Identification of potential natural inhibitors of SARS-CoV2 main protease by molecular docking and simulation studies

Abstract

Coronaviruses are contagious pathogens primarily responsible for respiratory and intestinal infections. Research efforts to develop antiviral agents against coronavirus demonstrated the main protease (Mpro) protein may represent effective drug target. X-ray crystallographic structure of the SARS-CoV2 Mpro protein demonstrated the significance of Glu166, Cys141, and His41 residues involved in protein dimerization and its catalytic function. We performed in silico screening of compounds from Curcuma longa L. (Zingiberaceae family) against Mpro protein inhibition. Employing a combination of molecular docking, scoring functions, and molecular dynamics simulations, 267 compounds were screened by docking on Mpro crystallographic structure. Docking score and interaction profile analysis exhibited strong binding on the Mpro catalytic domain with compounds C1 (1E,6E)-1,2,6,7-tetrahydroxy-1,7bis(4-hydroxy-3-methoxyphenyl)hepta-1,6-diene-3,5-dione) and C2 (4Z,6E)-1,5-dihydroxy-1,7-bis(4hydroxyphenyl)hepta-4,6-dien-3-one as lead agents. Compound C1 and C2 showed minimum binding score (-9.08 and -8.07 kcal/mole) against Mpro protein in comparison to shikonin and lopinavir (% À5.4 kcal/mole) a standard Mpro inhibitor. Furthermore, principal component analysis, free energy landscape and protein-ligand energy calculation studies revealed that these two compounds strongly bind to the catalytic core of the Mpro protein with higher efficacy than lopinavir, a standard antiretroviral of the protease inhibitor class. Taken together, this structure based optimization has provided lead on two natural Mpro inhibitors for further testing and development as therapeutics against human coronavirus.

Lopinavir-ritonavir is not an effective inhibitor of the main protease activity of SARS-CoV-2in vitro

“…Since lopinavir responds differently to SARS-CoV Mpro and SARS-CoV-2 Mpro, we wondered if structural differences between the two Mpro proteins could account for the disparity. Previous computational analysis studies listed the potential amino acid residues responsible for the interaction between Mpro and lopinavir [10,[14][15][16]. Because SARS-CoV-2 Mpro shares 96.08% identity with SARS-CoV Mpro, most of the listed amino acids are identical [12].…”

“…Among the potential amino acids responsible for the interaction with lopinavir, we found just one amino acid difference. Serine residue 46 of SARS-CoV-2 Mpro is one of the candidate amino acids for the interaction with lopinavir [10], however both SARS-CoV and MERS-CoV bear an alanine residue at that site in their Mpro protein sequences. Although the sequence differences are not substantial, these trivial sequence differences may contribute to the disparity in Mpro response to lopinavir.…”

“…Lopinavir is known to be an inhibitor of the SARS-CoV main protease (Mpro, also known as 3CL protease), and recent bioinformatics studies showed that lopinavir may interact with Mpro of SARS-CoV-2 [10,11]. For this reason, lopinavir was assumed to inhibit Mpro of SARS-CoV-2, however no evidence of this has been presented.…”

Identification of evolutionarily stable sites across the SARS-CoV-2 proteome

“…However, drug e cacy of top hits might be cell line speci c (17) and the mechanisms of drug action may be unclear or acting through modulation of the host cell rather than targeting the virus itself. In silico docking studies (19,62) take a more targeted approach towards speci c SARS-CoV-2 sites that may complement the results of experimental screens. Knowledge of the ligand binding site improves the chance of identifying drugs that inhibit protein function and although structural characterization of SARS-CoV-2 proteins is unprecedented, the structural information available is far from comprehensive.…”

“…However, the antiviral activity in these large-scale screens may, in part, be cell-line speci c (17), and therefore of unclear clinical relevance. Another approach to screen potential drugs for repurposing is to perform docking (18) of clinical-stage or FDA-approved drugs to the SARS-CoV-2 proteome (19,20). However, selection of the correct binding sites on the target proteins is crucial and di cult as protein surface cavities far exceed actual ligand binding sites that modulate function (21).…”