Journal Article

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

Liu, Keke, Boucher, Richard C., Radi, Rafael, Mallory, Michael L., Machado, Matías R., Carroll, Kate S., Sastre, Santiago, Zeida, Ari, Baric, Ralph S., Pickles, Raymond J., Yang, Jing, Edwards, Caitlin E., Shi, Yunlong, Fu, Ling

2022

Overview

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.

• Publisher: National Academy of Sciences
• Subject: ACE2 / Allosteric properties / Allosteric Regulation / Amino Alcohols - chemistry / Amino Alcohols - pharmacology / Angiotensin / Angiotensin-converting enzyme 2 / Angiotensin-Converting Enzyme 2 - antagonists & inhibitors / Angiotensin-Converting Enzyme 2 - chemistry / Angiotensin-Converting Enzyme 2 - genetics / Angiotensin-Converting Enzyme 2 - metabolism / Antibodies / Antiviral activity / Antiviral Agents - chemistry / Antiviral Agents - pharmacology / Binding / Binding Sites / Biological Sciences / Cell Line / Computer applications / Conformation / Coronaviridae / Coronaviruses / COVID-19 / COVID-19 - drug therapy / COVID-19 - virology / Disruption / Disulfides / Disulfides - antagonists & inhibitors / Disulfides - chemistry / Disulfides - metabolism / Dose-Response Relationship, Drug / Glycoproteins / Humans / Hydrophobicity / Microbiology / Molecular Docking Simulation / Nasal Mucosa - drug effects / Nasal Mucosa - metabolism / Nasal Mucosa - virology / Oxidation-Reduction / Pandemics / Peptidyl-dipeptidase A / Phenyl Ethers - chemistry / Phenyl Ethers - pharmacology / Probes / Protein Binding / Protein Conformation, alpha-Helical / Protein Conformation, beta-Strand / Protein Interaction Domains and Motifs / Proteomics / Receptors / Receptors, Virus - antagonists & inhibitors / Receptors, Virus - chemistry / Receptors, Virus - genetics / Receptors, Virus - metabolism / Recombinant Proteins - chemistry / Recombinant Proteins - genetics / Recombinant Proteins - metabolism / Reducing agents / SARS-CoV-2 - drug effects / SARS-CoV-2 - genetics / SARS-CoV-2 - metabolism / Severe acute respiratory syndrome coronavirus 2 / Spike glycoprotein / Spike Glycoprotein, Coronavirus - antagonists & inhibitors / Spike Glycoprotein, Coronavirus - chemistry / Spike Glycoprotein, Coronavirus - genetics / Spike Glycoprotein, Coronavirus - metabolism / Sulfhydryl Compounds - chemistry / Sulfhydryl Compounds - pharmacology / Vaccination / Viral diseases