Structural investigation of Keap1–Nrf2 protein–protein interaction (PPI) inhibitors for treating myocarditis through molecular simulations

Abstract

Myocarditis is classified as an inflammatory disease of the heart muscle and is a leading cause of sudden death. The Keap1-Nrf2-ARE pathway is an important antioxidant defense mechanism that protects cells from oxidative stress and the Keap1-Nrf2 protein–protein interaction (PPI) is considered as a potential drug target against myocarditis to upregulate the expression of ARE-controlled cytoprotective oxidative stress response enzymes. To gain insights into the relationship between the activity and structure of the compounds and design superior active novel inhibitors, 3D-QSAR, molecular docking and molecular dynamics (MD) simulation were combined to investigate the interaction between Keap1–Nrf2 PPI inhibitors and Keap1. The comparative molecular field analysis (CoMFA) model (q² = 0.907, n = 7, R² = 0.997) and the comparative molecular similarity index analysis (CoMSIA) model (q² = 0.900, n = 7, and R² = 0.993) showed that the 3D-QSAR models built were credible and predictable. Based on these models, 10 new compounds were discovered and their bioactivity was validated using molecular docking and MD simulation. Furthermore, the plausible ADME/T characteristics of new compounds were evaluated and the key residues (Arg415, Tyr334, Ser602, Ser363, Arg380, etc.) in the active site were also identified by free energy calculation. The binding energy results show that the structurally optimized compounds (N1: −65.409 kcal mol⁻¹, N3: −54.619 kcal mol⁻¹, N4: −62.627 kcal mol⁻¹, N5: −60.903 kcal mol⁻¹, and N8: −66.272 kcal mol⁻¹) have lower binding free energy values than compound 43 (ΔG_bind: −49.991 kcal mol⁻¹), indicating that they have a better affinity for the target. These findings provide necessary theoretical guidance for the discovery and design of highly active drugs against myocarditis.