In Silico and In Vitro Screening of Natural Compounds as Broad-Spectrum β -Lactamase Inhibitors against Acinetobacter baumannii New Delhi Metallo- β -lactamase-1 (NDM-1).
Aparna VasudevanDinesh Kumar KesavanLiang WuZhao-Liang SuShengjun WangMohan Kumar RamasamyWaheeta HopperHuaxi XuPublished in: BioMed research international (2022)
Antibiotic resistance is one of the significant problems globally; there is an increase in resistance with introducing every new class of antibiotics. Further, this has become one of the reasons for arising of new resistance mechanisms in Acinetobacter baumannii . In this study, we have screened natural compounds as a possible inhibitor against the NDM-1 β -lactamase enzyme from A. baumannii using a combination of in silico methods and in vitro evaluation. The database of natural compounds was screened against NDM-1 protein, using Glide docking, followed by QM-polarised ligand docking (QPLD). When the screened hits were validated in vitro , withaferin A and mangiferin had good IC 50 values in reducing the activity of NDM-1 enzymes, and their fractional inhibitory concentration index (FICI) was ascertained in combination with imipenem. The withaferin A and mangiferin-NDM-1 docking complexes were analyzed for structural stability by molecular dynamic simulation analysis using GROMACS for 100 ns. The molecular properties of the natural compounds were then calculated using density functional theory (DFT). Withaferin A and mangiferin showed promising inhibitory activity and can be a natural compound candidate inhibitor synergistically used along with carbapenems against NDM-1 producing A. baumannii .
Keyphrases
- klebsiella pneumoniae
- multidrug resistant
- acinetobacter baumannii
- gram negative
- drug resistant
- density functional theory
- molecular dynamics
- escherichia coli
- protein protein
- pseudomonas aeruginosa
- molecular dynamics simulations
- molecular docking
- small molecule
- emergency department
- single molecule
- electronic health record
- dengue virus
- drug induced
- zika virus
- adverse drug