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Manrique PD, Leus IV, López CA, Mehla J, Malloci G, Gervasoni S, Vargiu AV, Kinthada RK, Herndon L, Hengartner NW, Walker JK, Rybenkov VV, Ruggerone P, Zgurskaya HI, Gnanakaran S. Predicting permeation of compounds across the outer membrane of P. aeruginosa using molecular descriptors. Commun Chem 2024; 7:84. [PMID: 38609430 PMCID: PMC11015012 DOI: 10.1038/s42004-024-01161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The ability Gram-negative pathogens have at adapting and protecting themselves against antibiotics has increasingly become a public health threat. Data-driven models identifying molecular properties that correlate with outer membrane (OM) permeation and growth inhibition while avoiding efflux could guide the discovery of novel classes of antibiotics. Here we evaluate 174 molecular descriptors in 1260 antimicrobial compounds and study their correlations with antibacterial activity in Gram-negative Pseudomonas aeruginosa. The descriptors are derived from traditional approaches quantifying the compounds' intrinsic physicochemical properties, together with, bacterium-specific from ensemble docking of compounds targeting specific MexB binding pockets, and all-atom molecular dynamics simulations in different subregions of the OM model. Using these descriptors and the measured inhibitory concentrations, we design a statistical protocol to identify predictors of OM permeation/inhibition. We find consistent rules across most of our data highlighting the role of the interaction between the compounds and the OM. An implementation of the rules uncovered in our study is shown, and it demonstrates the accuracy of our approach in a set of previously unseen compounds. Our analysis sheds new light on the key properties drug candidates need to effectively permeate/inhibit P. aeruginosa, and opens the gate to similar data-driven studies in other Gram-negative pathogens.
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Affiliation(s)
- Pedro D Manrique
- Physics Department, George Washington University, Washington, 20052, DC, USA.
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - César A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Rama K Kinthada
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Liam Herndon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University, St. Louis, 63103, MO, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, 20052, CA, Italy
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, 73019, OK, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, 87545, NM, USA.
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2
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Leus IV, Roberts SR, Trinh A, W. Yu E, Zgurskaya HI. Nonadditive functional interactions between ligand-binding sites of the multidrug efflux pump AdeB from Acinetobacter baumannii. J Bacteriol 2024; 206:e0021723. [PMID: 37850798 PMCID: PMC10809976 DOI: 10.1128/jb.00217-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
Multidrug efflux is one of the major mechanisms of antibiotic resistance identified in clinical isolates of the human pathogen Acinetobacter baumannii. The multiple antibiotic resistance in this species is often enabled by the overproduction of the tripartite efflux pump AdeABC. In this pump, AdeB is the inner membrane transporter from the resistance-nodulation-division (RND) superfamily of proteins, which is responsible for the recognition and efflux of multiple structurally unrelated compounds. Like other RND transporters, AdeB is a trimeric protein with ligand-binding sites located in the large periplasmic domains. Previous structural studies, however, highlighted the uniqueness of AdeB interactions with ligands. Up to three ligand molecules were bound to one protomer of AdeB, mapping its substrate translocation path. In this study, we introduced single and double substitutions in the identified ligand-binding sites of AdeB. Our results show that the mechanism of substrate translocation by AdeB is different from that of other characterized RND transporters and that the functional interactions between the sites are nonadditive. We identified AdeB mutants with both the loss and the gain of antibiotic susceptibility phenotypes, as well as AdeB mutations making A. baumannii cells overproducing such pump variants even more susceptible to multiple antibiotics than efflux-deficient cells. IMPORTANCE Multidrug efflux pumps of the resistance-nodulation-division superfamily of proteins are important contributors to various aspects of bacterial physiology and antibiotic resistance. Studies of the best-characterized model transporter AcrB from Escherichia coli suggested that these transporters operate by a functional rotation mechanism in which various substrates bind to at least two different binding sites. This study suggests that the mechanism of AdeB is distinct and that the binding sites in this transporter are functionally linked.
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Affiliation(s)
- Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Sean R. Roberts
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Anhthu Trinh
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Leus IV, Olvera M, Adamiak JW, Nguyen LL, Zgurskaya HI. Acinetobacter baumannii Survival under Infection-Associated Stresses Depends on the Expression of Resistance-Nodulation-Division and Major Facilitator Superfamily Efflux Pumps. Antibiotics (Basel) 2023; 13:7. [PMID: 38275317 PMCID: PMC10812440 DOI: 10.3390/antibiotics13010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Multidrug efflux transporters are major contributors to the antibiotic resistance of Acinetobacter baumannii in clinical settings. Previous studies showed that these transporters are tightly integrated into the physiology of A. baumannii and have diverse functions. However, for many of the efflux pumps, such functions remain poorly defined. In this study, we characterized two putative drug efflux pumps, AmfAB and AmfCD (Acinetobacter Major Facilitator), that are homologous to EmrAB-like transporters from Escherichia coli and other Gram-negative bacteria. These pumps comprise the Major Facilitator Superfamily (MFS) transporters AmfB and AmfD and the periplasmic membrane fusion proteins AmfA and AmfC, respectively. We inactivated and overproduced these pumps in the wild-type ATCC 17978 strain and its derivative strains lacking the major efflux pumps from the Resistance-Nodulation-Division (RND) superfamily and characterized antibiotic susceptibilities and growth of the strains under stresses typical during human infections. We found that neither AmfAB nor AmfCD contribute to the antibiotic non-susceptibility phenotypes of A. baumannii. The two pumps, however, are critical for the adaptation and growth of the bacterium under acidic stress, whereas AmfCD also contributes to growth under conditions of low iron, high temperature, and in the presence of bile salts. These functions are dependent on the presence of the RND pumps, the inactivation of which further diminishes A. baumannii survival and growth. Our results suggest that MFS transporters contribute to stress survival by affecting the permeability properties of the A. baumannii cell envelope.
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Affiliation(s)
| | | | | | | | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73072, USA; (I.V.L.); (M.O.); (J.W.A.); (L.L.N.)
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Hu Z, Leus IV, Chandar B, Sherborne BS, Avila QP, Rybenkov VV, Zgurskaya HI, Duerfeldt AS. Correction to "Structure-Uptake Relationship Studies of Oxazolidinones in Gram-Negative ESKAPE Pathogens". J Med Chem 2023; 66:13858. [PMID: 37733930 DOI: 10.1021/acs.jmedchem.3c01679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
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Gervasoni S, Mehla J, Bergen CR, Leus IV, Margiotta E, Malloci G, Bosin A, Vargiu AV, Lomovskaya O, Rybenkov VV, Ruggerone P, Zgurskaya HI. Molecular determinants of avoidance and inhibition of Pseudomonas aeruginosa MexB efflux pump. mBio 2023; 14:e0140323. [PMID: 37493633 PMCID: PMC10470492 DOI: 10.1128/mbio.01403-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 07/27/2023] Open
Abstract
Transporters of the resistance-nodulation-cell division (RND) superfamily of proteins are the dominant multidrug efflux power of Gram-negative bacteria. The major RND efflux pump of Pseudomonas aeruginosa is MexAB-OprM, in which the inner membrane transporter MexB is responsible for the recognition and binding of compounds. The high importance of this pump in clinical antibiotic resistance made it a subject of intense investigations and a promising target for the discovery of efflux pump inhibitors. This study is focused on a series of peptidomimetic compounds developed as effective inhibitors of MexAB-OprM. We performed multi-copy molecular dynamics simulations, machine-learning (ML) analyses, and site-directed mutagenesis of MexB to investigate interactions of MexB with representatives of efflux avoiders, substrates, and inhibitors. The analysis of both direct and water-mediated protein-ligand interactions revealed characteristic patterns for each class, highlighting significant differences between them. We found that efflux avoiders poorly interact with the access binding site of MexB, and inhibition engages amino acid residues that are not directly involved in binding and transport of substrates. In agreement, machine-learning models selected different residues predictive of MexB substrates and inhibitors. The differences in interactions were further validated by site-directed mutagenesis. We conclude that the substrate translocation and inhibition pathways of MexB split at the interface (between the main putative binding sites) and at the deep binding pocket and that interactions outside of the hydrophobic patch contribute to the inhibition of MexB. This molecular-level information could help in the rational design of new inhibitors and antibiotics less susceptible to the efflux mechanism. IMPORTANCE Multidrug transporters recognize and expel from cells a broad range of ligands including their own inhibitors. The difference between the substrate translocation and inhibition routes remains unclear. In this study, machine learning and computational and experimental approaches were used to understand dynamics of MexB interactions with its ligands. Our results show that some ligands engage a certain combination of polar and charged residues in MexB binding sites to be effectively expelled into the exit funnel, whereas others engage aromatic and hydrophobic residues that slow down or hinder the next step in the transporter cycle. These findings suggest that all MexB ligands fit into this substrate-inhibitor spectrum depending on their physico-chemical structures and properties.
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Affiliation(s)
- Silvia Gervasoni
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Charles R. Bergen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Enrico Margiotta
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Andrea Bosin
- Department of Physics, University of Cagliari, Monserrato, Italy
| | | | | | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Italy
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nath D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Author Correction: Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2023; 13:8918. [PMID: 37264107 DOI: 10.1038/s41598-023-35960-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nath
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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Cao F, Kinthada R, Boehm T, D' Cunha N, Leus IV, Orth C, Zgurskaya HI, Walker JK. Identification and structure-activity relationships for a series of N, N-disubstituted 2-aminobenzothiazoles as potent inhibitors of S. aureus. Bioorg Med Chem Lett 2023; 89:129301. [PMID: 37094726 DOI: 10.1016/j.bmcl.2023.129301] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/02/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023]
Abstract
An internal collection of commercial and synthetically derived small molecule compounds was screened against several drug-resistant bacterial pathogens. Compound 1, a known N, N-disubstituted 2-aminobenzothiazole, was found to be a potent inhibitor of Staphylococcus aureus and several associated clinically relevant strains of methicillin-resistant S. aureus suggesting a possible novel mechanism of inhibition. It failed to show activity in any of the Gram-negative pathogens it was tested in. Evaluation in Escherichia coli BW25113 and Pseudomonas aeruginosa PAO1, as well as in their respective hyperporinated and efflux pump-deletion mutants revealed that activity in Gram-negative bacteria is diminished because this benzothiazole scaffold is a substrate for bacterial efflux pumps. Several analogs of 1 were synthesized to generate basic structure-activity relationships for the scaffold which highlighted that the N-propyl imidazole moiety was critical for the observed antibacterial activity.
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Affiliation(s)
- Feng Cao
- John Cochran Division, Department of Veteran Affairs Medical Center, St. Louis, MO, 63106, United States
| | - Ramakumar Kinthada
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO, 63110, United States
| | - Terri Boehm
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO, 63110, United States
| | - Napoleon D' Cunha
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO, 63110, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73072, United States
| | - Cari Orth
- John Cochran Division, Department of Veteran Affairs Medical Center, St. Louis, MO, 63106, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73072, United States
| | - John K Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, MO, 63110, United States.
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8
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Hu Z, Leus IV, Chandar B, Sherborne BS, Avila QP, Rybenkov VV, Zgurskaya HI, Duerfeldt AS. Structure-Uptake Relationship Studies of Oxazolidinones in Gram-Negative ESKAPE Pathogens. J Med Chem 2022; 65:14144-14179. [PMID: 36257060 PMCID: PMC9942527 DOI: 10.1021/acs.jmedchem.2c01349] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The clinical success of linezolid for treating Gram-positive infections paired with the high conservation of bacterial ribosomes predicts that if oxazolidinones were engineered to accumulate in Gram-negative bacteria, then this pharmacological class would find broad utility in eradicating infections. Here, we report an investigative study of a strategically designed library of oxazolidinones to determine the effects of molecular structure on accumulation and biological activity. Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa strains with varying degrees of compromise (in efflux and outer membrane) were used to identify motifs that hinder permeation across the outer membrane and/or enhance efflux susceptibility broadly and specifically between species. The results illustrate that small changes in molecular structure are enough to overcome the efflux and/or permeation issues of this scaffold. Three oxazolidinone analogues (3e, 8d, and 8o) were identified that exhibit activity against all three pathogens assessed, a biological profile not observed for linezolid.
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Affiliation(s)
- Ziwei Hu
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
| | - Inga V Leus
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Brinda Chandar
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | | | - Quentin P Avila
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Valentin V Rybenkov
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry & Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55414, United States
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9
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Zgurskaya HI, Adamiak JW, Leus IV. Making sense of drug-efflux transporters in the physiological environment. Curr Opin Microbiol 2022; 69:102179. [PMID: 35882103 PMCID: PMC9942525 DOI: 10.1016/j.mib.2022.102179] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]
Abstract
Bacterial drug-efflux transporters act synergistically with diffusion barriers of cellular membranes and other resistance mechanisms to protect cells from antibiotics and toxic metabolites. Their critical roles in clinical antibiotic and multidrug resistance are well established. In addition, a large body of evidence has been accumulated in support of their important contributions to bacterial growth and proliferation during infections. However, how these diverse functions of drug transporters are integrated at the level of bacterial cell physiology remains unclear. This opinion briefly summarizes the current understanding of substrate specificities and physiological roles of drug-efflux pumps from Resistance-Nodulation-Division (RND) superfamily of proteins in two ESKAPE pathogens Pseudomonas aeruginosa and Acinetobacter baumannii. Based on the analysis of phenotypic and transcriptomic studies in vitro and in vivo, we propose that RND pumps of Gram-negative bacteria fall into three categories: constitutively expressed, regulated, and silent. These three categories of efflux pumps participate in different physiological programs, which are not involved in the central metabolism and bacterial growth.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73072, USA.
| | - Justyna W Adamiak
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73072, USA
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73072, USA
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10
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2022; 12:8220. [PMID: 35581346 PMCID: PMC9114115 DOI: 10.1038/s41598-022-12376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023] Open
Abstract
Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nash
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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11
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Leimer N, Wu X, Imai Y, Morrissette M, Pitt N, Favre-Godal Q, Iinishi A, Jain S, Caboni M, Leus IV, Bonifay V, Niles S, Bargabos R, Ghiglieri M, Corsetti R, Krumpoch M, Fox G, Son S, Klepacki D, Polikanov YS, Freliech CA, McCarthy JE, Edmondson DG, Norris SJ, D'Onofrio A, Hu LT, Zgurskaya HI, Lewis K. A selective antibiotic for Lyme disease. Cell 2021; 184:5405-5418.e16. [PMID: 34619078 DOI: 10.1016/j.cell.2021.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 12/11/2022]
Abstract
Lyme disease is on the rise. Caused by a spirochete Borreliella burgdorferi, it affects an estimated 500,000 people in the United States alone. The antibiotics currently used to treat Lyme disease are broad spectrum, damage the microbiome, and select for resistance in non-target bacteria. We therefore sought to identify a compound acting selectively against B. burgdorferi. A screen of soil micro-organisms revealed a compound highly selective against spirochetes, including B. burgdorferi. Unexpectedly, this compound was determined to be hygromycin A, a known antimicrobial produced by Streptomyces hygroscopicus. Hygromycin A targets the ribosomes and is taken up by B. burgdorferi, explaining its selectivity. Hygromycin A cleared the B. burgdorferi infection in mice, including animals that ingested the compound in a bait, and was less disruptive to the fecal microbiome than clinically relevant antibiotics. This selective antibiotic holds the promise of providing a better therapeutic for Lyme disease and eradicating it in the environment.
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Affiliation(s)
- Nadja Leimer
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Xiaoqian Wu
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Yu Imai
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Madeleine Morrissette
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Norman Pitt
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Quentin Favre-Godal
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Akira Iinishi
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Samta Jain
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Mariaelena Caboni
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Samantha Niles
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Rachel Bargabos
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Meghan Ghiglieri
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Rachel Corsetti
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Megan Krumpoch
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Gabriel Fox
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Sangkeun Son
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Cecily A Freliech
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Julie E McCarthy
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Diane G Edmondson
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Steven J Norris
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Anthony D'Onofrio
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Linden T Hu
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, MA 02111, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA.
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12
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D’Cunha N, Moniruzzaman M, Haynes K, Malloci G, Cooper CJ, Margiotta E, Vargiu AV, Uddin MR, Leus IV, Cao F, Parks JM, Rybenkov VV, Ruggerone P, Zgurskaya HI, Walker JK. Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides. ACS Infect Dis 2021; 7:2650-2665. [PMID: 34379382 DOI: 10.1021/acsinfecdis.1c00100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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.
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Affiliation(s)
- Napoleon D’Cunha
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Keith Haynes
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Enrico Margiotta
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Attilio V. Vargiu
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Muhammad R. Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Feng Cao
- John Cochran Division, Department of Veteran Affairs Medical Center, St. Louis, Missouri 63106, United States
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Valentin V. Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Monserrato, Cagliari 09042, Italy
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - John K. Walker
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63110, United States
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13
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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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14
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Morgan CE, Glaza P, Leus IV, Trinh A, Su CC, Cui M, Zgurskaya HI, Yu EW. Cryoelectron Microscopy Structures of AdeB Illuminate Mechanisms of Simultaneous Binding and Exporting of Substrates. mBio 2021; 12:e03690-20. [PMID: 33622726 PMCID: PMC8545137 DOI: 10.1128/mbio.03690-20] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/31/2022] Open
Abstract
Acinetobacter baumannii is a Gram-negative pathogen that has emerged as one of the most highly antibiotic-resistant bacteria worldwide. Multidrug efflux within these highly drug-resistant strains and other opportunistic pathogens is a major cause of failure of drug-based treatments of infectious diseases. The best-characterized multidrug efflux system in A. baumannii is the prevalent Acinetobacterdrug efflux B (AdeB) pump, which is a member of the resistance-nodulation-cell division (RND) superfamily. Here, we report six structures of the trimeric AdeB multidrug efflux pump in the presence of ethidium bromide using single-particle cryoelectron microscopy (cryo-EM). These structures allow us to directly observe various novel conformational states of the AdeB trimer, including the transmembrane region of trimeric AdeB can be associated with form a trimer assembly or dissociated into "dimer plus monomer" and "monomer plus monomer plus monomer" configurations. We also discover that a single AdeB protomer can simultaneously anchor a number of ethidium ligands and that different AdeB protomers can bind ethidium molecules simultaneously. Combined with molecular dynamics (MD) simulations, we reveal a drug transport mechanism that involves multiple multidrug-binding sites and various transient states of the AdeB membrane protein. Our data suggest that each AdeB protomer within the trimer binds and exports drugs independently.IMPORTANCEAcinetobacter baumannii has emerged as one of the most highly antibiotic-resistant Gram-negative pathogens. The prevalent AdeB multidrug efflux pump mediates resistance to a broad spectrum of clinically relevant antimicrobial agents. Here, we report six cryo-EM structures of the trimeric AdeB pump in the presence of ethidium bromide. We discover that a single AdeB protomer can simultaneously anchor a number of ligands, and different AdeB protomers can bind ethidium molecules simultaneously. The results indicate that each AdeB protomer within the trimer recognizes and extrudes drugs independently.
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Affiliation(s)
- Christopher E Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Przemyslaw Glaza
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Anhthu Trinh
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Boston, Massachusetts, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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15
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Leus IV, Adamiak J, Trinh AN, Smith RD, Smith L, Richardson S, Ernst RK, Zgurskaya HI. Inactivation of AdeABC and AdeIJK efflux pumps elicits specific nonoverlapping transcriptional and phenotypic responses in Acinetobacter baumannii. Mol Microbiol 2020; 114:1049-1065. [PMID: 32858760 DOI: 10.1111/mmi.14594] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Multidrug resistant (MDR) strains of Acinetobacter baumannii present a serious clinical challenge. The development of antibiotic resistance in this species is enabled by efflux pumps of the Resistance-Nodulation-Division (RND) superfamily of proteins creating an efficient permeability barrier for antibiotics. At least three RND pumps, AdeABC, AdeIJK, and AdeFGH are encoded in the A. baumannii genome and are reported to contribute to antibiotic resistance in clinical isolates. In this study, we analyzed the contributions of AdeABC and AdeIJK in antibiotic resistance and growth physiology of the two MDR strains, AYE and AB5075. We found that not only the two pumps have nonoverlapping substrate specificities, their inactivation leads to specific nonoverlapping changes in gene expression as determined by RNA sequencing and confirmed by gene knockouts and growth phenotypes. Our results suggest that inactivation of AdeIJK elicits broader changes in the abundances of mRNAs and this response is modified in the absence of AdeB. In contrast, inactivation of AdeB leads to a focused cellular response, which is not sensitive to the activity of AdeIJK. We identified additional efflux pumps and transcriptional regulators that contribute to MDR phenotype of clinical A. baumannii isolates.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Justyna Adamiak
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Anhthu N Trinh
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Richard D Smith
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Lauren Smith
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Sophie Richardson
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
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16
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Fabre L, Ntreh AT, Yazidi A, Leus IV, Weeks JW, Bhattacharyya S, Ruickoldt J, Rouiller I, Zgurskaya HI, Sygusch J. A "Drug Sweeping" State of the TriABC Triclosan Efflux Pump from Pseudomonas aeruginosa. Structure 2020; 29:261-274.e6. [PMID: 32966762 DOI: 10.1016/j.str.2020.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/30/2020] [Accepted: 08/29/2020] [Indexed: 12/01/2022]
Abstract
The structure of the TriABC inner membrane component of the triclosan/SDS-specific efflux pump from Pseudomonas aeruginosa was determined by cryoelectron microscopy to 4.5 Å resolution. The complete structure of the inner membrane transporter TriC of the resistance-nodulation-division (RND) superfamily was solved, including a partial structure of the fused periplasmic membrane fusion subunits, TriA and TriB. The substrate-free conformation of TriABC represents an intermediate step in efflux complex assembly before the engagement of the outer membrane channel. Structural analysis identified a tunnel network whose constriction impedes substrate efflux, indicating inhibition of TriABC in the unengaged state. Blind docking studies revealed binding to TriC at the same loci by substrates and bulkier non-substrates. Together with functional analyses, we propose that selective substrate translocation involves conformational gating at the tunnel narrowing that, together with conformational ordering of TriA and TriB, creates an engaged state capable of mediating substrate efflux.
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Affiliation(s)
- Lucien Fabre
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada
| | - Abigail T Ntreh
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Amira Yazidi
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada
| | - Inga V Leus
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Jon W Weeks
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA
| | - Sudipta Bhattacharyya
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, India
| | - Jakob Ruickoldt
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Isabelle Rouiller
- McGill University, Department of Anatomy and Cell Biology, Montreal, QC H3A 0G4, Canada; Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, 101 Stephenson Parkway, Norman, OK 73019, USA.
| | - Jurgen Sygusch
- University of Montreal, Department of Biochemistry and Molecular Medicine, Medicine, CP 6128, Station Centre-ville, Montreal, QC H3C 3J7, Canada.
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17
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Mansbach RA, Leus IV, Mehla J, Lopez CA, Walker JK, Rybenkov VV, Hengartner NW, Zgurskaya HI, Gnanakaran S. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. J Chem Inf Model 2020; 60:2838-2847. [PMID: 32453589 DOI: 10.1021/acs.jcim.0c00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. In this work, we present proof of concept of an approach to rationally identify a "chemical vocabulary" related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.
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Affiliation(s)
- Rachael A Mansbach
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Cesar A Lopez
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - John K Walker
- Pharmacology and Physiological Science, School of Medicine, Saint Louis University, Schwitalla Hall, Room M362, St. Louis, Missouri 63104, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Nicolas W Hengartner
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - S Gnanakaran
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
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18
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Hazel AJ, Abdali N, Leus IV, Parks JM, Smith JC, Zgurskaya HI, Gumbart JC. Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly. ACS Infect Dis 2019; 5:1926-1935. [PMID: 31517484 DOI: 10.1021/acsinfecdis.9b00273] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. We determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.
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Affiliation(s)
- Anthony J. Hazel
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
| | - Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
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19
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Li Y, Gardner JJ, Fortney KR, Leus IV, Bonifay V, Zgurskaya HI, Pletnev AA, Zhang S, Zhang ZY, Gribble GW, Spinola SM, Duerfeldt AS. First-generation structure-activity relationship studies of 2,3,4,9-tetrahydro-1H-carbazol-1-amines as CpxA phosphatase inhibitors. Bioorg Med Chem Lett 2019; 29:1836-1841. [PMID: 31104993 DOI: 10.1016/j.bmcl.2019.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/26/2022]
Abstract
Genetic activation of the bacterial two-component signal transduction system, CpxRA, abolishes the virulence of a number of pathogens in human and murine infection models. Recently, 2,3,4,9-tetrahydro-1H-carbazol-1-amines were shown to activate the CpxRA system by inhibiting the phosphatase activity of CpxA. Herein we report the initial structure-activity relationships of this scaffold by focusing on three approaches 1) A-ring substitution, 2) B-ring deconstruction to provide N-arylated amino acid derivatives, and 3) C-ring elimination to give 2-ethylamino substituted indoles. These studies demonstrate that the A-ring is amenable to functionalization and provides a promising avenue for continued optimization of this chemotype. Further investigations revealed that the C-ring is not necessary for activity, although it likely provides conformational constraint that is beneficial to potency, and that the (R) stereochemistry is required at the primary amine. Simplification of the scaffold through deconstruction of the B-ring led to inactive compounds, highlighting the importance of the indole core. A new lead compound 26 was identified, which manifests a ∼30-fold improvement in CpxA phosphatase inhibition over the initial hit. Comparison of amino and des-amino derivatives in bacterial strains differing in membrane permeability and efflux capabilities demonstrate that the amine is required not only for target engagement but also for permeation and accumulation in Escherichia coli.
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Affiliation(s)
- Yangxiong Li
- Institute for Natural Products Applications and Research Technologies, Norman, OK 73019-5251, United States; Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, Norman, OK 73019-5251, United States
| | - Jessi J Gardner
- Institute for Natural Products Applications and Research Technologies, Norman, OK 73019-5251, United States; Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, Norman, OK 73019-5251, United States
| | - Katherine R Fortney
- Departments of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Inga V Leus
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, Norman, OK 73019-5251, United States
| | - Vincent Bonifay
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, Norman, OK 73019-5251, United States
| | - Helen I Zgurskaya
- Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, Norman, OK 73019-5251, United States
| | - Alexandre A Pletnev
- Department of Chemistry, Dartmouth College, Hanover New Hampshire, 03755, United States
| | - Sheng Zhang
- Biochemistry, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Zhong-Yin Zhang
- Biochemistry, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States; The Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
| | - Gordon W Gribble
- Department of Chemistry, Dartmouth College, Hanover New Hampshire, 03755, United States
| | - Stanley M Spinola
- Departments of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Adam S Duerfeldt
- Institute for Natural Products Applications and Research Technologies, Norman, OK 73019-5251, United States; Department of Chemistry & Biochemistry, Stephenson Life Sciences Research Center, Norman, OK 73019-5251, United States.
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20
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Leus IV, Weeks JW, Bonifay V, Smith L, Richardson S, Zgurskaya HI. Substrate Specificities and Efflux Efficiencies of RND Efflux Pumps of Acinetobacter baumannii. J Bacteriol 2018; 200:e00049-18. [PMID: 29661860 PMCID: PMC5996695 DOI: 10.1128/jb.00049-18] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 12/19/2022] Open
Abstract
Antibiotic-resistant Acinetobacter baumannii causes infections that are extremely difficult to treat. A significant role in these resistance profiles is attributed to multidrug efflux pumps, especially those belonging to the resistance-nodulation-cell division (RND) superfamily of transporters. In this study, we analyzed functions and properties of RND efflux pumps in A. baumannii ATCC 17978. This strain is susceptible to antibiotics and does not contain mutations that are commonly selected upon exposure to high concentrations of antibiotics. We constructed derivatives of ATCC 17978 lacking chromosomally encoded RND pumps and complemented these strains by the plasmid-borne genes. We analyzed the substrate selectivities and efficiencies of the individual pumps in the context of native outer membranes and their hyperporinated variants. Our results show that inactivation of AdeIJK provides the strongest potentiation of antibiotic activities, whereas inactivation of AdeFGH triggers the overexpression of AdeAB. The plasmid-borne overproduction complements the hypersusceptible phenotypes of the efflux deletion mutants to the levels of the parental ATCC 17978. Only a few antibiotics strongly benefitted from the overproduction of efflux pumps and antibacterial activities of some of those depended on the synergistic interaction with the low permeability barrier of the outer membrane. Either overproduction or inactivation of efflux pumps change dramatically the lipidome of ATCC 17978. We conclude that efflux pumps of A. baumannii are tightly integrated into physiology of this bacterium and that clinical levels of antibiotic resistance in A. baumannii isolates are unlikely to be reached solely due to the overproduction of RND efflux pumps.IMPORTANCE RND-type efflux pumps are important contributors in development of clinical antibiotic resistance in A. baumannii However, their specific roles and the extent of contribution to antibiotic resistance remain unclear. We analyzed antibacterial activities of antibiotics in strains with different permeability barriers and found that the role of active efflux in antibiotic resistance of A. baumannii is limited to a few select antibiotics. Our results further show that the impact of efflux pump overproduction on antibiotic susceptibility is significantly lower than the previously reported for clinical isolates. Additional mechanisms of resistance, in particular those that improve the permeability barriers of bacterial cells and act synergistically with active efflux pumps are likely involved in antibiotic resistance of clinical A. baumannii isolates.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Lauren Smith
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Sophie Richardson
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Leus IV, Shamelashvili KL, Skoryk OD, Tretiak SI, Golichenko OA, Shtemenko OV, Shtemenko NI. [Antioxidant and antitumor activity of dirhenium dicarboxylates in animals with guerin carcinoma]. Ukr Biokhim Zh (1999) 2012; 84:72-81. [PMID: 22860404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The antioxidant and anticancer properties of dirhenium dicarboxylates of cis- and transconfiguration with different organic ligands in a model of tumor growth (Guerin carcinoma) were studied. It was shown that compounds of different configuration had similar antitumor effect, and dirhenium (III) cis-dicarboxylates were characterized by higher antioxidant activity and degree of activation of erythrocyte superoxide dismutase (SOD) in comparison with trans-isomers. The dependence between the structure of dirhenium (III) dicarboxylates and their ability to activate erythrocyte SOD in the model of tumor growth was shown for the first time. The in vitro studies have shown that rhenium compounds of cis- and transconfiguration interacted similarly with erythrocyte SOD, changing the protein secondary structure. In contrast to trans-dicarboxylate, for cis-dicarboxylate the SOD-like activity was demonstrated to be on the first minutes of the xantine-oxidase reaction. The studied features of the interaction between rhenium compounds and SOD in vitro explain only partly the activation of SOD in experiments in vivo. The attempt is made to explain the differences in the mechanisms of antioxidant activity of dirhenium cis- and trans-dicarboxylates.
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