Structural basis for the inhibition of bacterial multidrug exporters

• Published in: Nature (London) Vol. 500; no. 7460; pp. 102 - 106
• Main Authors: Nakashima, Ryosuke, Sakurai, Keisuke, Yamasaki, Seiji, Hayashi, Katsuhiko, Nagata, Chikahiro, Hoshino, Kazuki, Onodera, Yoshikuni, Nishino, Kunihiko, Yamaguchi, Akihito
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.08.2013; Nature Publishing Group
• Subjects: 631/45/612/1237; 631/535/1266; 631/92/577; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - metabolism; Anti-Bacterial Agents - pharmacology; Antibiotics; Bacteria; Bacterial Outer Membrane Proteins - antagonists & inhibitors; Bacterial Outer Membrane Proteins - chemistry; Bacterial Outer Membrane Proteins - metabolism; Bacteriology; Binding Sites; Biological transport; Crystal structure; Crystallography, X-Ray; Crystals; Drug resistance in microorganisms; Escherichia coli - chemistry; Escherichia coli Proteins - antagonists & inhibitors; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Humanities and Social Sciences; Hydrophobic and Hydrophilic Interactions; Identification and classification; Inhibitors; letter; Membrane Transport Proteins - chemistry; Membrane Transport Proteins - metabolism; Microbiological research; Models, Molecular; multidisciplinary; Multidrug Resistance-Associated Proteins - antagonists & inhibitors; Multidrug Resistance-Associated Proteins - chemistry; Multidrug Resistance-Associated Proteins - metabolism; Physiological aspects; Protein Multimerization; Proteins; Pseudomonas aeruginosa; Pseudomonas aeruginosa - chemistry; Pseudomonas aeruginosa - metabolism; Pyridines - chemistry; Pyridines - metabolism; Pyridines - pharmacology; Pyrimidines - chemistry; Pyrimidines - metabolism; Pyrimidines - pharmacology; Pyrimidinones - chemistry; Pyrimidinones - metabolism; Pyrimidinones - pharmacology; Rotation; Science; Structure; Translocation
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature12300

The first inhibitor-bound X-ray crystal structures of the bacterial multidrug efflux transporter AcrB and its homologue MexB are presented, with the inhibitor shown to bind the transporter through a narrow hydrophobic pit, thereby preventing rotation of AcrB and MexB monomers. Bacterial multidrug exporter structures Inhibitors of bacterial multidrug efflux transporters are necessary to combat bacterial multidrug resistance, but no clinically useful inhibitors are currently available. The multidrug efflux transporter AcrB and its homologues facilitate the multidrug resistance of many Gram-negative pathogens, and in this paper Akihito Yamaguchi and colleagues describe the first X-ray crystal structures of inhibitor-bound AcrB and its homologue MexB. The inhibitor, a pyridopyrimidine derivative, binds in a narrow hydrophobic 'pit' and inhibits the functional rotation of the AcrB/MexB monomers. These inhibitor-bound structures may facilitate the development of new inhibitors of this family of multidrug efflux transporters, which could be used in conjunction with existing antibiotics to help make them more effective. The multidrug efflux transporter AcrB and its homologues are important in the multidrug resistance of Gram-negative pathogens 1 , 2 . However, despite efforts to develop efflux inhibitors 3 , clinically useful inhibitors are not available at present 4 , 5 . Pyridopyrimidine derivatives are AcrB- and MexB-specific inhibitors that do not inhibit MexY 6 , 7 ; MexB and MexY are principal multidrug exporters in Pseudomonas aeruginosa 8 , 9 , 10 . We have previously determined the crystal structure of AcrB in the absence and presence of antibiotics 11 , 12 , 13 . Drugs were shown to be exported by a functionally rotating mechanism 12 through tandem proximal and distal multisite drug-binding pockets 13 . Here we describe the first inhibitor-bound structures of AcrB and MexB, in which these proteins are bound by a pyridopyrimidine derivative. The pyridopyrimidine derivative binds tightly to a narrow pit composed of a phenylalanine cluster located in the distal pocket and sterically hinders the functional rotation. This pit is a hydrophobic trap that branches off from the substrate-translocation channel. Phe 178 is located at the edge of this trap in AcrB and MexB and contributes to the tight binding of the inhibitor molecule through a π–π interaction with the pyridopyrimidine ring. The voluminous side chain of Trp 177 located at the corresponding position in MexY prevents inhibitor binding. The structure of the hydrophobic trap described in this study will contribute to the development of universal inhibitors of MexB and MexY in P. aeruginosa .