statsyuk AV, Sotriffer C, Kisker C. ChemMedChem 13 2014-2023 (2018)
  33. Accelerating inhibitor discovery for deubiquitinating enzymes. Chan WC, Liu X, Magin RS, Girardi NM, Ficarro SB, Hu W, Tarazona Guzman MI, Starnbach CA, Felix A, Adelmant G, Varca AC, Hu B, Bratt AS, DaSilva E, Schauer NJ, Jaen Maisonet I, Dolen EK, Ayala AX, Marto JA, Buhrlage SJ. Nat Commun 14 686 (2023)
  34. New aspects of USP30 biology in the regulation of pexophagy. Marcassa E, Kallinos A, Jardine J, Rusilowicz-Jones EV, Clague MJ, Urbé S. Autophagy 15 1634-1637 (2019)
  35. Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity. Rossio V, Paulo JA, Chick J, Brasher B, Gygi SP, King RW. Cell Chem Biol 28 487-502.e5 (2021)
  36. Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint. Srivastava M, Mittal L, Kumari A, Agrahari AK, Singh M, Mathur R, Asthana S. Protein Sci 31 e4398 (2022)
  37. Discovery and Characterization of BAY-805, a Potent and Selective Inhibitor of Ubiquitin-Specific Protease USP21. Göricke F, Vu V, Smith L, Scheib U, Böhm R, Akkilic N, Wohlfahrt G, Weiske J, Bömer U, Brzezinka K, Lindner N, Lienau P, Gradl S, Beck H, Brown PJ, Santhakumar V, Vedadi M, Barsyte-Lovejoy D, Arrowsmith CH, Schmees N, Petersen K. J Med Chem 66 3431-3447 (2023)
  38. Halogen Substituents in the Isoquinoline Scaffold Switches the Selectivity of Inhibition between USP2 and USP7. Vamisetti GB, Meledin R, Gopinath P, Brik A. Chembiochem 20 282-286 (2019)
  39. Diarylcarbonates are a new class of deubiquitinating enzyme inhibitor. Long MJC, Lawson AP, Baggio R, Qian Y, Rozhansky L, Fasci D, El Oualid F, Weerapana E, Hedstrom L. Bioorg Med Chem Lett 29 204-211 (2019)
  40. Identification of deubiquitinase inhibitors via high-throughput screening using a fluorogenic ubiquitin-rhodamine assay. Varca AC, Casalena D, Auld D, Buhrlage SJ. STAR Protoc 2 100896 (2021)
  41. Backbone and ILV side-chain NMR resonance assignments of the catalytic domain of human deubiquitinating enzyme USP7. Valles G, Pozhidaeva A, Korzhnev DM, Bezsonova I. Biomol NMR Assign 16 197-203 (2022)
  42. In Silico Analysis of USP7 Inhibitors Based on Building QSAR Models and Fragment Design for Screening Marine Compound Libraries. Tan H, Li C, Lai T, Luo L. Mar Drugs 22 1 (2023)
  43. Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound. Giovannucci TA, Salomons FA, Haraldsson M, Elfman LHM, Wickström M, Young P, Lundbäck T, Eirich J, Altun M, Jafari R, Gustavsson AL, Johnsen JI, Dantuma NP. Cell Death Dis 12 914 (2021)
  44. On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA. Anal Chem 94 9508-9513 (2022)
  45. Structural and functional characterization of USP47 reveals a hot spot for inhibitor design. Shin SC, Park J, Kim KH, Yoon JM, Cho J, Ha BH, Oh Y, Choo H, Song EJ, Kim EE. Commun Biol 6 970 (2023)
  46. USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder. Cheron J, Beccari L, Hagué P, Icick R, Despontin C, Carusone T, Defrance M, Bhogaraju S, Martin-Garcia E, Capellan R, Maldonado R, Vorspan F, Bonnefont J, de Kerchove d'Exaerde A. Nat Commun 14 8481 (2023)
  47. USP8 inhibition regulates autophagy flux and controls Salmonella infection. Santelices J, Ou M, Maegawa GHB, Hercik K, Edelmann MJ. Front Cell Infect Microbiol 13 1070271 (2023)
  48. Ubiquitin specific protease 7 maintains pluripotency of mouse embryonic stem cells through stabilization of β-catenin. Hayal TB. Turk J Biol 46 82-94 (2022)