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Structural basis of RND-type multidrug exporters.

Yamaguchi A, Nakashima R, Sakurai K - Front Microbiol (2015)

Bottom Line: Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules.Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel.Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan.

ABSTRACT
Bacterial multidrug exporters are intrinsic membrane transporters that act as cellular self-defense mechanism. The most notable characteristics of multidrug exporters is that they export a wide range of drugs and toxic compounds. The overexpression of these exporters causes multidrug resistance. Multidrug-resistant pathogens have become a serious problem in modern chemotherapy. Over the past decade, investigations into the structure of bacterial multidrug exporters have revealed the multidrug recognition and export mechanisms. In this review, we primarily discuss RND-type multidrug exporters particularly AcrAB-TolC, major drug exporter in Gram-negative bacteria. RND-type drug exporters are tripartite complexes comprising a cell membrane transporter, an outer membrane channel and an adaptor protein. Cell membrane transporters and outer membrane channels are homo-trimers; however, there is no consensus on the number of adaptor proteins in these tripartite complexes. The three monomers of a cell membrane transporter have varying conformations (access, binding, and extrusion) during transport. Drugs are exported following an ordered conformational change in these three monomers, through a functional rotation mechanism coupled with the proton relay cycle in ion pairs, which is driven by proton translocation. Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules. The voluminous multidrug-binding pocket may have numerous binding sites even for a single substrate, suggesting that substrates may move between binding sites during transport, an idea named as multisite-drug-oscillation hypothesis. This hypothesis is consistent with the apparently broad substrate specificity of cell membrane exporters and their highly efficient ejection of drugs from the cell. Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel. Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.

No MeSH data available.


Related in: MedlinePlus

Magnified view of the ABI-PP binding site depicted as a surface model. ABI-PP is depicted in a stick model. F178 and W177 are depicted using a white space-filling model. V139, I138, and mutated Ala are depicted shown in magenta in the space-filling model. The symbols + and − indicate inhibition or the lack of inhibition by ABI-PP, respectively. (A,B,E,F) are crystal structures, and (C,D,G,H) are homology models. (A) ABI-PP-binding AcrB, (B) ABI-PP-binding MexB, (C) MexY overlapping with ABI-PP. (D) MexY W177F overlapping with ABI-PP, (E) AcrB F178W overlapping with ABI-PP, (F) ABI-PP-binding MexAB F178W, (G) AcrB F178W V139A overlapping with ABI-PP, (H) MexY I138A overlapping with ABI-PP.
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Figure 15: Magnified view of the ABI-PP binding site depicted as a surface model. ABI-PP is depicted in a stick model. F178 and W177 are depicted using a white space-filling model. V139, I138, and mutated Ala are depicted shown in magenta in the space-filling model. The symbols + and − indicate inhibition or the lack of inhibition by ABI-PP, respectively. (A,B,E,F) are crystal structures, and (C,D,G,H) are homology models. (A) ABI-PP-binding AcrB, (B) ABI-PP-binding MexB, (C) MexY overlapping with ABI-PP. (D) MexY W177F overlapping with ABI-PP, (E) AcrB F178W overlapping with ABI-PP, (F) ABI-PP-binding MexAB F178W, (G) AcrB F178W V139A overlapping with ABI-PP, (H) MexY I138A overlapping with ABI-PP.

Mentions: Although RND-type transporters display a broad substrate recognition spectrum, these proteins show strict specificity for some inhibitors. Pyridopyrimidine derivatives are good inhibitors of AcrB and MexB without toxic effects: however, these compounds do not inhibit MexY (Yoshida et al., 2007). The narrow spectrum of pyridopyrimidines limits the clinical usefulness of these molecules. The structural basis of inhibitor specificity has been revealed through an analysis of the inhibitor-bound crystal structure of AcrB and MexB (Nakashima et al., 2013). The pyridopyrimidine derivative ABI-PP binds to the distal pocket of AcrB and MexB. The hydrophobic tail of ABI-PP is inserted into a narrow hydrophobic pit branching off the substrate translocation path (Figure 14). The binding site of the relatively hydrophilic moiety of ABI-PP overlaps with the minocycline and doxorubicin binding sites. The branched pit is inconsistent with a hydrophobic trap in the distal binding pocket (Vargiu et al., 2011). The F610A mutation in this pit caused slip-in of substrates into this pit, resulting in decreased export activity. Phe178 is located at the edge of this pit in AcrB and MexB, and the benzene ring of this amino acid forms π - π interactions with the pyridopyrimidine bicyclic ring, thereby stabilizing ABI-PP binding (Figures 15A,B). The inhibitory activity of ABI-PP is based on strong binding to this pit, which terminates the functional-rotation cycle because this pit has to become closed off for transition to the extrusion stage.


Structural basis of RND-type multidrug exporters.

Yamaguchi A, Nakashima R, Sakurai K - Front Microbiol (2015)

Magnified view of the ABI-PP binding site depicted as a surface model. ABI-PP is depicted in a stick model. F178 and W177 are depicted using a white space-filling model. V139, I138, and mutated Ala are depicted shown in magenta in the space-filling model. The symbols + and − indicate inhibition or the lack of inhibition by ABI-PP, respectively. (A,B,E,F) are crystal structures, and (C,D,G,H) are homology models. (A) ABI-PP-binding AcrB, (B) ABI-PP-binding MexB, (C) MexY overlapping with ABI-PP. (D) MexY W177F overlapping with ABI-PP, (E) AcrB F178W overlapping with ABI-PP, (F) ABI-PP-binding MexAB F178W, (G) AcrB F178W V139A overlapping with ABI-PP, (H) MexY I138A overlapping with ABI-PP.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403515&req=5

Figure 15: Magnified view of the ABI-PP binding site depicted as a surface model. ABI-PP is depicted in a stick model. F178 and W177 are depicted using a white space-filling model. V139, I138, and mutated Ala are depicted shown in magenta in the space-filling model. The symbols + and − indicate inhibition or the lack of inhibition by ABI-PP, respectively. (A,B,E,F) are crystal structures, and (C,D,G,H) are homology models. (A) ABI-PP-binding AcrB, (B) ABI-PP-binding MexB, (C) MexY overlapping with ABI-PP. (D) MexY W177F overlapping with ABI-PP, (E) AcrB F178W overlapping with ABI-PP, (F) ABI-PP-binding MexAB F178W, (G) AcrB F178W V139A overlapping with ABI-PP, (H) MexY I138A overlapping with ABI-PP.
Mentions: Although RND-type transporters display a broad substrate recognition spectrum, these proteins show strict specificity for some inhibitors. Pyridopyrimidine derivatives are good inhibitors of AcrB and MexB without toxic effects: however, these compounds do not inhibit MexY (Yoshida et al., 2007). The narrow spectrum of pyridopyrimidines limits the clinical usefulness of these molecules. The structural basis of inhibitor specificity has been revealed through an analysis of the inhibitor-bound crystal structure of AcrB and MexB (Nakashima et al., 2013). The pyridopyrimidine derivative ABI-PP binds to the distal pocket of AcrB and MexB. The hydrophobic tail of ABI-PP is inserted into a narrow hydrophobic pit branching off the substrate translocation path (Figure 14). The binding site of the relatively hydrophilic moiety of ABI-PP overlaps with the minocycline and doxorubicin binding sites. The branched pit is inconsistent with a hydrophobic trap in the distal binding pocket (Vargiu et al., 2011). The F610A mutation in this pit caused slip-in of substrates into this pit, resulting in decreased export activity. Phe178 is located at the edge of this pit in AcrB and MexB, and the benzene ring of this amino acid forms π - π interactions with the pyridopyrimidine bicyclic ring, thereby stabilizing ABI-PP binding (Figures 15A,B). The inhibitory activity of ABI-PP is based on strong binding to this pit, which terminates the functional-rotation cycle because this pit has to become closed off for transition to the extrusion stage.

Bottom Line: Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules.Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel.Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University Ibaraki, Japan.

ABSTRACT
Bacterial multidrug exporters are intrinsic membrane transporters that act as cellular self-defense mechanism. The most notable characteristics of multidrug exporters is that they export a wide range of drugs and toxic compounds. The overexpression of these exporters causes multidrug resistance. Multidrug-resistant pathogens have become a serious problem in modern chemotherapy. Over the past decade, investigations into the structure of bacterial multidrug exporters have revealed the multidrug recognition and export mechanisms. In this review, we primarily discuss RND-type multidrug exporters particularly AcrAB-TolC, major drug exporter in Gram-negative bacteria. RND-type drug exporters are tripartite complexes comprising a cell membrane transporter, an outer membrane channel and an adaptor protein. Cell membrane transporters and outer membrane channels are homo-trimers; however, there is no consensus on the number of adaptor proteins in these tripartite complexes. The three monomers of a cell membrane transporter have varying conformations (access, binding, and extrusion) during transport. Drugs are exported following an ordered conformational change in these three monomers, through a functional rotation mechanism coupled with the proton relay cycle in ion pairs, which is driven by proton translocation. Multidrug recognition is based on a multisite drug-binding mechanism, in which two voluminous multidrug-binding pockets in cell membrane exporters recognize a wide range of substrates as a result of permutations at numerous binding sites that are specific for the partial structures of substrate molecules. The voluminous multidrug-binding pocket may have numerous binding sites even for a single substrate, suggesting that substrates may move between binding sites during transport, an idea named as multisite-drug-oscillation hypothesis. This hypothesis is consistent with the apparently broad substrate specificity of cell membrane exporters and their highly efficient ejection of drugs from the cell. Substrates are transported through dual multidrug-binding pockets via the peristaltic motion of the substrate translocation channel. Although there are no clinically available inhibitors of bacterial multidrug exporters, efforts to develop inhibitors based on structural information are underway.

No MeSH data available.


Related in: MedlinePlus