Next Generation Sequencing Analysis of NSP5 NSP6 and NSP7 SARS CoV-2 Nonstructural Protein with Bio-Python

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) an extremely pathogenic and transmissible virus that emerged in 2019, and caused global pandemic. The rapid mutation or evolution of various strains necessitates the analysis of its non-structural proteins using bioinformatics tools for therapeutic and drug design approaches. The virus consists of structural proteins like spike (S), nucleocapsid (N), membrane (M), and envelope (E). It binds to the ACE2 receptor via the S protein and uses the host's machinery to replicate and causes an immune response. This response can lead to cytokine storms and organ damage. Bioinformatics tools are used to analyse these proteins, and developed therapeutic development. Next-generation sequencing (NGS) and molecular docking tools accelerate drug discovery, while computational approaches help in predicting immune responses and developing vaccines. Initially protein samples of NSP 5 and NSP 6 and 7 were analysed with tool Prosite, to understand protein function, significant biological sites, and motifs. The ORF finder tool identified open reading frames in the RNA sequence, indicating potential viral replication sites. Potential docking sites for protein-ligand interactions were identified using the CB-Dock server, which evaluates binding affinity. The Deep Fold tool with GNN and RNN was used to predict protein structures, compatibility and compactness. Bio-python provided detailed structural information, including atom and residue distances and angles. For epitope prediction, the Bepipered linear epitope prediction tool identified B cell epitopes and developed reverse vaccinology and diagnostics. The analysis of protein samples 8OKB and 7MB6 of (NSP5, NSP6 and NSP7) for predicting protein structures and developing targeted drug delivery. This comprehensive approach offers significant insights into the structural and functional characteristics of SARS-CoV-2 non-structural proteins.