Drug Efflux Pump Inhibitors: A Promising Approach to Counter Multidrug Resistance in Gram-Negative Pathogens by Targeting AcrB Protein from AcrAB-TolC Multidrug Efflux Pump from Escherichia coli

Abstract

Infections caused by multidrug resistance (MDR) of Gram-negative bacteria have become one of the most severe public health problems worldwide. The main mechanism that confers MDR to bacteria is drug efflux pumps, as they expel a wide range of compounds, especially antibiotics. Among the different types of drug efflux pumps, the resistance nodulation division (RND) superfamily confers MDR to various Gram-negative bacteria species. The AcrAB-TolC multidrug efflux pump, from E. coli, a member of RND, is the best-characterized example and an excellent model for understanding MDR because of an abundance of functional and structural data. Small molecule inhibitors that target the AcrAB-TolC drug efflux pump represent a new solution to reversing MDR in Gram-negative bacteria and restoring the efficacy of various used drugs that are clinically relevant to these pathogens, especially in the high shortage of drugs for multidrug-resistant Gram-negative bacteria. This review will investigate solutions of MDR in Gram-negative bacteria by studying the inhibition of the AcrAB-TolC multidrug efflux pump.

Keywords: AcrAB-TolC drug efflux complex; AcrB protein; drug efflux pumps inhibitors; hydrophobic trap; mechanisms of antibiotic resistance; multidrug resistance; superfamily efflux pump RND.

Figure 1

WHO list of priority pathogens in most urgent need for antimicrobial development [17].

Figure 2

Schematic diagram highlighting the main antimicrobial resistance mechanisms in pathogenic bacteria, which include: (i) drug efflux systems, which expel the antimicrobials outside the bacterial cell and reduce their effectiveness to non-toxic levels. (ii) Antibiotic inactivation enzymes, which modify or destroy the structure of antibiotics. (iii) Alteration of the target site, which usually occurs in the cell envelope via spontaneous mutation via chemical modification of their molecular targets. (iv) Preventing drug entry by modifying the frequency, size and selectivity of porin channels, which are found in the bacterial envelope and play a crucial role in antibiotic entry into the bacterial cell.

Figure 3

Schematic diagram depicting representative structures of the resistance–nodulation–cell division (RND) family. The RND superfamily are tripartite drug transporters and are formed of three parts; an inner-membrane protein (IMP), an outer-membrane protein (OMP) and a periplasmic adapter protein (PAP), which works as a linker between IMP with OMP.

Figure 4

Schematic diagram showing the functional rotational mechanism of the tripartite complex AcrAB-TolC drug efflux pump. The upper and lower panels show the side and horizontal views of the complex, respectively. The three conformations of AcrB, defined as the loose (L: green), tight (T: blue) and open (O: red) are depicted that serve as the substrate access, binding and extrusion states, respectively. AcrA (light blue) and TolC (pale orange) are also shown. Substrates are indicated by black jagged circles. The movement of protons through AcrB is also shown.

Figure 5

Schematic diagram depicting drug pathways in AcrB and the drug-binding pockets and the two channels that transport substrates are depicted. The periplasmic entry site (channel 2) includes the proximal binding pocket (PBP) in the L protomer, while channel 1 guides substrates from the inner membrane leaflet. The binding sites for rifampicin and erythromycin, co-crystallized in the access pocket in the L monomer, are shown. Minocycline and doxorubicin bind in the deep binding pocket within the T monomer (not shown). The switch loop that separates the proximal and distal binding pockets is also shown. Moreover, the schematic diagram shows the proximal and distal binding pockets of AcrB and a switch loop that separates them, which assists in the unidirectional movement of substrates, whereas smaller substrates and low-molecular-mass drugs localize in the deeper DBP. The two entry channels for substrates connect together leading to the distal binding pocket shown, as is the exit channel that leads from the central cavity to TolC.

Figure 6

Chemical structure of PAβN.

Figure 7

Chemical structure of MBX2319.

Figure 8

Chemical structures of the phytochemicals shikonin and NDGA.

Figure 9

Schematic diagram showing the position of the hydrophobic trap relative to the proximal binding pocket (PBP) and the distal binding pocket (DBP). The switch loop that separates the PBP and DBP is shown in orange. Y327 which lies deep in the trap is highlighted, as is I277, which resides in the translocation tunnel. The yellow arrow depicts the direction substrates move through AcrB.