SARS-CoV–2 infects alveolar epithelial cells via receptor-mediated endocytosis by binding to the angiotensin-converting enzyme II (ACE2) receptor33. The viruses multiply following entry into host cells. The multiplication of RNA viruses depends upon the simple strategies of replication and transcription. The RDRP protein, encoded by the RdRp gene, plays a central role in the replication of RNA viruses7. Therefore, the RDRP protein is a potential antiviral drug target7. Furthermore, as the 2019-nCoV/SARS-CoV–2 share the highest nucleotide sequence identity34, the virus-human PPI networks were analysed using the SARS coronavirus database in STRING for identifying the potent druggable targets of SARS-CoV-2. Analysis of the virus-human PPI network revealed that the RDRP (NSP12) of SARS-CoV- 2 is associated with the human proteins, XPO1 and SPECC1, via the viral proteins 9b and nsp8, respectively. The human protein, XPO1, also known as exportin–1, mediates the nuclear export of proteins and certain RNAs29,31. The SPECC1 (sperm antigen with calponin homology and coiled-coil domains 1) protein, that is primarily expressed in the testes and plays a role in the organisation of the actin cytoskeleton30. The association of RDRP with the viral proteins, 9b and nsp8, indicated that it might be possible that RDRP mediates the interactions of 9b and nsp8 with XPO1 and SPECC1, respectively. This, combined with the fact that RDRP is a potential antiviral target7, led us to consider that the RDRP (NSP12) of SARS-CoV–2 was a potential target for drug discovery. We therefore selected RDRP as a potential target for drug repurposing against SARS-CoV–2. Analysis of the motifs in the NSP12 protein revealed that five copies of motif A are present in the NSP12 protein of SARS-CoV–2. A study by Chou and Wang in 2015 revealed that the presence of D/E-rich repeats in proteins in associated with transcriptional regulation, DNA mimicry, and mRNA processing39. It was found that motif A is rich in aspartic acid, and the presence of aspartic acid-rich repeats correlates with the fact that the RDRP domain catalyses RNA-dependent RNA transcription and plays a crucial role in viral replication. Several drugs, including chloroquine, baricitinib, remdesivir, lopinavir, and ritonavir, that are used to treat malaria, rheumatoid arthritis, and SARS-CoV infections, have been considered as potential drug candidates for the treatment of SARS-CoV–2 infections35,36.
SARS-CoV–2 is a novel strain of coronavirus that was first reported in Wuhan, China in December 2019, and has caused more than 21,031 deaths to date. The WHO is calling for “urgent, aggressive actions” for combating the pandemic. By employing a drug repurposing strategy, we aimed to identify plausible drug candidates from DrugBank against the NSP12 protein of SARS-CoV–2, which possesses the RDRP activity that is crucial for viral replication. We employed sequence-based and structure-based computational approaches for screening drug candidates from DrugBank. A homology model of the NSP12 protein of SARS-CoV–2 protein was constructed using the PDB template 6NUR, and refined by 10 ns MD simulations. Druggability analysis of the NSP12 protein of SARS-CoV–2 revealed the presence of two druggable sites. The druggable sites were mapped to the conserved domains in NSP12, which revealed that druggable site 2 mapped to the RDRP domain of NSP12. This indicated that site 2 would be a potential target site for inhibiting SARS-CoV–2, as targeting this site it would inhibit the RNA-dependent replication of viral RNA. We therefore selected site 2 as a potential druggable site for targeting SARS-CoV–2. Initially, the 13,533 entries in DrugBank were screened by performing a BLAST using the sequence of CoVID–19 NSP12 as target. The 7 drug hits that were obtained were docked to the druggable site in the RDRP protein, using a consensus docking and scoring approach. The rank of the top scoring hits, compound 5 and compound 3, agreed between the Glide SP and Glide XP hitlists, indicating that the binding of these two compounds did not occur randomly. The compounds interacted with the RDRP domain via hydrogen bonds, hydrophobic interactions, and pi-pi stacking interactions. Compounds 5 and 3 are experimental small molecules and the docking scores of the compounds were consistently better that compound 7, in both the docking platforms. Compound 7, remdesiver, is being presently studied in other clinical trials against 37. Previous studies have demonstrated that remdesivir (compound 7) can bind to the RDRP of SARS- CoV–2 and inhibit the virus in vitro35,38. We observed that the Glide SP and Glide XP scores of compounds 5 and 3 were higher than that of remdesivir (compound 7), indicating that these compounds might have better inhibitory properties against the RDRP activity of SARS- CoV–2.