Structural Landscape of nsp Coding Genomic Regions of SARS-CoV-2-ssRNA Genome: A Structural Genomics Approach Toward Identification of Druggable Genome, Ligand-Binding Pockets, and Structure-Based Druggability

SARS-CoV-2 has a single-stranded RNA genome (+ssRNA), and synthesizes structural and non-structural proteins (nsps). All 16 nsp are synthesized from the ORF1a, and ORF1b regions associated with different life cycle preprocesses, including replication. The regions of ORF1a synthesizes nsp1 to 11, and ORF1b synthesizes nsp12 to 16. In this paper, we have predicted the secondary structure conformations, entropy & mountain plots, RNA secondary structure in a linear fashion, and 3D structure of nsp coding genes of the SARS-CoV-2 genome. We have also analyzed the A, T, G, C, A+T, and G+C contents, GC-profiling of these genes, showing the range of the GC content from 34.23 to 48.52%. We have observed that the GC-profile value of the nsp coding genomic regions was less (about 0.375) compared to the whole genome (about 0.38). Additionally, druggable pockets were identified from the secondary structure-guided 3D structural conformations. For secondary structure generation of all the nsp coding genes (nsp 1-16), we used a recent algorithm-based tool (deep learning-based) along with the conventional algorithms (centroid and MFE-based) to develop secondary structural conformations, and we found stem-loop, multi-branch loop, pseudoknot, and the bulge structural components, etc. The 3D model shows bound and unbound forms, branched structures, duplex structures, three-way junctions, four-way junctions, etc. Finally, we identified binding pockets of nsp coding genes which will help as a fundamental resource for future researchers to develop RNA-targeted therapeutics using the druggable genome. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12033-022-00605-x.