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An expedited approach towards the rationale design of non-covalent SARS-CoV-2 main protease inhibitors with in vitro antiviral activity
Naoya Kitamura; Michael Dominic Sacco; Chunlong Ma; Yanmei Hu; Julia Townsend; Xiangzhi Meng; Fushun Zhang; Xiujun Zhang; Adis Kukuljac; Michael Marty; David Schultz; Sara Cherry; Yan Xiang; Yu Chen; Jun Wang.
Affiliation
  • Naoya Kitamura; University of Arizona
  • Michael Dominic Sacco; University of South Florida
  • Chunlong Ma; University of Arizona
  • Yanmei Hu; University of Arizona
  • Julia Townsend; University of Arizona
  • Xiangzhi Meng; University of Texas Health San Antonio
  • Fushun Zhang; University of Texas Health San Antonio
  • Xiujun Zhang; University of South Florida
  • Adis Kukuljac; University of South Florida
  • Michael Marty; University of Arizona
  • David Schultz; University of Pennsylvania
  • Sara Cherry; University of Pennsylvania
  • Yan Xiang; University of Texas Health Science Center at San Antonio
  • Yu Chen; University of South Florida
  • Jun Wang; University of Arizona
Preprint in English | bioRxiv | ID: ppbiorxiv-423537
ABSTRACT
The main protease (Mpro) of SARS-CoV-2 is a validated antiviral drug target. Several Mpro inhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including GC376, boceprevir, calpain inhibitors II and XII, each containing a reactive warhead that covalently modifies the catalytic Cys145. In this study, we report an expedited drug discovery approach by coupling structure-based design and Ugi four-component (Ugi-4CR) reaction methodology to the design of non-covalent Mpro inhibitors. The most potent compound 23R had cellular antiviral activity similar to covalent inhibitors such as GC376. Our designs were guided by overlaying the structure of SARS-CoV Mpro + ML188 (R), a non-covalent inhibitor derived from Ug-4CR, with the X-ray crystal structures of SARS-CoV-2 Mpro + calpain inhibitor XII/GC376/UAWJ247. Binding site analysis suggests a strategy of extending the P2 and P3 substitutions in ML188 (R) to achieve optimal shape complementary with SARS-CoV-2 Mpro. Lead optimization led to the discovery of 23R, which inhibits SARS-CoV-2 Mpro and SARS-CoV-2 viral replication with an IC50 of 0.31 M and EC50 of 1.27 M, respectively. The binding and specificity of 23R to SARS-CoV-2 Mpro were confirmed in a thermal shift assay and native mass spectrometry assay. The co-crystal structure of SARS-CoV-2 Mpro with 23R revealed the P2 biphenyl fits snuggly into the S2 pocket and the benzyl group in the -methylbenzyl faces towards the core of the enzyme, occupying a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study revealed the most potent non-covalent SARS-CoV-2 Mpro inhibitors reported to date and a novel binding pocket that can be explored for Mpro inhibitor design.
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Full text: Available Collection: Preprints Database: bioRxiv Type of study: Prognostic study Language: English Year: 2020 Document type: Preprint
Full text: Available Collection: Preprints Database: bioRxiv Type of study: Prognostic study Language: English Year: 2020 Document type: Preprint
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