Computational Investigation of Rifampicin as a Multitarget Inhibitor of Melanin Biosynthesis via Molecular Docking and Dynamics Simulations

Hyperpigmentation disorders, characterized by aberrant melanin accumulation, pose a significant clinical challenge, driving the search for novel therapeutic agents. Rifampicin, a clinically approved antibiotic, has recently emerged as a potential candidate for regulating melanogenesis, with preliminary evidence indicating it may target key proteins involved in melanin synthesis and signaling pathways—specifically tyrosinase-related protein 1 (TYRP1), phosphoinositide 3-kinase (PI3K), protein kinase A (PKA), p38 mitogen-activated protein kinase (p38 MAPK), and glycogen synthase kinase-3β (GSK-3β).​ To elucidate the underlying molecular mechanism, this study employed molecular docking and molecular dynamics (MD) simulations. Molecular docking analyses revealed strong binding of rifampicin to TYRP1 (−6.6 kcal/mol), p38 MAPK (−9.6 kcal/mol), PKA (−9.2 kcal/mol), and GSK-3β (−8.5 kcal/mol), with affinities comparable to or exceeding those of their native ligands. In contrast, its affinity for PI3K was lower (−7.8 kcal/mol), suggesting limited involvement in the PI3K/AKT pathway.​ MD simulations confirmed the stability of rifampicin-protein complexes, as evidenced by consistent root-mean-square deviation (RMSD), radius of gyration, and solvent-accessible surface area (SASA) values, alongside minimal residue fluctuations and stable hydrogen bonds. Gibbs free energy landscape analysis further validated the compact, stable nature of these complexes. MM/GBSA calculations yielded favorable binding free energies (ΔG_total: –50.07 to –30.8 kcal/mol), with van der Waals interactions identified as the primary driver of binding. Key interacting residues included Leu382 (TYRP1), Tyr35 (p38 MAPK), Lys896 (PKA), Ile62 (GSK-3β), and Phe439 (PI3K).​ These findings support a multitarget mechanism for rifampicin in melanogenesis regulation and underscore its potential for repurposing as a therapeutic agent for hyperpigmentation.​