Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline

Edmond Y. Lau, Oscar A. Negrete, W. F.Drew Bennett, Brian Bennion, Monica Borucki, Feliza Bourguet, Aidan Epstein, Magdalena Franco, Brooke Harmon, Stewart He, Derek Jones, Hyojin Kim, Daniel Kirshner, Victoria Lao, Jacky Lo, Kevin McLoughlin, Richard Mosesso, Deepa K. Murugesh, Edwin A. Saada, Brent SegelkeMaxwell A. Stefan, Garrett A. Stevenson, Marisa W. Torres, Dina R. Weilhammer, Sergio Wong, Yue Yang, Adam Zemla, Xiaohua Zhang, Fangqiang Zhu, Jonathan E. Allen, Felice C. Lightstone

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

A rapid response is necessary to contain emergent biological outbreaks before they can become pandemics. The novel coronavirus (SARS-CoV-2) that causes COVID-19 was first reported in December of 2019 in Wuhan, China and reached most corners of the globe in less than two months. In just over a year since the initial infections, COVID-19 infected almost 100 million people worldwide. Although similar to SARS-CoV and MERS-CoV, SARS-CoV-2 has resisted treatments that are effective against other coronaviruses. Crystal structures of two SARS-CoV-2 proteins, spike protein and main protease, have been reported and can serve as targets for studies in neutralizing this threat. We have employed molecular docking, molecular dynamics simulations, and machine learning to identify from a library of 26 million molecules possible candidate compounds that may attenuate or neutralize the effects of this virus. The viability of selected candidate compounds against SARS-CoV-2 was determined experimentally by biolayer interferometry and FRET-based activity protein assays along with virus-based assays. In the pseudovirus assay, imatinib and lapatinib had IC50 values below 10 μM, while candesartan cilexetil had an IC50 value of approximately 67 µM against Mpro in a FRET-based activity assay. Comparatively, candesartan cilexetil had the highest selectivity index of all compounds tested as its half-maximal cytotoxicity concentration 50 (CC50) value was the only one greater than the limit of the assay (>100 μM).

Original languageEnglish (US)
Article number678701
JournalFrontiers in Molecular Biosciences
Volume8
DOIs
StatePublished - Jul 9 2021
Externally publishedYes

Keywords

  • COVID-19
  • FRET
  • live virus
  • machine-learning
  • main protease
  • molecular simulations
  • protein assays
  • spike protein

ASJC Scopus subject areas

  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Molecular Biology

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