Molecular docking of SARS-CoV-2 proteins against selected ligands
1M. Ibtisam Khan, 1N. Rajesh, 2Anu Prasanna Vankara and 1*K. Riazunnisa
1*Department of Biotechnology and Bioinformatics, 2*Department of Zoology, Yogi Vemana University, Vemanapuram, YSR district -516005 (India) *Corresponding author: E-mail khateefriaz@gmail.com; krbtbi@yogivemanauniversity.ac.in Contact: 09966863416
ABSTRACT
The outburst of COVID-19 (SARS-CoV-2) creates an unrivalled cause to human health all across the world and society. The growth of proper treatments is criticized in condition. Available drugs were present but with severe adverse effects. Hence in order to reduce an alternative medication is needed. Spike protein, Nucleocapsid protein, RNAdependent- RNA-polymerase (RdRp), Mpro (Main protease), PLpro (Papain-like protease) are the proteins coronavirus (COVID-19) has various functions in its life cycle. Spike protein is an envelope protein that mostly interacts with the assembly of the virus and plays a crucial role in propounding the host cells and starting off with infection. RdRp is involved in genome expression like RNA synthesis, capping and proofreading. Mpro mediates the replication of virus and transcription. PLpro plays an important role in processing polyproteins of virus, maturation and virus assemblage. Hence in order to reduce the side effects, the present study focused on the molecular docking of selected ligands with coronavirus proteins. Autodock vina was used for docking proteins and ligands of COVID-19. Among various ligands, carbamic acid shows the least binding affinities i.e., -10.7 kcal/mol with spike protein. The docking results indicate that the active binding pockets presuppose the amino acid residues – Asn142, Asp2, Thr24, Thr25, Thr26, Thr45, Asn37, Arg80, Trp29, Thr84, Arg188, Thr190, Arg262, Arg259, Arg88, Arg107, Arg319, Ile292, Glu323, Thr332, Ile357, Ala4, Ala40, Thr49, Thr57, Ile94, Ile130 and Glu118. Eventually, for the initial time, this computational study assumes the perspective of carbamic acid as a therapeutic strategy that acts against SARS-CoV-2. Network interactions of spike protein reveal that transmembrane proteases were involved in protein-protein interaction with spike protein of SARS-CoV-2. Further optimization of these protein-protein interactions and docking could lead to promising drugs against SARS-CoV-2.