In Silico Investigation of Phytochemicals From Clinically Tested Herbal Extracts as Potential Dihydrofolate Reductase Inhibitors for Buruli Ulcer.

Abstract

Buruli ulcer (BU), a neglected tropical disease caused by Mycobacterium ulcerans, requires more effective and accessible treatments. Clinical trials have shown the efficacy of herbal formulations containing Nicotiana tabacum, Mangifera indica, Carica papaya, and Solanum rugosum, although the active phytochemicals remain unstudied. In the present study, we employed an in silico approach to identify the active phytochemicals from these plants that could inhibit M. ulcerans dihydrofolate reductase (MuDHFR), a crucial enzyme for mycobacterial survival. A library of 172 phytochemicals was screened using molecular docking, followed by 300-ns molecular dynamics (MD) simulations using AMBER for the top hits and standard drugs (methotrexate and trimethoprim). Binding free energies were calculated using the molecular mechanics/generalized born surface area (MM/GBSA) method. The extended MD simulations and post hoc MM/GBSA analysis revealed that kaempferol-3-O-rutinoside (Δ G _bind -51.62 kcal/mol) and neochlorogenic acid (ΔG_bind -49.44 kcal/mol) exhibited the strongest and most stable binding to MuDHFR. The binding energies were more favorable than both methotrexate (Δ G _bind -44.18 kcal/mol) and trimethoprim (Δ G _bind -41.01 kcal/mol) used as positive controls. Stability analyses (RMSD and RMSF) and principal component analysis (PCA) confirmed that these compounds form stable complexes and induce specific conformational states in the enzyme. Favorable ADMET profiles, particularly the lack of predicted skin sensitization, support their potential for topical use. This study identifies kaempferol-3-O-rutinoside and neochlorogenic acid as the most promising lead candidates for developing novel BU therapies, warranting their prioritization for experimental validation.