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A Phytochemical-based Medication Search for the SARS-CoV-2 Infection by Molecular Docking Models towards Spike Glycoproteins and Main Proteases

Publication Type : Journal Article

Thematic Areas : Nanosciences and Molecular Medicine

Publisher : RSC Adv,

Source : RSC Adv, Volume 11, 12003-12014 (2021)

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Campus : Amritapuri, Kochi

School : Center for Nanosciences, School of Biotechnology

Center : Amrita Centre for Advanced Research in Ayurveda (ĀCĀRA), Amrita Center for Nanosciences and Molecular Medicine Move

Department : Nanosciences and Molecular Medicine

Year : 2021

Abstract : Identifying best bioactive phytochemicals from different medicinal plants using molecular docking techniques demonstrates a potential pre-clinical compound discovery against SARS-CoV-2 viral infection. The in silico screening of bioactive phytochemicals with the two druggable targets of SARS-CoV-2 by simple precision/extra precision molecular docking methods was used to compute binding affinity at its active sites. phyllaemblicin and cinnamtannin class of phytocompounds showed a better binding affinity range (−9.0 to −8.0 kcal mol−1) towards both these SARS-CoV-2 targets; the corresponding active site residues in the spike protein were predicted as: Y453, Q496, Q498, N501, Y449, Q493, G496, T500, Y505, L455, Q493, and K417; and Mpro: Q189, H164, H163, P168, H41, L167, Q192, M165, C145, Y54, M49, and Q189. Molecular dynamics simulation further established the structural and energetic stability of protein–phytocompound complexes and their interactions with their key residues supporting the molecular docking analysis. Protein–protein docking using ZDOCK and Prodigy server predicted the binding pose and affinity (−13.8 kcal mol−1) of the spike glycoprotein towards the human ACE2 enzyme and also showed significant structural variations in the ACE2 recognition site upon the binding of phyllaemblicin C compound at their binding interface. The phyllaemblicin and cinnamtannin class of phytochemicals can be potential inhibitors of both the spike and Mpro proteins of SARS-CoV-2; furthermore, its pharmacology and clinical optimization would lead towards novel COVID-19 small-molecule therapy.

Cite this Research Publication : Anju Choorakott Pushkaran, Prajeesh Nath EN, Ram Manohar P., Anu R. Melge, and Dr. Gopi Mohan C., “A phytochemical-based medication search for the SARS-CoV-2 infection by molecular docking models towards spike glycoproteins and main proteases”, RSC Adv, vol. 11, 12003-12014, 2021.

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