Plant-Based Phytochemical Screening by Targeting Main Protease of SARS-CoV-2 to Design Effective Potent Inhibitors

SIMPLE SUMMARY: Virtual screening schemes, including molecular docking in conjunction with molecular dynamics simulation, were accomplished, as they extend an ample opportunity to screen plausible inhibitors of the main protease from an extensive phytochemical library. The preferential phytochemicals were retrieved from Asian plants through the data mining procedure and comprehensive literature study. The three preeminent reliable phytochemical exhibited toxicity by no means during the scrutinization of ADMET prominences. Moreover, pharmacologically distinguishing characteristics and the biological activity of the lead phytochemicals were satisfying as a repurposing antiviral drug contender. Additionally, the molecular dynamics simulation exhibited thermal stability and a stable binding affinity of the protein-compound complex that refers to the appreciable efficacy of the lead optimization. Therefore, the preferable phytochemicals are worth substantial evaluation in the biological laboratory to recommend plausible antiviral drug contenders. ABSTRACT: Currently, a worldwide pandemic has been declared in response to the spread of coronavirus disease 2019 (COVID-19), a fatal and fast-spreading viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The low availability of efficient vaccines and treatment options has resulted in a high mortality rate, bringing the world economy to its knees. Thus, mechanistic investigations of drugs capable of counteracting this disease are in high demand. The main protease (M(pro)) expressed by SARS-CoV-2 has been targeted for the development of potential drug candidates due to the crucial role played by M(pro) in viral replication and transcription. We generated a phytochemical library containing 1672 phytochemicals derived from 56 plants, which have been reported as having antiviral, antibacterial, and antifungal activity. A molecular docking program was used to screen the top three candidate compounds: epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate, which had respective binding affinities of −8.4, −8.5, and −8.8 kcal/mol. Several active sites in the targeted protein, including Cys145, His41, Met49, Glu66, and Met165, were found to interact with the top three candidate compounds. The multiple simulation profile, root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and solvent-accessible surface area values supported the inflexible nature of the docked protein–compound complexes. The toxicity and carcinogenicity profiles were assessed, which showed that epicatechin-3-O-gallate, psi-taraxasterol, and catechin gallate had favorable pharmacological properties with no adverse effects. These findings suggest that these compounds could be developed as part of an effective drug development pathway to treat COVID-19.