In silico identification and design of 2-(3-methoxyphenoxy)-N-methylacetamide analogs as anti-tuberculosis transcriptional regulator (EthR) inhibitors via E-pharmacophore modeling, QSAR, docking, MMGBSA, ADMET, and molecular dynamics

Abstract

Tuberculosis (TB) remains a leading cause of infectious mortality worldwide, exacerbated by the emergence of multidrug-resistant strains and the dose-limiting toxicity of existing chemotherapeutics. Targeting regulatory mechanisms that potentiate current drugs offers a promising alternative strategy. EthR, a TetR-family transcriptional repressor that downregulates ethA and thereby limits ethionamide activation, has emerged as an attractive molecular target. Inhibiting EthR can enhance ethionamide efficacy while potentially reducing required dosage. Although 2-(3-methoxyphenoxy)-N-methylacetamide derivatives have been reported as EthR binders, their pharmacophoric features, structure–activity relationships, and dynamic interaction profiles remain insufficiently characterized. In this study, a comprehensive in silico workflow was employed to design and evaluate novel 2-(3-methoxyphenoxy)-N-methylacetamide analogs as EthR inhibitors. An energetically optimized e-pharmacophore model was developed and used to virtually screen a curated compound library. Quantitative structure–activity relationship (QSAR) modeling was performed to elucidate key molecular descriptors governing inhibitory activity. High-ranking compounds were subjected to molecular docking, MM-GBSA binding free-energy calculations, ADMET prediction, and 100 ns molecular dynamics (MD) simulations to assess binding stability and drug-likeness. The generated e-pharmacophore hypothesis effectively captured essential steric and electronic features required for EthR inhibition. The QSAR model demonstrated robust predictive performance (R² = 0.8289; Q² = 0.6383), revealing a strong correlation between functional-group distribution and bioactivity. Docking studies identified several analogs with high affinity for the hydrophobic regulatory pocket of EthR, stabilized by persistent hydrogen-bond interactions with key residues including Trp103, Asn179, and Phe184. MMGBSA analysis confirmed favorable binding free energies ranging from − 71.43 to − 96.28 kcal/mol. The selected hits exhibited acceptable pharmacokinetic properties and low predicted toxicity. MD simulations further demonstrated conformational stability of the protein-ligand complexes, with low RMSD fluctuations and sustained intermolecular interactions throughout the simulation period. This integrative computational investigation identifies 2-(3-methoxyphenoxy)-N-methylacetamide analogs as promising EthR inhibitors with favorable binding energetics, stability, and drug-like characteristics. By elucidating their pharmacophoric requirements and dynamic binding behavior, the study provides a mechanistically informed framework for the rational development of EthR-targeted adjunct therapies, offering a viable pathway toward improved anti-tuberculosis treatment strategies.