Research
Research Interest
We are investigating the inhibitors for the structural protein of the SARS CoV-2 and characterising their effect on the protein's structural and functional stability through biophysical approaches. We have set up a high-throughput virtual screening to find suitable inhibitors and validate the inhibitors through molecular dynamic simulation against the conserved binding pocket of the SARS CoV-2 structural protein. Based on binding energy, affinity, and residues involved in binding, the best inhibitors will be selected and further validated by biophysical techniques like absorption spectroscopy, fluorescence quenching, ITC, CD, and DLS. The selected antiviral agents will be evaluated in cell cultures using an engineered pseudotyped virus expressing the structural gene for antiviral activity, efficacy, toxicity, etc. The in vitro result will be utilised to evaluate the therapeutic potential of the inhibitors in the animal model. The results will likely help frame future contributions toward formulating therapeutic agents against Covid19 infection.
pH induced structural and conformational changes in Nucleocapsid protein leads to intermediate like conformation
In this study, we report conformational measurements of N protein at different pH by observing transition in secondary and tertiary structural contents by biophysical and computational approaches. Spectroscopic measurements revealed that N protein loses its secondary and tertiary structure at extreme acidic pH while maintaining its native conformation at mild acidic and alkaline pH. MD simulation studies validated spectroscopic findings. Secondary structure estimation confirmed CD findings that participation of total number of average residues in formation of native structure is higher at physiological pH, and coil percentage is higher at acidic pH. In MG state, secondary structure is conserved but here, CD data reveals more random structure at low pH. In PMG, ANS binds weakly to protein as compared to MG but here, ANS binds strongly to protein. All the above-mentioned findings suggested formation of intermediary like state at low pH, which can be attributed to an off-pathway species. Unravelling structural characteristics of N protein will help understand phase-separation, protein-protein interaction, and host-immune response modulation behavior, which will eventually help in designing novel therapeutic target against COVID-19.
(Published in JBSD 2024)
