Comparative evaluation of antimicrobial activities and molecular docking of selected medicinal plants used in arab countries using zamzam water and conventional solvents

The increasing prevalence of antimicrobial resistance has renewed interest in plant-derived bioactive compounds as alternative therapeutic agents. Although medicinal plants are widely studied, limited research has examined the comparative efficacy of Zamzam water as an extraction solvent or integrated in vitro antimicrobial findings with molecular docking analysis to explore potential mechanisms of action. This study aimed to evaluate the antimicrobial activity of ethanol, methanol, petroleum ether, aqueous, and Zamzam water extracts of Origanum majorana, Costus speciosus, Lepidium sativum, and Linum usitatissimum, and to investigate potential molecular interactions of selected phytocompounds with key bacterial targets. Antimicrobial activity was assessed using agar well diffusion and microbroth dilution methods against five standard microorganisms: Bacillus subtilis (ATCC 11774), Staphylococcus aureus (ATCC 25923), Proteus vulgaris (ATCC 33420), Klebsiella pneumoniae (ATCC 10031), and Candida albicans (ATCC 10231). Molecular docking was performed using FLARE software to evaluate selected plant-derived compounds against DNA gyrase (Gram-negative target) and dihydrofolate reductase (DHFR, Gram-positive target). Ethanol, methanol, and Zamzam water extracts produced larger inhibition zones than aqueous extracts, with greater activity observed at higher concentrations. L. usitatissimum seed extracts demonstrated strong activity against P. vulgaris and K. pneumoniae. Docking analysis revealed that β-caryophyllene from O. majorana exhibited high predicted binding affinities to DNA gyrase (− 11.549 kcal/mol) and DHFR (− 13.169 kcal/mol). Flavonoids, including quercetin and kaempferol, also showed favorable binding interactions. These in silico results provide supportive mechanistic insight into the observed antimicrobial effects. The findings indicate that selected medicinal plant extracts, particularly those obtained using alcohol-based and Zamzam water solvents, demonstrate notable antimicrobial activity. The combined experimental and computational approach suggests that specific phytocompounds merit further investigation for the development of novel antibacterial agents.