An insight into the simulation directed understanding of the mechanism in SARS CoV-2 N-CTD, dimer integrity, and RNA-binding: Identifying potential antiviral inhibitors

Abstract

Coronavirus 2019 is a transmissible disease and has caused havoc throughout the world. The present study identifies the novel potential antiviral inhibitors against the nucleocapsid C-terminal domain that aids in RNA-binding and replication. A total of 485,629 compounds were screened, and MD was performed. The trajectory analysis (DCCM & PCA), structural integrity, and degree of compaction depicted the protein-ligand complex stability (PDB-PISA and R_gyr). Results obtained from screening shortlists 13 compounds possessing high Docking score. Further, seven compounds had a permissible RMSD limit (3 Å), with robust RMSF. Post-MD analysis of the top two compounds (204 and 502), DCCM & PCA analysis show a positive atomic displacements correlation among residues of active sites-dimer (Chain A and Chain B) & residual clustering. The ΔG_int of RNA-bound (-83.5 kcal/mol) and drug-bound N-CTD-204 (-40.8 kcal/mol) and 502(-39.7 kcal/mol) as compared to Apo (-35.95 kcal/mol) suggests stabilization of protein, with less RNA-binding possibility. The R_gyr values depict the loss of compactness on RNA-binding when compared to the drug-bound N-CTD complex. Further, overlapping the protein complexes (0 ns and 100 ns) display significant changes in RMSD of the protein (204-2.07 Å and 502-1.89 Å) as compared to the Apo (1.72 Å) and RNA-bound form (1.76 Å), suggesting strong interaction for compound 204 as compared to 502. ADMET profiling indicates that these compounds can be used for further experiments (in vitro and pre-clinical). Compound 204 could be a promising candidate for targeting the N-protein-RNA assembly and viral replication.

Graphical abstract

Communicated by Ramaswamy H. Sarma

Keywords:

• Dimer structural integrity
• molecular dynamics simulations (MD)
• nucleocapsid C terminal domain
• radius of gyration (R_gyr)
• severe acute respiratory syndrome coronavirus 2 (SARS CoV-2)

Disclosure statement

All the authors declare no conflict of interest.

Data and software availability

The X-RAY crystallized structure of the nucleocapsid protein chosen was PDB-ID (7C22) (https://www.rcsb.org/structure/7C22). The protein preparation, modeling, molecular docking simulations operations were performed on Maestro (release 2020-4), Schrödinger, LLC, New York, NY, the USA. The ligand libraries were retrieved from www.asinex.com/libraries-html/. PDBePISA v.1.48 (open source) was used to explore the macromolecular interfaces and calculate the protein assembly interaction energy https://www.ebi.ac.uk/pdbe/pisa/. Using the Bio3d v.2.4-1.9000 (http://thegrantlab.org/bio3d/) package in R studio v1.4.1103, MD trajectories of protein-ligand complexes was obtained by examining the Dynamical Cross-Correlation Matrix (DCCM) and Principal Component Analysis (PCA) (https://rstudio.com/products/rstudio/download-commercial-desktop/)