21
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives.

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The Escherichia coli AcrAB-TolC efflux pump is the archetype of the resistance nodulation cell division (RND) exporters from Gram-negative bacteria. Overexpression of RND-type efflux pumps is a major factor in multidrug resistance (MDR), which makes these pumps important antibacterial drug discovery targets. We have recently developed novel pyranopyridine-based inhibitors of AcrB, which are orders of magnitude more powerful than the previously known inhibitors. However, further development of such inhibitors has been hindered by the lack of structural information for rational drug design. Although only the soluble, periplasmic part of AcrB binds and exports the ligands, the presence of the membrane-embedded domain in AcrB and its polyspecific binding behavior have made cocrystallization with drugs challenging. To overcome this obstacle, we have engineered and produced a soluble version of AcrB [AcrB periplasmic domain (AcrBper)], which is highly congruent in structure with the periplasmic part of the full-length protein, and is capable of binding substrates and potent inhibitors. Here, we describe the molecular basis for pyranopyridine-based inhibition of AcrB using a combination of cellular, X-ray crystallographic, and molecular dynamics (MD) simulations studies. The pyranopyridines bind within a phenylalanine-rich cage that branches from the deep binding pocket of AcrB, where they form extensive hydrophobic interactions. Moreover, the increasing potency of improved inhibitors correlates with the formation of a delicate protein- and water-mediated hydrogen bond network. These detailed insights provide a molecular platform for the development of novel combinational therapies using efflux pump inhibitors for combating multidrug resistant Gram-negative pathogens.

          Related collections

          Author and article information

          Journal
          Proc. Natl. Acad. Sci. U.S.A.
          Proceedings of the National Academy of Sciences of the United States of America
          Proceedings of the National Academy of Sciences
          1091-6490
          0027-8424
          Mar 29 2016
          : 113
          : 13
          Affiliations
          [1 ] Institute of Biochemistry, Goethe University Frankfurt, D-60438 Frankfurt, Germany;
          [2 ] Department of Physics, University of Cagliari, I-09042 Monserrato (CA), Italy; vargiu@dsf.unica.it nhiroshi@berkeley.edu pos@em.uni-frankfurt.de topperman@microbiotix.com.
          [3 ] Department of Molecular and Cell Biology, Microbiotix, Inc., Worcester, MA 01605;
          [4 ] University of California, Berkeley, CA 94720-3202.
          [5 ] Department of Physics, University of Cagliari, I-09042 Monserrato (CA), Italy;
          [6 ] University of California, Berkeley, CA 94720-3202 vargiu@dsf.unica.it nhiroshi@berkeley.edu pos@em.uni-frankfurt.de topperman@microbiotix.com.
          [7 ] Institute of Biochemistry, Goethe University Frankfurt, D-60438 Frankfurt, Germany; vargiu@dsf.unica.it nhiroshi@berkeley.edu pos@em.uni-frankfurt.de topperman@microbiotix.com.
          [8 ] Department of Molecular and Cell Biology, Microbiotix, Inc., Worcester, MA 01605; vargiu@dsf.unica.it nhiroshi@berkeley.edu pos@em.uni-frankfurt.de topperman@microbiotix.com.
          Article
          1602472113
          10.1073/pnas.1602472113
          4822567
          26976576
          f5f16bae-2b27-47b9-aa63-5217455b0909
          History

          RND efflux transporters,X-ray crystallography,efflux pump inhibitors,molecular dynamics simulation,multidrug resistance

          Comments

          Comment on this article