Functional annotation of PBK missense SNPs and dysregulation in multiple myeloma: A bioinformatics approach integrating identification of natural inhibitors

Abstract

T-LAK cell-originated protein kinase (PBK/TOPK) is a serine/threonine kinase that is essential for DNA damage repair, cell division, mitosis, and tumor growth. Deleterious missense single nucleotide polymorphisms (nsSNPs) may alter the biological activity of PBK and structural stability, thus contributing to cancer progression. Therefore, this study aimed to use an integrated computational strategy to thoroughly identify and characterize pathogenic nsSNPs in the PBK gene and evaluate their potential clinical and therapeutic relevance in multiple myeloma. Additionally, compounds from Camellia sinensis were screened to identify potential inhibitors of three PBK mutants. Multiple computational approaches were employed to evaluate the drug-likeness and binding stability of these compounds. To identify missense variations, we employed multiple prediction tools, including SIFT, SNPs&GO, PolyPhen-2, PROVEAN, MetaSNP, and FATHMM. DeepREx-WS was used to assess sequence conservation, while MutPred2 and HOPE were employed for structural evaluation. SWISS-MODEL was used to construct structural models; HDOCK, PyRx 0.8, and PyMOL (v2.3.3) were used for molecular docking, virtual screening, and docked complex visualization; and CScape and Dr. Cancer were used to predict cancer-related alterations. Among the 421 missense SNPs identified in the NCBI dbSNP database, three variants — H158P, G188E, and G188R were found to be highly conserved across species, located in protein regions forming helices or strands, and associated with decreased protein stability. Structural analysis revealed that the three mutations altered the size, charge, and hydrophobicity of the PBK protein. Docking analyses revealed differences in the binding interactions and energies of TP53 with wild-type and mutant PBK proteins. Among the seven compounds screened from Camellia sinensis, Brassinolide was the most promising candidate for the PBK mutants H158P and G188R, whereas Castasterone showed the highest affinity for the G188E mutant, indicating its potential as a targeted therapeutic agent. Analysis of muTarget gene expression and Kaplan–Meier survival data indicated that PBK mutations were associated with specific gene expression changes. However, elevated PBK expression, rather than mutation status, was significantly correlated with poor prognosis in multiple myeloma. Our comprehensive in silico research provided insights into the structural and functional consequences of the identified PBK alterations. These findings support the hypothesis that PBK may serve as a potential prognostic biomarker and therapeutic target for treating multiple myeloma.