DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides

Journal Article · · ACS Infectious Diseases
 [1];  [2];  [1]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [3]; ORCiD logo [3];  [2];  [2]; ORCiD logo [5]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [2]; ORCiD logo [1]
  1. Saint Louis University School of Medicine, St. Louis, MO (United States). Dept. of Pharmacology and Physiology
  2. Univ. of Oklahoma, Norman, OK (United States). Dept. of Chemistry and Biochemistry
  3. Univ. of Cagliari, Monserrato, Cagliari (Italy). Dept. of Physics
  4. Univ. of Tennessee, Knoxville, TN (United States). Graduate School of Genome Science and Technology; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  5. Dept. of Veteran Affairs Medical Center, St. Louis, MO (United States)

Antibiotic resistance poses an immediate and growing threat to human health. Multidrug efflux pumps are promising targets for overcoming antibiotic resistance with small-molecule therapeutics. Previously, we identified a diaminoquinoline acrylamide, NSC-33353, as a potent inhibitor of the AcrAB–TolC efflux pump in Escherichia coli. This inhibitor potentiates the antibacterial activities of novobiocin and erythromycin upon binding to the membrane fusion protein AcrA. It is also a substrate for efflux and lacks appreciable intrinsic antibacterial activity of its own in wild-type cells. Here, we have modified the substituents of the cinnamoyl group of NSC-33353, giving rise to analogs that retain the ability to inhibit efflux, lost the features of the efflux substrates, and gained antibacterial activity in wild-type cells. The replacement of the cinnamoyl group with naphthyl isosteres generated compounds that lack antibacterial activity but are both excellent efflux pump inhibitors and substrates. Surprisingly, these inhibitors potentiate the antibacterial activity of novobiocin but not erythromycin. Surface plasmon resonance experiments and molecular docking suggest that the replacement of the cinnamoyl group with naphthyl shifts the affinity of the compounds away from AcrA to the AcrB transporter, making them better efflux substrates and changing their mechanism of inhibition. These results provide new insights into the duality of efflux substrate/inhibitor features in chemical scaffolds that will facilitate the development of new efflux pump inhibitors.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
National Institutes of Health (NIH); National Science Foundation (NSF); USDOE Office of Science (SC)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1820794
Journal Information:
ACS Infectious Diseases, Journal Name: ACS Infectious Diseases Journal Issue: 9 Vol. 7; ISSN 2373-8227
Publisher:
American Chemical Society (ACS)Copyright Statement
Country of Publication:
United States
Language:
English

References (65)

UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility journal December 2009
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading journal January 2009
AcrA is a highly asymmetric protein capable of spanning the periplasm 1 1Edited by I. B. Holland journal January 1999
3-Arylpiperidines as potentiators of existing antibacterial agents journal July 2001
Conformationally-restricted analogues of efflux pump inhibitors that potentiate the activity of levofloxacin in Pseudomonas aeruginosa journal August 2003
Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold journal June 2020
Kinetic analysis of the inhibition of the drug efflux protein AcrB using surface plasmon resonance journal April 2018
MexAB-OprM specific efflux pump inhibitors in Pseudomonas aeruginosa. Part 7: Highly soluble and in vivo active quaternary ammonium analogue D13-9001, a potential preclinical candidate journal November 2007
Structure–activity relationships of a novel pyranopyridine series of Gram-negative bacterial efflux pump inhibitors journal May 2015
Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA journal February 2019
Sequential Mechanism of Assembly of Multidrug Efflux Pump AcrAB-TolC journal April 2011
Toward the Rational Design of Carbapenem Uptake in Pseudomonas aeruginosa journal April 2015
The hydrophobic trap—the Achilles heel of RND efflux pumps journal September 2018
Computer simulations of the activity of RND efflux pumps journal September 2018
Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC journal February 2016
Identification and Structure–Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli journal July 2017
Molecular Interactions of Cephalosporins with the Deep Binding Pocket of the RND Transporter AcrB journal May 2019
Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump journal November 2016
Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins journal July 2018
Small Molecule Condensin Inhibitors journal October 2018
Direct Inhibition of MmpL3 by Novel Antitubercular Compounds journal March 2019
Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly journal September 2019
Drug Permeation against Efflux by Two Transporters journal February 2020
Drug Uptake Pathways of Multidrug Transporter AcrB Studied by Molecular Simulations and Site-Directed Mutagenesis Experiments journal May 2013
Trends and Exceptions of Physical Properties on Antibacterial Activity for Gram-Positive and Gram-Negative Pathogens journal November 2014
Physicochemical Properties of Antibacterial Compounds: Implications for Drug Discovery journal May 2008
Multi-Conformer Ensemble Docking to Difficult Protein Targets journal August 2014
The antibiotic paradox: why companies can’t afford to create life-saving drugs journal August 2020
Crystal structures of a multidrug transporter reveal a functionally rotating mechanism journal August 2006
Structures of the multidrug exporter AcrB reveal a proximal multisite drug-binding pocket journal November 2011
Structural basis for the inhibition of bacterial multidrug exporters journal June 2013
Antibacterial resistance worldwide: causes, challenges and responses journal November 2004
Drugs for bad bugs: confronting the challenges of antibacterial discovery journal December 2006
Multiple entry pathways within the efflux transporter AcrB contribute to multidrug recognition journal January 2018
Structures of the wild-type MexAB–OprM tripartite pump reveal its complex formation and drug efflux mechanism journal April 2019
Regulation of Salmonella typhimurium virulence gene expression by cationic antimicrobial peptides: Salmonella response to antimicrobial peptides journal August 2003
Kinetic control of TolC recruitment by multidrug efflux complexes journal September 2009
Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli journal March 2010
Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations journal November 2012
AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity journal March 2015
Aminoacyl β-naphthylamides as substrates and modulators of AcrB multidrug efflux pump journal January 2016
Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives journal March 2016
The emergence of pan-resistant Gram-negative pathogens merits a rapid global political response journal October 2011
The need for new antibiotics journal January 2004
On the role of TolC in multidrug efflux: the function and assembly of AcrAB-TolC tolerate significant depletion of intracellular TolC protein: Role of TolC in multidrug efflux journal January 2013
Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism journal September 2006
Breaking the permeability barrier of Escherichia coli by controlled hyperporination of the outer membrane. journal October 2016
Troponoids Can Inhibit Growth of the Human Fungal Pathogen Cryptococcus neoformans journal April 2017
Identification and Characterization of Inhibitors of Multidrug Resistance Efflux Pumps in Pseudomonas aeruginosa: Novel Agents for Combination Therapy journal January 2001
Multidrug Efflux Pumps: Expression Patterns and Contribution to Antibiotic Resistance in Pseudomonas aeruginosa Biofilms journal June 2001
Selected Arylpiperazines Are Capable of Reversing Multidrug Resistance in Escherichia coli Overexpressing RND Efflux Pumps journal February 2005
The Challenge of Efflux-Mediated Antibiotic Resistance in Gram-Negative Bacteria journal March 2015
The C-Terminal Domain of AcrA Is Essential for the Assembly and Function of the Multidrug Efflux Pump AcrAB-TolC journal May 2009
Site-Directed Mutagenesis Reveals Putative Substrate Binding Residues in the Escherichia coli RND Efflux Pump AcrB journal October 2008
Chimeric Analysis of the Multicomponent Multidrug Efflux Transporters from Gram-Negative Bacteria journal December 2002
Synergy between Active Efflux and Outer Membrane Diffusion Defines Rules of Antibiotic Permeation into Gram-Negative Bacteria journal October 2017
Structures of Gate Loop Variants of the AcrB Drug Efflux Pump Bound by Erythromycin Substrate journal July 2016
Bifurcation kinetics of drug uptake by Gram-negative bacteria journal September 2017
Impact of multi-drug resistant bacteria on economic and clinical outcomes of healthcare-associated infections in adults: Systematic review and meta-analysis journal January 2020
Mutation and Evolution of Antibiotic Resistance: Antibiotics as Promoters of Antibiotic Resistance? journal August 2002
RND Efflux Pumps: Structural Information Translated into Function and Inhibition Mechanisms journal December 2013
Potential strategies for the eradication of multidrug-resistant Gram-negative bacterial infections journal July 2016
Challenges of antibacterial drug discovery journal July 2019
An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump journal March 2017