Novel inhibitors of the main protease enzyme of SARS-CoV-2 identified via molecular dynamics simulation-guided in vitro assay

Abstract

For the COVID-19 pandemic caused by SARS-CoV-2, there are currently no effective drugs or vaccines to treat this coronavirus infection. In this study, we focus on the main protease enzyme of SARS-CoV-2, 3CL pro , which is critical for viral replication. We employ explicit solvent molecular dynamics simulations of about 150 compounds docked into 3CL pro ’s binding site and that had emerged as good main protease ligands from our previous in silico screening of over 1.2 million compounds. By incoporating protein dynamics and applying a range of structural descriptors, such as the ability to form specific contacts with the catalytic dyad residues of 3CL pro and the structural fluctuations of the ligands in the binding site, we are able to further refine our compound selection. Fourteen compounds including estradiol shown to be the most promising based on our calculations were procured and screened against recombinant 3CL pro in a fluorescence assay. Eight of these compounds have significant activity in inhibiting the SARS-CoV-2 main protease. Among these are corilagin, a gallotannin, and lurasidone, an antipsychotic drug, which emerged as the most promising natural product and drug, respectively, and might thus be candidates for drug repurposing for the treatment of COVID-19. In addition, we also tested the inhibitory activity of testosterone, and our results reveal testosterone as possessing moderate inhibitory potency against the 3CL pro enzyme, which may thus provide an explanation why older men are more severely affected by COVID-19.

Discovery of SARS-CoV-2 MproPeptide Inhibitors from Modelling Substrate and Ligand Binding

“…6 and Figure S3. 19). Docking of p13 and p15 remained challenging, possibly due to the difficulty of recognising a larger Leu (p13) or Ile (p15) residue in the S4 pocket, which originally accommodates a Val side chain.…”

“…11,12 Multiple crystallographic and computational modelling studies concerning the M pro mechanism [13][14][15][16] and inhibition are available. [17][18][19][20][21][22] (For a list of modelling studies on M pro and related coronaviruses, see the CORD-19 database 23 ). It is proposed that during M pro catalysis, His-41 deprotonates the Cys-145 thiol, which then reacts with the carbonyl of the scissile amide to give an acyl-enzyme intermediate stabilised by a hydrogen bond network that includes the scissile amide carbonyl in an 'oxyanion hole'.…”

Potential Mechanisms of Action of Chinese Patent Medicines for COVID-19: A Review

“…The responsibility of SARS-CoV-2 3CLpro is to cleave polyproteins and generate functional enzymes. Without it, the entire replication architecture will not work properly (Loschwitz et al, 2021). So 3CLpro is considered to be a necessary target in the process of viral replication.…”

Natural Products, Alone or in Combination with FDA-Approved Drugs, to Treat COVID-19 and Lung Cancer

“…Corilagin has been reported to inhibit SARS-CoV-2 infection with an EC 50 value of 0.13 μM in a concentration-dependent manner by preventing the conformational change of RdRp and inhibits SARS-CoV-2 replication [ 36 ]. Furthermore, corilagin, as identified via molecular dynamics simulation-guided studies, could also be used as an endogenous M pro candidate, with an 88% anti-SARS-CoV-2 M pro activity at concentrations of 20 μM in vitro [ 37 ].…”