Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop

Emerging roles of i-motif in gene expression and disease treatment

As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.

Identification of potential inhibitors, conformational dynamics, and mechanistic insights into mutant Kirsten rat sarcoma virus (G13D) driven cancers

The mutations at the hotspot region of K-Ras result in the progression of cancer types. Our study aimed to explore the small molecule inhibitors against the G13D mutant K-Ras model with anti-cancerous activity from food and drug administration (FDA)-approved drug compounds. We implemented several computational strategies such as pharmacophore-based virtual screening, molecular docking, absorption, distribution, metabolism and excretion features, and molecular simulation to ensure the identified hit compounds have potential efficacy against G13D K-Ras. We found that the FDA-approved compounds, namely, azelastine, dihydrocodeine, paroxetine, and tramadol, are potential candidates to inhibit the action of G13D mutant K-Ras. All four compounds exhibited similar binding patterns of sotorasib, and a structural binding mechanism with significant hydrophobic contacts. The descriptor features from the QikProp of all four compounds are within allowable limits compared to sotorasib drug. Consequently, a molecular simulation result emphasized that the dihydrocodeine and tramadol exhibited less fluctuation, minimal basin, significant h-bonds, and potent inhibition against G13D K-Ras. As a result, the current research identifies prospective K-Ras inhibitors that could be further improved with biochemical analysis for precision medicine against K-Ras-driven cancers.

Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes

Understanding the molecular mechanism of the GTP-KRAS binding is significant for improving the target roles of KRAS in cancer treatment. In this work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations were applied to decode the effect of Q61A, Q61H and Q61L on the activity of KRAS. Dynamics analyses based on MR-GaMD trajectory reveal that motion modes and dynamics behavior of the switch domain in KRAS are heavily affected by the three Q61 mutants. Information of free energy landscapes (FELs) shows that Q61A, Q61H and Q61L induce structural disorder of the switch domain and disturb the activity of KRAS. Analysis of the interaction network uncovers that the decrease in the stability of hydrogen bonding interactions (HBIs) of GTP with residues V29 and D30 induced by Q61A, Q61H and Q61L is responsible for the structural disorder of the switch-I and that in the occupancy of the hydrogen bond between GTP and residue G60 leads to the structural disorder of the switch-II. Thus, the high disorder of the switch domain caused by three current Q61 mutants produces a significant effect on binding of KRAS to its effectors. This work is expected to provide useful information for further understanding function and target roles of KRAS in anti-cancer drug development.

Computational investigation to identify potent inhibitors of the GTPase-Kirsten RAt sarcoma virus (K-Ras) mutants G12C and G12D

K-Ras mutations are frequent in various cancer types, and according to recent research, K-Ras possesses four-drug targeting sites. This increased our interest in finding potential small molecule inhibitors with anticancer activity to treat K-Ras-driven cancers. We utilized integrated bioinformatic strategies, such as XP docking, MM-GBSA, cell-line cytotoxicity prediction, ADMET, and molecular simulation, to discover potential inhibitors of G12C and G12D mutants compared to sotorasib, which is a recent FDA-approved inhibitor of G12C. We identified compounds, such as flupentixol, amlodipine, and fluvoxamine, for the G12C mutant and paroxetine, flupentixol, and zuclopenthixol for the G12D mutant with significant inhibitory functions. All five compounds bound to the H95 cryptic groove of mutant K-Ras with high efficiency and, like sotorasib, retained a novel binding mechanism with additional hydrophobic interactions at the molecular level. Furthermore, the simulation studies suggested that the binding of flupentixol and amlodipine to G12C stabilizes switch I and switch II. In contrast, paroxetine and flupentixol to G12D showed a similar trend compared to sotorasib complexes. Thus, despite the very dynamic functionality of K-Ras switches I and II, the binding of shortlisted compounds is highly stable. Therefore, the reported study provides potential drug candidates for K-Ras inhibition that can be further developed with in vitro and in vivo evidence for targeted therapy.