2. Academic Validation
  3. Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors

  • ACS Infect Dis. 2023 Oct 13;9(10):1918-1931. doi: 10.1021/acsinfecdis.3c00203.
Nicole L Inniss 1,  Ján Kozic 2,  Fengling Li 3,  Monica Rosas-Lemus 1,  George Minasov 1,  Jiří Rybáček 2,  Yingjie Zhu 4,  Radek Pohl 2,  Ludmilla Shuvalova 5,  Lubomír Rulíšek 2,  Joseph S Brunzelle 6,  Lucie Bednárová 2,  Milan Štefek 2,  Ján Michael Kormaník 2,  Erik Andris 2,  Jaroslav Šebestík 2,  Alice Shi Ming Li 7 8,  Peter J Brown 3,  Uli Schmitz 9,  Kumar Saikatendu 10,  Edcon Chang 10,  Radim Nencka 2,  Masoud Vedadi 7 8,  Karla J F Satchell 1
Affiliations

Affiliations

  • 1 Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States.
  • 2 Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic.
  • 3 Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
  • 4 WuXi AppTec Co., Ltd, China (Shanghai) Pilot Free Trade Zone, Shanghai, 201308, China.
  • 5 Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, United States.
  • 6 Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States.
  • 7 Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
  • 8 Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
  • 9 Structural Chemistry, Gilead Pharmaceuticals, San Mateo, California 94404, United States.
  • 10 Takeda Development Center Americas, Inc., San Diego, California 92121, United States.
PMID: 37728236 DOI: 10.1021/acsinfecdis.3c00203
Abstract

A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 Infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.

Keywords

antiviral; coronavirus; covalent inhibitors; nsp16 methyltransferase; structural biology.

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