Thiol-based chemical probes exhibit antiviral activity against SARS-CoV-2 via allosteric disulfide disruption in the spike glycoprotein.

Abstract

The development of small-molecules targeting different components of SARS-CoV-2 is a key strategy to complement antibody-based treatments and vaccination campaigns in managing the COVID-19 pandemic. Here, we show that two thiol-based chemical probes that act as reducing agents, P2119 and P2165, inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease the binding of spike glycoprotein to its receptor, the angiotensin-converting enzyme 2 (ACE2). Proteomics and reactive cysteine profiling link the antiviral activity to the reduction of key disulfides, specifically by disruption of the Cys379-Cys432 and Cys391-Cys525 pairs distal to the receptor binding motif in the receptor binding domain (RBD) of the spike glycoprotein. Computational analyses provide insight into conformation changes that occur when these disulfides break or form, consistent with an allosteric role, and indicate that P2119/P2165 target a conserved hydrophobic binding pocket in the RBD with the benzyl thiol-reducing moiety pointed directly toward Cys432. These collective findings establish the vulnerability of human coronaviruses to thiol-based chemical probes and lay the groundwork for developing compounds of this class, as a strategy to inhibit the SARS-CoV-2 infection by shifting the spike glycoprotein redox scaffold.

• Authors: Yunlong Shi, Ari Zeida, Caitlin E Edwards, Michael L Mallory, Santiago Sastre, Matías R Machado, Raymond J Pickles, Ling Fu, Keke Liu, Jing Yang, Ralph S Baric, Richard C Boucher, Rafael Radi, Kate S Carroll
• Journal: Proceedings of the National Academy of Sciences of the United States of America (Proc Natl Acad Sci U S A) Vol. 119 Issue 6 (02 08 2022) ISSN: 1091-6490 [Electronic] United States
• PMID: 35074895 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)
• Copyright: Copyright © 2022 the Author(s). Published by PNAS.

Chemical References

• (2R,3R,4R,5S)-6-(((2S,3R,4R,5R)-2,3,4,5,6-pentahydroxyhexyl)-(2-(4-(sulfanylmethyl)phenoxy)ethyl)amino)hexane-1,2,3,4,5-pentol
• Amino Alcohols
• Antiviral Agents
• Disulfides
• P-2165
• Phenyl Ethers
• Receptors, Virus
• Recombinant Proteins
• Spike Glycoprotein, Coronavirus
• Sulfhydryl Compounds
• spike protein, SARS-CoV-2
• ACE2 protein, human
• Angiotensin-Converting Enzyme 2

Topics

• Allosteric Regulation
• Amino Alcohols (chemistry, pharmacology)
• Angiotensin-Converting Enzyme 2 (antagonists & inhibitors, chemistry, genetics, metabolism)
• Antiviral Agents (chemistry, pharmacology)
• Binding Sites
• COVID-19 (virology)
• Cell Line
• Disulfides (antagonists & inhibitors, chemistry, metabolism)
• Dose-Response Relationship, Drug
• Humans
• Molecular Docking Simulation
• Nasal Mucosa (drug effects, metabolism, virology)
• Oxidation-Reduction
• Phenyl Ethers (chemistry, pharmacology)
• Protein Binding
• Protein Conformation, alpha-Helical
• Protein Conformation, beta-Strand
• Protein Interaction Domains and Motifs
• Receptors, Virus (antagonists & inhibitors, chemistry, genetics, metabolism)
• Recombinant Proteins (chemistry, genetics, metabolism)
• SARS-CoV-2 (drug effects, genetics, metabolism)
• Spike Glycoprotein, Coronavirus (antagonists & inhibitors, chemistry, genetics, metabolism)
• Sulfhydryl Compounds (chemistry, pharmacology)
• COVID-19 Drug Treatment