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In-silico interaction studies suggest RND efflux pump mediates polymyxin resistance in Acinetobacter baumannii
Privita Verma1, Pramila Maurya1, Monalisa Tiwari1
1a Department of Biochemistry , Central University of Rajasthan , Bandarsindri, Ajmer - 305817 , India.
Abstract:
Bacterial efflux pumps have emerged as antibiotic resistance determinants and confers multi-drug resistance to a broad range of antimicrobials as well as non-antibiotic substances. A study about translocation of antibiotic molecules through the efflux transporter, will contribute in determining substrate specificity. In the present study, we have explored RND family efflux pump extensively found in Acinetobacter baumannii i.e. AdeABC. Besides, another well studied RND efflux pump, AcrAB-TolC together with a non-RND efflux pump, NorM was investigated for comparative analysis. We employed a series of computational techniques ranging from molecular docking to binding free energy estimation and molecular dynamics simulations to determine the binding affinity for different classes of drugs, namely aminoglycosides, polymyxins, β-lactams, tetracyclines, glycylcyclines, quinolones and metronidazole with AdeB, AcrB, and NorM efflux proteins. Our results revealed that class polymyxins has the highest binding affinity with the RND efflux pumps i.e. AcrAB-TolC and AdeABC as well as non-RND efflux pump, NorM. The experimental validation study demonstrated bigger zone of inhibition in presence of efflux pump inhibitor than polymyxin alone thus unveiling its specificity toward efflux pump. The reported experimental data comprising of minimum inhibitory concentration of antibiotics toward these efflux pumps also support our finding based on in silico approach. To recapitulate the outcome, polymyxins shows maximum specificity toward RND as well as non-RND efflux pump and may unlatch the way to rationally develop new potential antibacterial agents as well as efflux pump inhibitors in order to combat resistance.
Insights
Polymyxins exhibit the highest binding affinity with bacterial efflux pumps, including RND and non-RND types. This finding suggests polymyxins
Area of Science:
- Microbiology and Molecular Biology
- Computational Chemistry
- Drug Discovery
Background:
- Bacterial efflux pumps are key mechanisms conferring multidrug resistance (MDR).
- Understanding efflux pump substrate specificity is crucial for developing new antibacterial strategies.
- Acinetobacter baumannii harbors the RND efflux pump AdeABC, a significant contributor to its MDR phenotype.
Purpose of the Study:
- To investigate the substrate specificity of the AdeABC efflux pump from Acinetobacter baumannii.
- To conduct a comparative analysis of the RND efflux pumps AdeABC and AcrAB-TolC alongside the non-RND pump NorM.
- To determine the binding affinities of various antibiotic classes with these efflux proteins using computational and experimental methods.
Main Methods:
- In silico approaches including molecular docking, binding free energy estimation, and molecular dynamics simulations.
- Evaluation of binding affinities for drug classes: aminoglycosides, polymyxins, β-lactams, tetracyclines, glycylcyclines, quinolones, and metronidazole.
- Experimental validation using zone of inhibition assays and minimum inhibitory concentration (MIC) determination.
Main Results:
- Polymyxins demonstrated the highest binding affinity across both RND (AdeABC, AcrAB-TolC) and non-RND (NorM) efflux pumps.
- Experimental validation confirmed polymyxin's specificity towards efflux pumps, indicated by enhanced inhibition zones in the presence of efflux pump inhibitors.
- In silico findings were corroborated by experimental data on antibiotic MICs against these efflux pumps.
Conclusions:
- Polymyxins exhibit broad specificity for both RND and non-RND bacterial efflux pumps.
- This high specificity suggests polymyxins as a promising lead for developing novel antibacterial agents and efflux pump inhibitors.
- Targeting efflux pumps with agents like polymyxins could be a viable strategy to combat antibiotic resistance.
