Integrated in silico and in vitro assessment of Azadirachta indica leaf extract against multi-drug resistant Citrobacter koseri and Staphylococcus saprophyticus.

Azadirachta indica (Neem) is well-known for its therapeutic potential against bacteria, while Staphylococcus saprophyticus and Citrobacter koseri are significant public health threats due to their potential to cause skin infections. This study aims to identify phytocompounds from the methanolic extract of A. indica leaves and evaluate their efficacy to inhibit those bacteria through in vitro and computational approaches. The bacteria were isolated from boil-derived pus, and the extract's growth-inhibitory effect was examined by the disc diffusion method. Additionally, GC-MS identified phytochemicals remaining in the extract. The pharmacokinetic and ADMET properties of those phytochemicals were assessed via PKCSM and SwissADME servers. Screened phytocompounds were docked with functional proteins using AutoDock Vina and GLIDE. Following that, molecular dynamics simulation in GROMACS, post-simulation, and DFT analysis were conducted. Five of the sixteen phytocompounds with favorable pharmacokinetics and toxicity profiles were docked with Peptidoglycan D, D-transpeptidase MrdA of Citrobacter koseri, and D-alanine--D-alanine ligase of Staphylococcus saprophyticus. Among them, 2-(Acetoxymethyl)-3-(methoxycarbonyl)biphenylene, and Cyclopropane-1-carboxamide, 2-butyl-N-(5,6,7,8-tetrahydro-7,7-dimethyl-5-oxoquinazolin-2-yl)- demonstrated higher binding affinity, greater stability, and smaller energy gap in docking, simulation, and DFT analysis, respectively. This study highlights the two compounds as promising lead phytocompounds to inhibit those bacteria. Further in vivo investigations are essential to validate their therapeutic effectiveness.