Molecular Docking Studies of Coronavirus Proteins with Medicinal Plant Based Phytochemicals

Avinash Marwal; Mukesh Meena; RK Gaur

doi:10.14429/dlsj.6.15704

Avinash Marwal Assistant Professor, Department of Biotechnology, Vigyan Bhawan - Block B New Campus, Mohanlal Sukhadia University, Udaipur - 313001, Rajasthan, India Mobile: +917023005538, Office: +912942470071, http://orcid.org/0000-0003-2163-8057
Mukesh Meena Mohanlal Sukhadia University, Udaipur – 313 001, India https://orcid.org/0000-0002-6336-1140
RK Gaur Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur – 273 009, India https://orcid.org/0000-0003-4550-0730

DOI: https://doi.org/10.14429/dlsj.6.15704

Keywords: SARS-CoV-2, COVID-19, Docking, Coronavirus, Proteins, Medicinal plants, Phytochemicals, Ligand, DockThor, Antivirals

Abstract

In this study, we presented an in silico molecular docking between the SARS-CoV-2 four proteins [(a) SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (6M3M), (b) Nsp9 RNA binding protein of SARS CoV-2 (6W4B), (c) The crystal structure of COVID-19 main protease in apo form (6M03), and (d) Structure of the 2019-nCoV HR2 Domain (6LVN)] available in the PDB (Protein Data Bank), and the medicinal plant-based phytochemicals (retrieved from PubChem database) as ligand molecules i.e. Piperine (Black Pepper), Eugenol (Clove), Alliin (Garlic), Gingerol (Ginger) and Curcumin (Turmeric). All these ligand molecules showed good docking with their respective receptor molecules and their scores range from -8.195 to -5.263. DockThor Portal (a receptor ligand-docking server) which was recently developed and published this year were used in the current study. The obtained results might help in the wet lab conditions to develop better antiviral compounds against SARS-CoV-2.