The global increase in antimicrobial resistance among Gram-negative hospital pathogens creates an urgent need for new antibacterial candidates that combine whole-cell activity with mechanistic evidence. The principal alkaloid canadine (tetrahydroberberine), derived from Hydrastis canadensis L., was evaluated as a lead compound and compared with the related natural product berberine. The investigation sought both phenotypic antibacterial effects and mechanistic corroboration at a defined molecular target to support further optimization and translational assessment.
A reverse pharmacophore-mapping approach (PharmMapper), followed by filtering for bacterial-relevant targets, prioritized DNA gyrase subunit B (GyrB) as the putative target for canadine. This computational target nomination guided subsequent structure-based and biochemical studies focused on GyrB from Acinetobacter baumannii.
Antibacterial activity was assessed by broth microdilution across a panel of pathogenic bacterial strains. The study reports that canadine displayed consistently superior whole-cell activity relative to berberine and in particular exhibited enhanced inhibition of Acinetobacter baumannii. The abstract summarizes these comparative phenotypic results but does not list MIC values or the complete panel composition in the abstract text; those specific experimental details were not reported in the source summary.
Structure-based docking was performed against the A. baumannii GyrB crystal structure (PDB: 7PQL). The docking protocol was validated by redocking the co-crystallized inhibitor, which produced a root-mean-square deviation (RMSD) of 1.68 Å for the redocked pose versus the crystal ligand, supporting the docking setup.
Canadine achieved a favorable docking score of -10.5 kcal/mol. For context, the co-crystallized ligand scored -10.8 kcal/mol under the same docking conditions, and canadine outperformed berberine in docking score. These docking results supported the computational plausibility of canadine binding in the GyrB active site with an energetics profile approaching that of the known inhibitor present in the crystal structure.
Molecular dynamics (MD) simulations were carried out for 100 ns to evaluate complex stability and dynamic behavior. Over the simulation timeframe, canadine–GyrB complexes showed stable interactions with lower conformational deviation and reduced energetic fluctuation compared with berberine–GyrB complexes.
Interaction-energy decomposition identified van der Waals forces as the main stabilizing contribution to the canadine–GyrB complex, while electrostatic interactions were reported as secondary modulators. Binding free-energy calculations further supported a favorable association, with a calculated ΔG of -9.57 kcal/mol for canadine bound to GyrB. Together, the MD and energetic analyses corroborated the docking prediction and indicated a stable binding mode for canadine at GyrB.
Biochemical validation used an in vitro DNA gyrase inhibition assay with E. coli enzyme preparations. These assays confirmed that canadine had greater inhibitory potency than berberine against the DNA gyrase tested. The abstract states the comparative outcome but does not report specific IC50 or inhibition percentages in the abstract text; such numeric assay endpoints were not provided in the source summary.
Collectively, phenotypic testing, structure-based docking, molecular dynamics and binding-energy analyses, and in vitro enzyme inhibition assays converge to establish canadine as a mechanistically credible GyrB-targeting antibacterial lead with superior performance to berberine.
The authors recommend additional work including structure–activity relationship (SAR) studies, selectivity profiling, and translational evaluation against multidrug-resistant Acinetobacter baumannii. These next steps are proposed to optimize potency, assess bacterial selectivity and off-target liabilities, and determine the translational potential of canadine-derived leads for treatment of resistant Gram-negative infections.
Note: The abstract provides key comparative scores (docking scores, RMSD, MD duration, and calculated ΔG) and reports enhanced phenotypic and enzymatic inhibition by canadine relative to berberine, but detailed experimental values for whole-cell MICs and enzyme inhibition metrics were not included in the abstract text and therefore are not reported here.