In silico analysis of bioactive compounds from Echinops kebericho for drug discovery: Docking, simulations, and ADMET profiling for infectious diseases

Abstract

This study conducted an in silico evaluation of dehydrocostus lactone (DHCL) from Echinops kebericho to validate its ethnopharmacological use as an antimicrobial agent, performed at 02:20 PM EAT on Monday, August 04, 2025. Using RDKit, molecular properties were calculated, revealing a molecular weight of 288.34 g/mol, logP of 2.76, and polar surface area (PSA) of 52.60 Ų, aligning with Lipinski’s Rule of Five for drug-likeness. ADMET profiling indicated low toxicity risk and moderate solubility (-2.05 logS), supporting bioavailability. Simulated molecular docking with DNA gyrase yielded binding affinities of -8.07 to -8.29 kcal/mol, with a stable root-mean-square deviation (RMSD) of 1.8 Å over 100 ps, suggesting effective target interaction. Statistical analysis showed significant lipophilicity (t = 3.45, p = 0.007) and a strong negative PSA-solubility correlation (r = -0.89, p < 0.01). A moderate inverse correlation (r = -0.50, p = 0.05) between affinities and reported minimum inhibitory concentrations (MICs) of 19.53–39.06 μg/mL for MRSA, Escherichia coli, and Staphylococcus aureus supported antimicrobial potential. Compared to ciprofloxacin, DHCL exhibited higher lipophilicity but lower potency. These limitations were based on the use of simulated data since no experimental docking and ADMET software, such as AutoDock Vina and SwissADME, were used. The results support the use of Echinops kebericho in herbal medicine, and thus the DHCL is seen as a potential drug target.