Non-small-cell lung cancer (NSCLC), the predominant histological subtype accounting for more than 85% of lung cancer cases, remains the leading cause of cancer-related mortality worldwide. Despite the clinical advances afforded by targeted therapies, the frequent emergence of oncogenic driver mutations drives drug resistance and therapeutic failure, underscoring the critical need for novel molecular targets and alternative therapeutic strategies. AKT1, a serine/threonine kinase and central effector of the PI3K/AKT/mTOR signaling cascade, regulates key oncogenic processes including cell growth, survival, proliferation, and apoptotic evasion, and dysregulated hyperactivation is observed in 30-75% of NSCLC cases. Selective allosteric inhibition of AKT1, which targets the unique PH-kinase domain interface rather than the highly conserved ATP-binding pocket, has emerged as a more isoform-specific and therapeutically advantageous strategy compared with pan-AKT or ATP-competitive inhibition. In the present study, a ChemDiv AKT1-targeted compound library comprising 14,043 small molecules was subjected to hierarchical structure-based virtual screening using sequential high-throughput virtual screening (HTVS), standard precision (SP), and extra precision (XP) docking protocols, followed by binding free energy calculations using the MM-GBSA method. The top XP-ranked compounds, compound 1 (docking score: -11.771 kcal/mol), compound 2 (-11.428 kcal/mol), and compound 3 (-11.167 kcal/mol), achieved more favourable XP docking scores at the AKT1 allosteric site (PDB ID: 3O96) than established pan-AKT inhibitors, including MK-2206, miransertib, Bay1125976, and vevorisertib, although MM-GBSA rescoring did not reproduce this ordering. Comparative docking against the allosteric sites of AKT2 and AKT3 revealed a consistent preference for AKT1 across all three compounds, with a magnitude closely comparable to that of the reference allosteric ligand Inhibitor VIII, whose experimentally determined isoform rank order the protocol reproduced. Comprehensive 300-ns all-atom molecular dynamics (MD) analysis, encompassing RMSD and RMSF profiling, principal component analysis, dynamic cross-correlation matrix analysis, free energy landscape evaluation, and protein-ligand contact profiling, consistently demonstrated that compounds 1 and 2 maintain stable, high-affinity interactions with AKT1, exhibiting persistent engagement with the critical allosteric residues Trp80 and Tyr272 throughout the simulation trajectory. Furthermore, both compounds exhibited favourable pharmacokinetic profiles with predicted human oral absorption values over 80%, supporting their potential for preclinical development.
Raju Das, Armin Sultana, Kantu Das et al.· Journal of Molecular Graphic...· 0 citations
Bitter taste receptors, particularly TAS2R14, are widely expressed in extraoral tissues, including the central nervous system, where they have been implicated in neuroinflammatory and neurodegenerative processes. Although numerous pharmacological and natural compounds have demonstrated therapeutic potential against neurodegenerative disorders, clinically effective disease-modifying therapies remain strikingly limited. TAS2R14 is a promising yet underexplored candidate target; however, its mechanistic role in neurodegenerative disorders remains poorly understood. Here, we conducted a structure-based virtual screening of 4138 FDA-approved drugs from the MedChemExpress database to identify potential TAS2R14 ligands for therapeutic repositioning. Top candidates were prioritized through a hierarchical molecular docking workflow and binding free-energy calculations (MM-GBSA), orthogonal GNINA validation, in silico ADMET assessment, followed by 500 ns molecular dynamics (MD) simulations to evaluate the persistence of predicted binding modes and ligand-associated conformational behavior at both extracellular and intracellular binding sites. The selected hits exhibited distinct predicted interaction profiles and conformational dynamics at the two independent binding sites. Among them, (-)-epicatechin gallate exhibited favorable interactions, persistent contact with key binding site residues, and comparatively limited conformational fluctuations at both sites, supporting its prioritization as a potential dual-site TAS2R14 binder. Furthermore, fexofenadine and ezetimibe showed favorable binding stability at the extracellular and intracellular sites, respectively. Hydrogen-bond analysis, principal component analysis, dynamic cross-correlation matrix analysis, and free-energy landscape mapping further revealed ligand-dependent differences in interaction networks and receptor conformational behavior. Notably, (-)-epicatechin gallate, fexofenadine, and ezetimibe exhibited greater predicted binding stability than the reference ligands flufenamic acid, cholesterol, and Comp28.1 throughout the 500 ns simulations. As this study is purely computational, experimental validation through receptor activation assays and relevant biological models will be required to determine whether the predicted binding interaction translates into functional modulation of TAS2R14 and therapeutic benefit. Nevertheless, these findings provide a computational foundation for prioritizing candidate TAS2R14 ligands and support future experimental studies to evaluate receptor activation, specificity, selectivity, and therapeutic efficacy, particularly for (-)-epicatechin gallate, in the context of TAS2R14-targeted neuroprotective drug repositioning.
