An in silico approach to target RNA-dependent RNA polymerase of COVID-19 with naturally occurring phytochemicals

The novel coronavirus disease 2019 (COVID-19) was firstly reported from Wuhan city of China and found as a highly contagious, transmittable and pathogenic viral infection. The World Health Organization declared COVID-19 as a pandemic since its emergence from China. The RNA-dependent RNA polymerase (nsp-12) is a complex with nsp-7 and nsp-8 cofactors and is a major constituent of viral replication and RNA synthesis machinery. In the current study, the RdRp of the virus was selected as a receptor protein for computational drug discovery. Computational homology modelling was done in order to find the hidden secondary structures and structural assessment of the viral protein to target them via antiviral drugs. The study was based on molecular docking of different phytochemicals to check their potentials against viral replicative proteins. Out of 200 ligands used in this study from different plants, the best ten were selected based on drug discovery parameters such as S-score, ligand interactions, hydrophobic interactions and druglikeness. The ten best selected ligands were found to be verbenalin, epigallocatechin, swertisin, nobiletin, pinoresinol, caftaric acid, hesperetin, islandicin, neochlorogenic acid and sesamin that exploit the potency as antagonists of viral protein. Among binding interactions of all ligands, Arg339 centred as the main interacting residue among almost all the ligands. Till now, many antiviral agents have shown potency in only mild cases of SARS-CoV-2, but no effective drug has been found for critical pulmonary cases. In clinical trials, many broad-spectrum antiviral agents have been still in trial periods of testing against SARS-CoV-2. Till date, no effective drug or vaccine has been validated with significant efficacy and potency against the SARS-CoV-2; therefore, there is an urgent need to design effective vaccine against nCoV-19 infection.