Identification of novel AKT1 inhibitors from Sapria himalayana bioactive compounds using structure-based virtual screening and molecular dynamics simulations

Theoretical investigation of AKT1 mutations in breast cancer: a computational approach to structural and functional insights

Breast cancer is a complex disease primarily driven by genetic mutations that disrupt crucial signaling pathways, with the AKT1 gene playing a central role in its progression. This study explores the impact of AKT1 mutations using Whole Exome Sequencing (WES), bioinformatics, and computational modeling. Using WES, we identified and prioritized significant mutations in patient samples, specifically D3N, V337M, and D3N-E169G. Comprehensive sequence and structural analyses were conducted to understand how these mutations affect specific functional domains of the AKT1 protein. To investigate the molecular consequences, molecular docking studies were performed to assess the binding affinity of AKT1 mutations with MK2206, a known allosteric inhibitor of AKT1. The docking results revealed substantial differences in interaction energies, indicating impaired inhibitor binding due to these mutations. Additionally, molecular dynamics simulations over a 500-nanosecond trajectory provided detailed insights into the structural perturbations caused by these mutations. This integrated study, combining genomic and computational approaches, offers a comprehensive understanding of how AKT1 mutations contribute to BC pathogenesis. These findings enhance our knowledge of the molecular mechanisms underlying the disease and support the development of targeted therapies to address the altered behavior of mutated AKT1, advancing personalized treatment strategies for BC.

Anticancer activity of Stemona tuberosa (wild asparagus) against type-II human lung adenocarcinoma (A549) cells and identification of SRC inhibitor using integrated network pharmacology and molecular dynamic simulation

Stemona tuberosa is widely recognized for its traditional applications as an anti-cancer agent. This study aimed to assess the anti-cancer properties of S. tuberosa in human lung adenocarcinoma A549 cells. Among the various solvent extracts of S. tuberosa, the methanolic extract showed the highest toxicity against A549 cells. The S. tuberosa extract elicited cytotoxic effects and suppressed colony formation in A549 cells in a dose-dependent manner. S. tuberosa activity was further supported by AO/EtBr staining, increased caspase 3/6 activity, upregulation of pro-apoptotic genes, DNA damage, and elevated lipid peroxidation, with decreasing antioxidant levels. LC-MS analysis identified 80 predominant secondary metabolites in the methanolic extracts of S. tuberosa. A network pharmacology study identified SRC as the primary target of compounds identified from S. tuberosa. SRC protein is crucial for advancing lung cancer because of its function in cell proliferation, survival, and metastasis. Among the various compounds identified from S. tuberosa extract, 4-Azatricyclo [4.3.1.13,8] undecan-5-one (ADE) (- 10.88 kcal/mol) and Dihydro-normorphine, 3-desoxy- (DNY) (- 10.83 kcal/mol) exhibited notable binding affinities for SRC. Further analysis using molecular dynamics simulations (100 ns) validated the stability of SRC-ligand complexes, with RMSD of 1.8 and 2.2 Å for ADE and DNY, respectively, alongside the establishment of essential hydrogen bonds with pivotal residues, including ASP408, ALA403, and THR438. Finally, gmx._MMPBSA showed favourable ΔGbind values for ADE (- 15.06 ± 0.11 kcal/mol) and DNY (- 15.66 ± 0.25 kcal/mol), which highlights the significant potential of ADE and DNY as effective SRC inhibitors, suggesting S. tuberosa as a novel candidate for cancer therapy.

Binding patterns of inhibitors to different pockets of kinesin Eg5

The kinesin-5 family member, Eg5, plays very important role in the mitosis. As a mitotic protein, Eg5 is the target of various mitotic inhibitors. There are two targeting pockets in the motor domain of Eg5, which locates in the α2/L5/α3 region and the α4/α6 region respectively. We investigated the interactions between the different inhibitors and the two binding pockets of Eg5 by using all-atom molecular dynamics method. Combined the conformational analysis with the free-energy calculation, the binding patterns of inhibitors to the two binding pockets are shown. The α2/L5/α3 pocket can be divided into 4 regions. The structures and binding conformations of inhibitors in region 1 and 2 are highly conserved. The shape of α4/α6 pocket is alterable. The space of this pocket in ADP-binding state of Eg5 is larger than that in ADP·Pi-binding state due to the limitation of a hydrogen bond formed in the ADP·Pi-binding state. The results of this investigation provide the structural basis of the inhibitor-Eg5 interaction and offer a reference for the Eg5-targeted drug design.