Shalini SwamiUniversity of Delhi, India
Title: In Silico therapeutic approach for potential interventions against SARS CoV-2 Receptor Binding Domain of Delta variant (B.1.617.2)
The availability of few effective interventions and the acquisition of novel variants of severe acute respiratory syndrome coronavirus (SARS-CoV-2) has caused an increase in the death toll. The conventional/existing therapeutic agents respond poorly to the novel variants of SARS-CoV-2. The mandate to develop newer and more effective therapeutics to combat the spread of this deadly virus is a strict requirement. The computational structure-based drug design method is one of the robust therapeutic approaches and design strategies. Structure-based therapeutic approaches rely on the interaction between the molecule and the target protein. The virtual screening of the chemical database to retrieve 3200 drug-like molecules was performed. PDB ID 7SBO was used to create the binding pockets using SeeSAR. Ten docked poses for each molecule were generated on the RBD of the spike proteins of the Delta variant (B. 1. 617.2) of SARS-CoV-2 and ranked using the HYDE scoring function of SeeSAR. The molecules exhibiting good binding affinity, ligand-lipophilicity efficiency, minimum torsion, and intramolecular/intermolecular clashes were shortlisted and redocked to generate 100 poses. Sixty leads with a good binding affinity of <300nm, without torsional and intermolecular clashes, were analyzed and selected. Five molecules, namely Z366605568 and Z414796914, have shown a predictive binding affinity of 1.92-191.53 nm and 3.01-299.30 nm. Moreover, Z434334252, Z1143051815, and Z1360092881 were shown to have a binding affinity of 3.61-359.19 nm, 3.67-364.73 nm, and 3.87-384.95 nm, respectively. The binding affinity in the nanomolar range with key residues CYS379, THR376, LEU425, ALA435, LYS378, ILE402, VAL510, GLY431, PHE429 PRO412 ALA411, VAL433, VAL407, ARG408, and TYR380 of RBD of the spike protein is suggestive of strong interaction could be a potential anti-viral therapeutics to impede the SARS CoV-2 infection.
Shalini Swami has completed her PHD From the University of Manchester, United Kingdom. She has done her Postdoctoral studies from Texas Agriculture and Mechanical University, Texas, USA. She is also the awardee of “National Overseas Scholarship” from Ministry of Social Justice and Empowerment, Government of India. Presently she is working as an Assistant Professor in the Department of Microbiology, Ram Lal Anand College, University of Delhi and she has supervised many students in the projects as Principal Investigator. She has publications in international and national journals of high repute.