In silico screening of phytochemical inhibitors against Agrobacterium proteins using ADMET prediction, molecular docking, molecular dynamics simulation, and in vitro antimicrobial evaluation.

PURPOSE/

Objective

Multidrug resistance (MDR) in Agrobacterium tumefaciens poses significant challenges to agriculture and health. This study aimed to identify safe, plant-derived phytochemicals that inhibit essential Agrobacterium proteins, using an integrated in silico and in vitro approach.

Methods

A library of 1816 phytocompounds was screened for drug-likeness and ADMET properties. Key bacterial target proteins including MotA, Enolase, Malate dehydrogenase, Penicillin V acylase, ABC transporter, D-β-lactamase, TetR, and TraR were selected for molecular docking. Both phytochemicals and reference antibiotics (tetracycline, ampicillin, carbenicillin, chloramphenicol, kanamycin) were docked and compared. For top-binding complexes underwent molecular dynamics (MD) simulations and MM/GBSA binding free energy analysis to assess the stability and energetics of ligand-protein interactions. Experimental validation was performed using MIC, MBC, and resazurin based-cell viability assays against MDR Agrobacterium strain.

Results

Piperine, curcumin, and quercetin demonstrated high drug-likeness, favorable ADMET and toxicity, and strong binding affinities (up to -9.9 kcal/mol) with target proteins. MD simulations and MM/GBSA analysis confirmed the stable binding and favorable energetics of the piperine-TraR complex. In vitro, these phytochemicals inhibited growth of both sensitive and resistant strains, with piperine exhibiting the lowest MIC among the tested phytocompounds.

Conclusions

This integrative in silico and experimental strategy identified safe, multi-target phytochemicals, especially piperine as promising alternatives to antibiotics for combating MDR Agrobacterium. The use of MD simulation and in vitro experiments provided robust support of binding stability and biological activity, supporting further optimization and in vivo studies.