Phytochemicals from Selective Plants Have Promising Potential against SARS-CoV-2: Investigation and Corroboration through Molecular Docking, MD Simulations, and Quantum Computations

Abstract

Coronaviruses have been reported previously due to their association with the severe acute respiratory syndrome (SARS). After SARS, these viruses were known to be causing Middle East respiratory syndrome (MERS) and caused 35% evanescence amid victims pursuing remedial care. Nowadays, beta coronaviruses, members of Coronaviridae, family order Nidovirales, have become subjects of great importance due to their latest pandemic originating from Wuhan, China. The virus named as human-SARS-like coronavirus-2 contains four structural as well as sixteen nonstructural proteins encoded by single-stranded ribonucleic acid of positive polarity. As there is no vaccine available to treat the infection caused by these viruses, there is a dire need for taking necessary steps against this virus. Herein, we have targeted two nonstructural proteins of SARS-CoV-2, namely, methyltransferase (nsp16) and helicase (nsp13), respectively, due to their substantial activity in viral pathogenesis. A total of 2035 compounds were analyzed for their pharmacokinetics and pharmacological properties. The screened 108 compounds were docked against both targeted proteins and were compared with previously reported known compounds. Compounds with high binding affinity were analyzed for their reactivity through DFT analysis, and binding was analyzed using molecular dynamics simulations. Through the analyses performed in this study, it is concluded that EryvarinM, Silydianin, Osajin, and Raddeanine can be considered potential inhibitors for MTase, while TomentodiplaconeB, Osajin, Sesquiterpene Glycoside, Rhamnetin, and Silydianin for helicase after these compounds are validated thoroughly using in vitro and in vivo protocols.

Structure-Based Designing, Solvent Less Synthesis of 1,2,3,4-Tetrahydropyrimidine-5-carboxylate Derivatives: A Combined In Vitro and In Silico Screening Approach

“…The average RMSD descriptor of all the docked compounds were calculated to corroborate their stability in biological system [ 28 , 29 , 30 ]. As the justified threshold for RMSD calculation is 2 Å, its mean average RMSD value of all the complexes less than this threshold provides us with the proof that our docking process is validated, as having RMSD for anti-cancer docking protocol 2.0 Å, for anti-diabetic 1.35 Å and for anti-oxidant 0.71 Å [ 31 , 32 , 33 , 34 ].…”

Analysis of SYK Gene as a Prognostic Biomarker and Suggested Potential Bioactive Phytochemicals as an Alternative Therapeutic Option for Colorectal Cancer: An In-Silico Pharmaco-Informatics Investigation

“…Therefore, this parameter measures the compactness of the protein molecule and gives us a deeper understanding of the protein’s folding properties [ 80 ]. Additionally, a higher Rg value signifies slackpacking, whereas a lower Rg value reveals compact packing [ 81 ]. Figure 8 shows all the Rg values, among which glabridin had the best matching capacity (28.4) compared to the control ligand (CAP, 28.45).…”

Evaluation of SYK Gene as a Prognostic Biomarker and Suggested Aromatic Potential Phytochemicals to Halt the Colorectal Cancer

“…Molecular docking is the process that estimates how two or more molecules bind together with the best structural confirmation as well as the lowest binding energy. More significant and efficient drug candidates were selected depending on the scoring value of molecular docking via the PyRx virtual screening tool [Version: 0.8] [82]. The docking operation for five phytochemicals as well as a control molecule with receptor 4GX3 and found the docking score of control was -6.5 Kcal/mol.…”