Configuration Flipping in Distal Pocket of Multidrug Transporter MexB Impacts the Efflux Inhibitory Mechanism

Abstract

MexAB-OprM efflux pumps, found in Pseudomonas aeruginosa, play a major role in drug resistance by extruding out drugs and antibiotic molecules from cells. Inhibitors are used to cease the potency of the efflux pumps. In this study, in-silico models are used to investigate the nature of the binding pocket of the MexAB-OprM efflux pump. First, we have performed classical molecular dynamics (MD) simulations to shed light on different aspects of protein-inhibitor interaction in the binding pocket of the pump. Using classical MD simulations, quantum mechanics/ molecular mechanics (QM/MM), and various types of analyses, it is found that D13-9001 has a higher binding affinity towards the binding pocket compared to D1 and D2; the results are in sync with the experimental dat. Two stable configurations of D13-9001 are discovered inside the distal pocket which could be one of the primary reasons for the greater efficacy of D13-9001. The free energy barrier upon changing one state to another is calculated by employing umbrella sampling method. Finally, F178 is mutated to have the complete picture as it contributes significantly to the binding energy irrespective of the three inhibitors. Our results may help to design a new generation of inhibitors for such an efflux pump.

Machine Learning-Guided Discovery of AcrB and MexB Efflux Pump Inhibitors

“…Careful analyses of rmsd data of the porter domain consisting of PN1, PN2, PC1, and PC2 subdomains over the last 100 ns trajectory showed almost similar trends of average positional fluctuations. Also, the rmsd values were almost constant over time and within the accepted range of deviation , from the native protein structure (Supporting Information, Figure S7). Furthermore, the average rmsd values of the PN2 and PC1 subdomains were calculated for each ligand-bound AcrB and MexB system to gain insights about the structural changes of the DBP region.…”

Common recognition topology of mex transporters of Pseudomonas aeruginosa revealed by molecular modelling

“…Furthermore, we have observed that two channels among all, namely CH2 and CH5, are endowed with MFS in all the transporters (the latter mostly in MexY), suggesting their possible involvement in the early recognition of several small organic probes (and thus substrates, such as antibiotics, functionalized with these chemical groups). This is relevant also from a pharmaceutical perspective, as it points to the possibility of targeting these sites in drug design efforts (Collu et al, 2012;Kumar Roy and Patra, 2020)-for instance to inhibit the translocation of substrates from the periplasm to the AP L and DP T binding pockets-and protein engineering (Mao et al, 2002;Middlemiss and Poole, 2004;Krishnamoorthy et al, 2008;Ohene-Agyei et al, 2012;Wang et al, 2015;Kumar Roy and Patra, 2020;Marshall and Bavro, 2020;Zwama and Nishino, 2021;Cacciotto et al, 2022).…”

Uncovering the Structural and Binding Insights of Dual Inhibitors Simultaneously Targeting Two Distinct Sites on EGFR Kinase

“…Binding free energies (Δ G bind ) of protein–ligand complexes were calculated by using molecular mechanics–generalized Born surface area (MM-GBSA) implicit solvent models. MM-GBSA is a more widely used method to date for calculation of the binding free energies among biomolecular complexes . The general MM-GBSA is used to determine significant conformational fluctuations and the entropic contribution to the binding energy.…”

“…MM-GBSA is a more widely used method to date for calculation of the binding free energies among biomolecular complexes. 70 The general MM-GBSA is used to determine significant conformational fluctuations and the entropic contribution to the binding energy. The binding free energy was calculated based on the following equations…”