Design of SARS-CoV-2 PLpro Inhibitors for COVID-19 Antiviral Therapy Leveraging Binding Cooperativity

Overview

Journal J Med Chem

Publisher American Chemical Society

Specialty Chemistry

Date 2021 Oct 19

PMID 34665619

Citations 83

Authors

Zhengnan Shen

Kiira Ratia

Laura Cooper

Deyu Kong

Hyun Lee

Youngjin Kwon

Yangfeng Li

Saad Alqarni

Fei Huang

Oleksii Dubrovskyi

Lijun Rong

Gregory R J Thatcher

Rui Xiong

Affiliations

Soon will be listed here.

Abstract

Antiviral agents that complement vaccination are urgently needed to end the COVID-19 pandemic. The SARS-CoV-2 papain-like protease (PLpro), one of only two essential cysteine proteases that regulate viral replication, also dysregulates host immune sensing by binding and deubiquitination of host protein substrates. PLpro is a promising therapeutic target, albeit challenging owing to featureless P1 and P2 sites recognizing glycine. To overcome this challenge, we leveraged the cooperativity of multiple shallow binding sites on the PLpro surface, yielding novel 2-phenylthiophenes with nanomolar inhibitory potency. New cocrystal structures confirmed that ligand binding induces new interactions with PLpro: by closing of the BL2 loop of PLpro forming a novel "BL2 groove" and by mimicking the binding interaction of ubiquitin with Glu167 of PLpro. Together, this binding cooperativity translates to the most potent PLpro inhibitors reported to date, with slow off-rates, improved binding affinities, and low micromolar antiviral potency in SARS-CoV-2-infected human cells.

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References

Lafleur K, Huang D, Zhou T, Caflisch A, Nevado C . Structure-based optimization of potent and selective inhibitors of the tyrosine kinase erythropoietin producing human hepatocellular carcinoma receptor B4 (EphB4). J Med Chem. 2009; 52(20):6433-46. DOI: 10.1021/jm9009444. View

Smith E, Davis-Gardner M, Garcia-Ordonez R, Nguyen T, Hull M, Chen E . High-Throughput Screening for Drugs That Inhibit Papain-Like Protease in SARS-CoV-2. SLAS Discov. 2020; 25(10):1152-1161. PMC: 7550789. DOI: 10.1177/2472555220963667. View

Murshudov G, Vagin A, Dodson E . Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997; 53(Pt 3):240-55. DOI: 10.1107/S0907444996012255. View

Ratia K, Saikatendu K, Santarsiero B, Barretto N, Baker S, Stevens R . Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci U S A. 2006; 103(15):5717-22. PMC: 1458639. DOI: 10.1073/pnas.0510851103. View

Baez-Santos Y, Barraza S, Wilson M, Agius M, Mielech A, Davis N . X-ray structural and biological evaluation of a series of potent and highly selective inhibitors of human coronavirus papain-like proteases. J Med Chem. 2014; 57(6):2393-412. PMC: 3983375. DOI: 10.1021/jm401712t. View

Vabret N, Britton G, Gruber C, Hegde S, Kim J, Kuksin M . Immunology of COVID-19: Current State of the Science. Immunity. 2020; 52(6):910-941. PMC: 7200337. DOI: 10.1016/j.immuni.2020.05.002. View

Kabsch W . Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 2):133-44. PMC: 2815666. DOI: 10.1107/S0907444909047374. View

Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A . Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature. 2020; 587(7835):657-662. PMC: 7116779. DOI: 10.1038/s41586-020-2601-5. View

Ghosh A, Brindisi M, Shahabi D, Chapman M, Mesecar A . Drug Development and Medicinal Chemistry Efforts toward SARS-Coronavirus and Covid-19 Therapeutics. ChemMedChem. 2020; 15(11):907-932. PMC: 7264561. DOI: 10.1002/cmdc.202000223. View

10.

Barretto N, Jukneliene D, Ratia K, Chen Z, Mesecar A, Baker S . The papain-like protease of severe acute respiratory syndrome coronavirus has deubiquitinating activity. J Virol. 2005; 79(24):15189-98. PMC: 1316023. DOI: 10.1128/JVI.79.24.15189-15198.2005. View

11.

Klemm T, Ebert G, Calleja D, Allison C, Richardson L, Bernardini J . Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. EMBO J. 2020; 39(18):e106275. PMC: 7461020. DOI: 10.15252/embj.2020106275. View

12.

Del Ser T, Fernandez-Blazquez M, Valenti M, Zea-Sevilla M, Frades B, Alfayate E . Residence, Clinical Features, and Genetic Risk Factors Associated with Symptoms of COVID-19 in a Cohort of Older People in Madrid. Gerontology. 2021; 67(3):281-289. PMC: 7900450. DOI: 10.1159/000513182. View

13.

Wrapp D, Wang N, Corbett K, Goldsmith J, Hsieh C, Abiona O . Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020; 367(6483):1260-1263. PMC: 7164637. DOI: 10.1126/science.abb2507. View

14.

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

15.

Vagin A, Teplyakov A . Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr. 2010; 66(Pt 1):22-5. DOI: 10.1107/S0907444909042589. View

16.

Ratia K, Kilianski A, Baez-Santos Y, Baker S, Mesecar A . Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease. PLoS Pathog. 2014; 10(5):e1004113. PMC: 4031219. DOI: 10.1371/journal.ppat.1004113. View

17.

Muley L, Baum B, Smolinski M, Freindorf M, Heine A, Klebe G . Enhancement of hydrophobic interactions and hydrogen bond strength by cooperativity: synthesis, modeling, and molecular dynamics simulations of a congeneric series of thrombin inhibitors. J Med Chem. 2010; 53(5):2126-35. DOI: 10.1021/jm9016416. View

18.

Freitas B, Durie I, Murray J, Longo J, Miller H, Crich D . Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease. ACS Infect Dis. 2020; 6(8):2099-2109. DOI: 10.1021/acsinfecdis.0c00168. View

19.

Ghosh A, Takayama J, Venkateswara Rao K, Ratia K, Chaudhuri R, Mulhearn D . Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation. J Med Chem. 2010; 53(13):4968-79. PMC: 2918394. DOI: 10.1021/jm1004489. View

20.

Tonge P . Drug-Target Kinetics in Drug Discovery. ACS Chem Neurosci. 2017; 9(1):29-39. PMC: 5767540. DOI: 10.1021/acschemneuro.7b00185. View