In Silico Exploration of Novel Tubulin Inhibitors: A Combination of Docking and Molecular Dynamics Simulations, Pharmacophore Modeling, and Virtual Screening

Impact of mutations on KAT6A enzyme and inhibitory potential of compounds from Withania somnifera using computational approaches

KAT6A is an enzyme that regulates biological processes that are linked to cancer cell proliferation and metastasis. Recent studies suggest that certain compounds from Withania somnifera may inhibit cancer growth by targeting KAT6A. However, the impact of mutations on KAT6A's structure and the inhibitory potential of compounds obtained from W. somnifera remain unclear. This study investigated three mutations, K181N, R242P and R325C, using molecular docking, molecular dynamics simulations and network pharmacology to assess their effects on KAT6A's interaction with its coenzyme, acetyl-CoA (CoA), and inhibitors (WM8014, withasomniferol B, withanolide E and sitoindoside IX). The results showed that R242P and R325C mutations significantly reduced binding affinity (from -12.94 kcal/mol to -9.96 and -7.00 kcal/mol, respectively) and increased RMSD values (from 1.860 to 2.296 and 2.373, respectively) compared to K181N (-11.86 kcal/mol and 1.698), suggesting altered enzyme activity. Notably, these mutations enhanced the inhibitory effects of the compounds from W. somnifera, particularly withanolide E, which showed reduced RMSD values (2.259-2.211, 2.045 and 1.985 for K181N, R242P, and R325C, respectively). Additionally, mutant complexes showed higher binding energies, including R325C-WM8014 (-90.53 kcal/mol), K181N-CoA (-90.50 kcal/mol) and R242P-withanolide E (-82.06 kcal/mol) compared to their corresponding wild-type complexes, which exhibited -85.25 kcal/mol, -69.30 kcal/mol and -57.08 kcal/mol, respectively. Network pharmacology also revealed that the compounds from Withania somnifera target KAT6A through multiple cancer pathways like PI3K-Akt signaling, apoptosis and chemical carcinogenesis. These findings suggest that specific KAT6A mutations may enhance the efficacy of the compounds from W. somnifera. However, further research is needed to validate these results, which could advance clinical applications and drug development for KAT6A-targeted cancer therapies.

Investigation on the mechanisms by which the herbal remedies induce anti-prostate cancer activity: uncovering the most practical natural compound

Prostate cancer (PCa) is one of the most reported cancers among men worldwide. Targeting the essential proteins associated with PCa could be a promising method for cancer treatment. Traditional and herbal remedies (HRs) are the most practical approaches for PCa treatment. Here, the proteins and enzymes associated with PCa were determined based on the information obtained from the DisGeNET database. The proteins with a gene-disease association (GDA) score greater than 0.7 and the genes that have a disease specificity index (DSI) = 1 were selected as the target proteins. 28 HRs with anti-PCa activity as a traditional treatment for PCa were chosen as potential bioactive compounds. More than 500 compound-protein complexes were screened to find the top-ranked bioactives. The results were further evaluated using the molecular dynamics (MD) simulation and binding free energy calculations. The outcomes revealed that procyanidin B2 3,3'-di-O-gallate (B2G2), the most active ingredient of grape seed extract (GSE), can act as an agonist for PTEN. PTEN has a key role in suppressing PCa cells by applying phosphatase activity and inhibiting cell proliferation. B2G2 exhibited a considerable binding affinity to PTEN (11.643 kcal/mol). The MD results indicated that B2G2 could stabilize the key residues of the phosphatase domain of PTEN and increase its activity. Based on the obtained results, the active ingredient of GSE, B2G2, could play an agonist role and effectively increase the phosphatase activity of PTEN. The grape seed extract is a useful nutrition that can be used in men's diets to inhibit PCa in their bodies.Communicated by Ramaswamy H. Sarma.

Application of molecular dynamics simulation in self-assembled cancer nanomedicine

Self-assembled nanomedicine holds great potential in cancer theragnostic. The structures and dynamics of nanomedicine can be affected by a variety of non-covalent interactions, so it is essential to ensure the self-assembly process at atomic level. Molecular dynamics (MD) simulation is a key technology to link microcosm and macroscale. Along with the rapid development of computational power and simulation methods, scientists could simulate the specific process of intermolecular interactions. Thus, some experimental observations could be explained at microscopic level and the nanomedicine synthesis process would have traces to follow. This review not only outlines the concept, basic principle, and the parameter setting of MD simulation, but also highlights the recent progress in MD simulation for self-assembled cancer nanomedicine. In addition, the physicochemical parameters of self-assembly structure and interaction between various assembled molecules under MD simulation are also discussed. Therefore, this review will help advanced and novice researchers to quickly zoom in on fundamental information and gather some thought-provoking ideas to advance this subfield of self-assembled cancer nanomedicine.

Systematic Studies on Anti-Cancer Evaluation of Stilbene and Dibenzo[b,f]oxepine Derivatives

Cancer is one of the most common causes of human death worldwide; thus, numerous therapies, including chemotherapy, have been and are being continuously developed. In cancer cells, an aberrant mitotic spindle-a microtubule-based structure necessary for the equal splitting of genetic material between daughter cells-leads to genetic instability, one of the hallmarks of cancer. Thus, the building block of microtubules, tubulin, which is a heterodimer formed from α- and β-tubulin proteins, is a useful target in anti-cancer research. The surface of tubulin forms several pockets, i.e., sites that can bind factors that affect microtubules' stability. Colchicine pockets accommodate agents that induce microtubule depolymerization and, in contrast to factors that bind to other tubulin pockets, overcome multi-drug resistance. Therefore, colchicine-pocket-binding agents are of interest as anti-cancer drugs. Among the various colchicine-site-binding compounds, stilbenoids and their derivatives have been extensively studied. Herein, we report systematic studies on the antiproliferative activity of selected stilbenes and oxepine derivatives against two cancer cell lines-HCT116 and MCF-7-and two normal cell lines-HEK293 and HDF-A. The results of molecular modeling, antiproliferative activity, and immunofluorescence analyses revealed that compounds 1a, 1c, 1d, 1i, 2i, 2j, and 3h were the most cytotoxic and acted by interacting with tubulin heterodimers, leading to the disruption of the microtubular cytoskeleton.

Computational Approaches to the Rational Design of Tubulin-Targeting Agents

Microtubules are highly dynamic polymers of α,β-tubulin dimers which play an essential role in numerous cellular processes such as cell proliferation and intracellular transport, making them an attractive target for cancer and neurodegeneration research. To date, a large number of known tubulin binders were derived from natural products, while only one was developed by rational structure-based drug design. Several of these tubulin binders show promising in vitro profiles while presenting unacceptable off-target effects when tested in patients. Therefore, there is a continuing demand for the discovery of safer and more efficient tubulin-targeting agents. Since tubulin structural data is readily available, the employment of computer-aided design techniques can be a key element to focus on the relevant chemical space and guide the design process. Due to the high diversity and quantity of structural data available, we compiled here a guide to the accessible tubulin-ligand structures. Furthermore, we review different ligand and structure-based methods recently used for the successful selection and design of new tubulin-targeting agents.