Chemico-biological evaluation of carpachromene against key antimicrobial protein targets: an integrated in-silico, in-vitro approach for mechanistic insights

Ethnopharmacological Relevance Verbascum thapsus L. is a prized medicinal plant from the Kashmir Himalaya traditionally utilized to treat many ailments, yet its active metabolites against antimicrobial mechanisms remain unclear. Aim of the Study This work envisages an integrated in-silico and in-vitro approach to mechanistically investigate broad-spectrum antimicrobial activity of carpachromene, a supradecorated phytochemical from V . thapsus . Materials and Methods Carpachromene was isolated through cold extraction from V . thapsus , followed by silica gel column chromatography with an optimized polarity solvent system, yielding a whitish amorphous solid confirmed by XRD, FTIR, 1 H NMR and 13 C NMR spectroscopy. In-silico analyses encompassed molecular docking of carpachromene against key microbial drug targets like sterol 14-α demethylase (CYP51), Dihydropteroate synthase (DHPS), GyrB ATPase domain, and Penicillin-Binding Protein 1 (PBP-1) followed by 100 ns molecular dynamics simulations assessing RMSD, RMSF, dynamic cross-correlation matrix (DCCM), principal component analysis (PCA), radius of gyration (Rg), and solvent accessible surface area (SASA). In-vitro antimicrobial activity was assessed using the agar well-diffusion method against clinical isolates: bacterial pathogens ( Escherichia coli OP268610, Staphylococcus aureus OP268597, Salmonella enterica OP268585, Pseudomonas aeruginosa OP268614, Klebsiella pneumoniae OP268611, Bacillus cereus OP268602) and fungal pathogens ( Aspergillus niger MTCC183, A. fumigatus MTCC282, Candida albicans MTCC343), evaluating concentration-dependent inhibition zones relative to standard controls (ciprofloxacin for bacteria; fluconazole for fungi). Results Docking studies revealed robust binding affinities for carpachromene, ranging from −9.3 to −10.5 kcal/mol across targets (CYP51: −10.5 kcal/mol; E. coli DHPS: −9.6 kcal/mol; S. aureus GyrB: −9.4 kcal/mol; PBP-1: −9.3 kcal/mol) driven by hydrogen bonding (e.g., with active-site residues like Asp 73, Thr 165, Gly 77 in GyrB ATPase) and other hydrophobic interactions. MD simulations affirmed complex stability (RMSD: 1.2–1.5 Å; RMSF: 0.69–1.07 Å), with persistent intermolecular contacts, and coordinated residue motions via DCCM/PCA. In-vitro results revealed potent, dose-dependent activity, yielding maximum inhibition zones of 21 mm against S. enterica (50 μg/mL) and 10 mm against C. albicans . Conclusion The mechanistic insights from computational analysis corroborated with in-vitro observations, highlighting carpachromene as a promising multi-target antimicrobial scaffold. These findings support supradecoration strategies for advancing carpachromene toward novel drug development against antimicrobial resistance.