Pharmacophore modelling-based screening of natural allosteric EGFR inhibitors using molecular docking, DFT, and molecular dynamics simulations

Abstract

The development of allosteric inhibitors is a promising strategy for targeting epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC), especially in cases where orthosteric inhibitors face resistance. However, despite their selective inhibition of EGFR mutations, fourth-generation allosteric inhibitors show limited antiproliferative efficacy without cetuximab. The present study aims to identify potent natural product-derived allosteric inhibitors for NSCLC using a comprehensive approach, including pharmacophore modelling, Lipinski's Rule of Five (Ro5), ADMET profiling, density functional theory, and molecular docking. Experimentally validated EGFR tyrosine kinase inhibitors (TKIs) were used to build a pharmacophore model. The validated pharmacophore model was used to screen the Natural Product Activity and Species Source database. Drug-likeness was assessed using Ro5 and ADMET to predict pharmacokinetic and toxicity profiles for further drug development. Molecular docking studies revealed that the identified natural compounds exhibited more favorable docking scores (−8.74 to −7.87 kcal/mol) than the co-crystallized ligand (−7.32 kcal/mol), indicating significant interactions with the receptor residues. Geometry optimization, electrostatic potential, and frontier molecular orbital analyses were performed to assess potential reactive sites and molecular stability. Molecular dynamics (MD) simulations, subsequent post-MD analyses, and binding free energy calculations provided additional support for these findings. The free-energy landscape revealed stable, favorable binding conformations, suggesting that they may act as allosteric inhibitors. These results highlight the potential of natural compounds to combat resistance to EGFR-TKIs in NSCLC. In particular, compounds 1 and 2 emerged as promising candidates targeting mutant EGFR and warrant further experimental validation as potential leads for NSCLC treatment.