Research Article: In Silico Identification of Potential Inhibitors Targeting NUSAP1, A Hub Gene in Hepatocellular...

Nucleolar-spindle-associated protein 1 (NUSAP1) participates in the assembly of microtubules and the mitotic spindle. Mitotic spindles are microtubule-based structures that segregate chromosomes during mitosis. Its overexpression and knockdown caused alterations in gene expression programs linked to tumor progression. It was also identified as one of the potential hub genes in various cancers, including the mediation of hepatocellular carcinoma. The present research addresses the NUSAP1 protein structure refinement and its targeting by the lead molecules identified using various computational approaches. The initial structure of NUSAP1 from the Alpha fold database is evaluated using the Ramachandran plot and subjected to multiple energy minimization steps through the YASARA program. The best-optimized structure of NUSAP1 is obtained and subjected to binding site analysis and virtual screening studies using I-TASSER and Mcule webservers, respectively. From the binding site analysis, His293 was considered the ligand binding site for docking ligands by AutoDock Vina. Selected ligands from the Mcule chemical library were chosen through various filters, and 50 hits were identified for further studies. Among the 50 hits, 27 were identified as non-toxic molecules using a toxicity checker. Further, based on the RO5 violation check, 18 hits exhibited no RO5 violations. Further, for all 18 hits, LigPlot analysis was performed, and 11 hits exhibited hydrogen and hydrophobic interactions with the NUSAP1 protein. Among 11, three hits showed promising hydrogen and hydrophobic interactions near the potential binding site His293. For the promising three hits with Mcule IDs 9300000909-0-6, 9753624331-0-3, and 1764527053-0-4, ADMET properties were predicted using the PreADMET server. The comparative studies of drug-likeness properties found that all three hits do not violate Lipinski's rule of 5. The comparative studies of ADME properties of three hits found that the 9753624331-0-3 compound exhibits non-inhibiting properties in liver enzymes and p-glycoprotein inhibition. Furthermore, 9753624331-0-3 is computed as the lowest solvation-free energy of -18.1300000 and found to be non-mutagenic, negative for all toxicity studies, including the Ames test, fishes, rats, mice, and daphnia. Based on the drug-likeness, ADME, and toxicity predictions, the 9753624331-0-3 presented favorable properties and hence may be considered the potential lead targeting the NUSAP1 protein.