Targeting the N- and C-terminal of nucleocapsid protein of SARS-CoV-2 for identification of small molecules through virtual screening
SARS-CoVnucleocapsid (N) protein is the most abundant protein in the virus-infected cells. The N protein is involved in packing the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. The n- and c-terminal domains are responsible for viral genome binding and nucleocapsid dimerization/oligomerization, respectively. Targeting both the terminal requires homology modeling of n- and c-terminal using XRay PDB templates. The robustness of the homology model should be evaluated by the Ramachandran plot and carry out MD simulation to check the stability of backbone. Furthermore, the RNA binding site at n-terminal and dimer formation site at c-terminal may be used for binding site characterization prior to screen the chemical libraries. Submit at least top 25% (max. 100) or top 100 hits fulfilling the listed parameters as per the guidelines.