Novel Inhibitors of the Main Protease of SARS-CoV-2 Identified via a Molecular Dynamics Simulation-Guided in Vitro Assay

Abstract

<div>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.</div>

Therapeutic Potentials of Antiviral Plants Used in Traditional African Medicine With COVID-19 in Focus: A Nigerian Perspective

“…A recent CADD-directed fluorogenic enzyme inhibition assay reported corilagin and rhoifolin, two natural products of African origin, with micromolar range inhibitory activity against the main protease (3CLpro) enzyme of the SARS-CoV2 ( Loschwitz et al, 2020 ). Interestingly, the investigation which had commenced with the screening of an over 1.2 million virtual compound library ( Olubiyi et al, 2020 ) identified corilagin and rhoifolin in the top eight compounds with respect to main protease inhibitory activity.…”

Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS

“…To test the reliability of the resulting force field parameters, we applied them in energy minimizations of the 160 molecules using their structures as obtained from docking to 3CL pro [15] , which were also used for the force field parameterization as starting structures. These calculations were realized with GROMACS 2018 [16] .…”

“…Afterwards, we applied the newly derived force field parameters in 20 ns MD simulations of the molecules docked to 3CL pro using GROMACS 2018 and AMBER14SB [18] as force field for the protein. For 99 of the ligands that fulfilled specific structural requirements for inhibitor design reported in [15] , the MD simulations were extended to 100 ns. All MD simulations (whether 20 ns or 100 ns) finished successfully without any stability or incompatibility issues arising.…”