Antibacterial efficacy and molecular docking analysis of Huang-Lian-Jie-Du Decoction against the phytopathogenic bacteria P. carotovorum PC1

•The main active ingredients and their antibacterial efficacies were analyzed.•Molecular docking and SAR study were performed to identify the lead compound.•Antibacterial mechanism against the P. carotovorum PC1 was revealed.•The bioactive ingredients with lipophilic groups might need to be studied further. The inhibitory effect of the Traditional Chinese Prescription HLJDD against the phytopathogenic bacteria P. carotovorum PC1 has been investigated by HPLC-ESI-MS analysis, FTIR spectroscopy, SEM and computational analysis. It was suggested that HLJDD changed the intracellular membrane permeability of the P. carotovorum PC1 and cause the release of DNA, RNA and intracellular protein. The main ingredients berberine, coptisine, epiberberine and berberubine showed relatively lower MIC values (200-400 µg/ml) when compared with the positive control of 50% carbendazim wettable powder. Further FTIR and SEM analysis showed that the cell wall of the bacteria is damaged after treatment with HLJDD, thus the sunken cell surface and hollow holes are noticed. The MESP diagram clearly tells that the presence of electron rich oxygen atom (-23.18 Kcal/mol) of the 1,3-dioxolane ring makes Berberine as donor, which can chelate the catalytic Zn2+-ion at the active site of the deacetylase LpxC. Molecular docking suggested that the electrostatic interaction, hydrophobic interaction and van der Waals interactions are significant in the active site. [Display omitted]