Development of DHODH inhibitors incorporating virtual screening, pharmacophore modeling, fragment-based optimization methods, ADMET, molecular docking, molecular dynamics, PCA analysis, and free energy landscape

Abstract

The overexpression of dihydroorotate dehydrogenase (DHODH) in various malignant tumor cells is significantly associated with ferroptosis, making DHODH inhibition a promising strategy for cancer therapy. In this study, we employed an integrated approach to screen and optimize DHODH inhibitor candidates. First, virtual screening of the FDA-approved drug library identified 20 potential compounds (with the positive control AG-636 as a benchmark, docking score: 133.166). Subsequent pharmacophore modeling (ROC curve value >0.8) further narrowed the candidates to six compounds, which underwent fragment displacement optimization. All optimized compounds were evaluated for absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Molecular docking identified compounds 65:[(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 3-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) (docking score: 197.362) and 66: [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 4-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) (docking score: 202.623) as high-affinity candidates. Molecular dynamics (MD) simulations, principal component analysis (PCA), and free energy landscape (FEL) analyses confirmed stable binding conformations for both compounds. Notably, compound 66: [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 4-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) exhibited minimal conformational changes, suggesting superior binding stability. This study advances compound 66: [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 4-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) as a promising DHODH inhibitor candidate through a multimodal workflow integrating structure-based pharmacophore design, fragment optimization, ADMET profiling, and advanced molecular simulations, providing a novel avenue for DHODH-targeted antitumor therapies.