Targeting Omicron (B.1.1.529) SARS CoV-2 spike protein with selected phytochemicals:  an in-silico approach for identification of potential drug

Hardeep Tuli; Poonam Bansal; Varruchi  Sharma; Ranjan K.  Mohapatra; Kuldeep  Dhama; Priti; Anil K Sharma

doi:10.18006/2022.10(2).396.404

Authors

Hardeep Tuli Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, Haryana, India
Poonam Bansal Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, Haryana, India
Varruchi Sharma Department of Biotechnology & Bioinformatics, Sri Guru Gobind Singh College, Chandigarh
Ranjan K. Mohapatra Department of Chemistry, Government College of Engineering, Keonjhar-758002, Odisha, India
Kuldeep Dhama Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly-243 122, Uttar Pradesh, India
Priti Department of Biotechnology, K.L. Mehta Dayanand College for Women, Faridabad
Anil K Sharma Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, Haryana, India

DOI:

https://doi.org/10.18006/2022.10(2).396.404

Keywords:

SARS-CoV-2, Omicron variant, Phytochemicals, Molecular docking, Drugs

Abstract

Severe acute respiratory syndrome coronavirus -2 (S ARS-CoV-2) emerging variants particularly those of concern contain numerous mutations that influence the behavior and transmissibility of the virus and could adversely affect the efficacies of existing coronavirus disease 2019 (COVID-19) vaccines and immunotherapies. The emerging SARS-CoV-2 variants have resulted in different waves of the pandemic within the ongoing COVID-19 pandemic. On 26 November 2021 World Health Organization designated omicron (B.1.1.529) as the fifth variant of concern which was first reported from South Africa on November 24, 2021, and thereafter rapidly spread across the globe owing to its very high transmission rates along with impeding efficacies of existing vaccines and immunotherapies. Omicron contains more than 50 mutations with many mutations (26-32) in spike protein that might be associated with high transmissibility. Natural compounds particularly phytochemicals have been used since ancient times for the treatment of different diseases, and owing to their potent anti-viral properties have also been explored recently against COVID-19. In the present study, molecular docking of nine phytochemicals (Oleocanthal, Tangeritin, Coumarin, Malvidin, Glycitein, Piceatannol, Pinosylnin, Daidzein, and Naringenin) with omicron spike protein (7QNW (electron microscopy, resolution 2.40 Å) was done. The docking study revealed that selected ligands interact with the receptor with binding energy in the range of -6.2 to-7.0 kcal/mol. Pinosylnin showed the highest binding energy of -7.0 kcal/mol which may be used as potential ligands against omicron spike protein. Based on the docking studies, it was suggested that these phytochemicals are potential molecules to be tested against omicron SARS-CoV-2 and can be used to develop effective antiviral drugs.

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