title: Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors.
abstract: Efflux pumps of the resistance nodulation division (RND) superfamily, such as AcrB, make a major contribution to multidrug resistance in Gram-negative bacteria. The development of inhibitors of the RND pumps would improve the efficacy of current and next-generation antibiotics. To date, however, only one inhibitor has been cocrystallized with AcrB. Thus, in silico structure-based analysis is essential for elucidating the interaction between other inhibitors and the efflux pumps. In this work, we used computer docking and molecular dynamics simulations to study the interaction between AcrB and the compound MBX2319, a novel pyranopyridine efflux pump inhibitor with potent activity against RND efflux pumps of Enterobacteriaceae species, as well as other known inhibitors (D13-9001, 1-[1-naphthylmethyl]-piperazine, and phenylalanylarginine-β-naphthylamide) and the binding of doxorubicin to the efflux-defective F610A variant of AcrB. We also analyzed the binding of a substrate, minocycline, for comparison. Our results show that MBX2319 binds very tightly to the lower part of the distal pocket in the B protomer of AcrB, strongly interacting with the phenylalanines lining the hydrophobic trap, where the hydrophobic portion of D13-9001 was found to bind by X-ray crystallography. Additionally, MBX2319 binds to AcrB in a manner that is similar to the way in which doxorubicin binds to the F610A variant of AcrB. In contrast, 1-(1-naphthylmethyl)-piperazine and phenylalanylarginine-β-naphthylamide appear to bind to somewhat different areas of the distal pocket in the B protomer of AcrB than does MBX2319. However, all inhibitors (except D13-9001) appear to distort the structure of the distal pocket, impairing the proper binding of substrates.
authors.affiliation: Department of Physics, University of Cagliari, Monserrato, Cagliari, Italy.
authors.forename: Attilio V
authors.initials: AV
authors.lastname: Vargiu
authors.affiliation: Department of Physics, University of Cagliari, Monserrato, Cagliari, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ruggerone
authors.affiliation: Microbiotix, Inc., Worcester, Massachusetts, USA.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Opperman
authors.affiliation: Microbiotix, Inc., Worcester, Massachusetts, USA.
authors.forename: Son T
authors.initials: ST
authors.lastname: Nguyen
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, California, USA nhiroshi@berkeley.edu.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Nikaido
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D004151:Dipeptides / Q000494:pharmacology; D004926:Escherichia coli / Q000187:drug effects* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors*; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000037:antagonists & inhibitors*; D010879:Piperazines / Q000494:pharmacology; D011714:Pyrans / Q000494:pharmacology*; D011725:Pyridines / Q000494:pharmacology*
chemical_list: D000900:Anti-Bacterial Agents; D004151:Dipeptides; D029968:Escherichia coli Proteins; D027425:ATP-Binding Cassette, Sub-Family C Proteins; D010879:Piperazines; D011714:Pyrans; D011725:Pyridines; C511391:1-(1-naphthylmethyl)piperazine; C083496:AcrB protein, E coli; C000591634:MBX2319; C474925:phenylalanylarginine-naphthylamide
references.citation: Nature. 2011 Nov 27;480(7378):565-9
references.pmid: 22121023
references.citation: Recent Pat Antiinfect Drug Discov. 2012 Apr;7(1):73-89
references.pmid: 22353004
references.citation: Antimicrob Agents Chemother. 2010 Sep;54(9):3717-22
references.pmid: 20585122
references.citation: Recent Pat Antiinfect Drug Discov. 2009 Jan;4(1):37-50
references.pmid: 19149695
references.citation: Antimicrob Agents Chemother. 2001 Jan;45(1):105-16
references.pmid: 11120952
references.citation: J Antimicrob Chemother. 2007 Jun;59(6):1223-9
references.pmid: 17229832
references.citation: Open Microbiol J. 2013;7:34-52
references.pmid: 23569468
references.citation: J Bacteriol. 2011 Oct;193(20):5847-9
references.pmid: 21856849
references.citation: J Am Chem Soc. 2011 Jul 20;133(28):10704-7
references.pmid: 21707050
references.citation: J Antimicrob Chemother. 2007 Jun;59(6):1247-60
references.pmid: 17145734
references.citation: Biochemistry. 2013 May 28;52(21):3752-64
references.pmid: 23627712
references.citation: J Bacteriol. 1997 Oct;179(19):6122-6
references.pmid: 9324261
references.citation: J Antimicrob Chemother. 2010 Jun;65(6):1215-23
references.pmid: 20304975
references.citation: J Phys Chem B. 2011 Jun 30;115(25):8278-87
references.pmid: 21657235
references.citation: Curr Top Med Chem. 2013;13(24):3079-100
references.pmid: 24200360
references.citation: Antimicrob Agents Chemother. 2009 Jan;53(1):329-30
references.pmid: 18936189
references.citation: Curr Opin Microbiol. 2009 Oct;12(5):512-9
references.pmid: 19664953
references.citation: Antimicrob Agents Chemother. 2005 Feb;49(2):849-52
references.pmid: 15673787
references.citation: Adv Enzymol Relat Areas Mol Biol. 2011;77:1-60
references.pmid: 21692366
references.citation: Trends Biochem Sci. 2014 Jan;39(1):8-16
references.pmid: 24316304
references.citation: J Bacteriol. 2005 Oct;187(19):6804-15
references.pmid: 16166543
references.citation: Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20637-42
references.pmid: 23175790
references.citation: J Bacteriol. 1993 Oct;175(19):6299-313
references.pmid: 8407802
references.citation: Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16696-701
references.pmid: 23010927
references.citation: PLoS One. 2011 Apr 12;6(4):e18547
references.pmid: 21533264
references.citation: J Bacteriol. 1996 Oct;178(20):5853-9
references.pmid: 8830678
references.citation: Drugs. 2009 Aug 20;69(12):1555-623
references.pmid: 19678712
references.citation: Curr Pharm Des. 2011;17(13):1291-302
references.pmid: 21470111
references.citation: Biochim Biophys Acta. 2009 May;1794(5):769-81
references.pmid: 19026770
references.citation: Science. 2006 Sep 1;313(5791):1295-8
references.pmid: 16946072
references.citation: J Comput Chem. 2005 Dec;26(16):1781-802
references.pmid: 16222654
references.citation: Nature. 2002 Oct 10;419(6907):587-93
references.pmid: 12374972
references.citation: J Am Chem Soc. 2012 Nov 21;134(46):19146-58
references.pmid: 23146101
references.citation: PLoS Comput Biol. 2010 Jun 10;6(6):e1000806
references.pmid: 20548943
references.citation: Annu Rev Biochem. 2009;78:119-46
references.pmid: 19231985
references.citation: Nat Struct Mol Biol. 2008 Feb;15(2):199-205
references.pmid: 18223659
references.citation: J Mol Biol. 2011 Aug 5;411(1):264-74
references.pmid: 21664361
references.citation: Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6559-65
references.pmid: 20212112
references.citation: Biochemistry. 2013 Nov 19;52(46):8342-51
references.pmid: 24205856
references.citation: Nature. 2006 Sep 14;443(7108):173-9
references.pmid: 16915237
references.citation: J Bacteriol. 2008 Dec;190(24):8225-9
references.pmid: 18849422
references.citation: J Comput Chem. 2010 Jan 30;31(2):455-61
references.pmid: 19499576
references.citation: Antimicrob Agents Chemother. 2010 Sep;54(9):3770-5
references.pmid: 20606071
references.citation: PLoS One. 2011;6(6):e21196
references.pmid: 21698261
references.citation: Nat Commun. 2010 Nov 16;1:117
references.pmid: 21081915
references.citation: Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5687-92
references.pmid: 22451937
references.citation: Antimicrob Agents Chemother. 2014;58(2):722-33
references.pmid: 24247144
references.citation: J Bacteriol. 2007 Dec;189(23):8677-84
references.pmid: 17905989
references.citation: J Antimicrob Chemother. 2007 Jun;59(6):1216-22
references.pmid: 17062614
references.citation: PLoS Biol. 2007 Jan;5(1):e7
references.pmid: 17194213
references.citation: Nat Rev Microbiol. 2011 Nov 02;9(12):894-6
references.pmid: 22048738
references.citation: J Bacteriol. 2009 Mar;191(6):1729-37
references.pmid: 19060146
references.citation: Curr Med Chem. 2007;14(4):393-415
references.pmid: 17305542
references.citation: Mol Microbiol. 2010 Oct;78(2):320-30
references.pmid: 20804453
references.citation: Nature. 2014 May 22;509(7501):512-5
references.pmid: 24747401
references.citation: J Antimicrob Chemother. 2006 Feb;57(2):339-43
references.pmid: 16354747
references.citation: Biochem Pharmacol. 2006 Mar 30;71(7):910-8
references.pmid: 16427026
references.citation: Annu Rep Comput Chem. 2009 Jan 1;5:23-48
references.pmid: 20454547
references.citation: Acc Chem Res. 2000 Dec;33(12):889-97
references.pmid: 11123888
references.citation: J Mol Recognit. 2002 Nov-Dec;15(6):377-92
references.pmid: 12501158
references.citation: FEMS Microbiol Rev. 2012 Mar;36(2):340-63
references.pmid: 21707670
references.citation: Bioorg Med Chem. 2007 Nov 15;15(22):7087-97
references.pmid: 17869116
references.citation: J Bacteriol. 2000 Sep;182(17):4803-10
references.pmid: 10940021
references.citation: Comput Struct Biotechnol J. 2013 Mar 03;5:e201302008
references.pmid: 24688701
references.citation: Nature. 2013 Aug 1;500(7460):102-6
references.pmid: 23812586