Integrative docking and molecular dynamics identify potential allosteric modulators of AKT1.

Abstract

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.