1
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Adolph C, Cheung CY, McNeil MB, Jowsey WJ, Williams ZC, Hards K, Harold LK, Aboelela A, Bujaroski RS, Buckley BJ, Tyndall JDA, Li Z, Langer JD, Preiss L, Meier T, Steyn AJC, Rhee KY, Berney M, Kelso MJ, Cook GM. A dual-targeting succinate dehydrogenase and F 1F o-ATP synthase inhibitor rapidly sterilizes replicating and non-replicating Mycobacterium tuberculosis. Cell Chem Biol 2024; 31:683-698.e7. [PMID: 38151019 DOI: 10.1016/j.chembiol.2023.12.002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023]
Abstract
Mycobacterial bioenergetics is a validated target space for antitubercular drug development. Here, we identify BB2-50F, a 6-substituted 5-(N,N-hexamethylene)amiloride derivative as a potent, multi-targeting bioenergetic inhibitor of Mycobacterium tuberculosis. We show that BB2-50F rapidly sterilizes both replicating and non-replicating cultures of M. tuberculosis and synergizes with several tuberculosis drugs. Target identification experiments, supported by docking studies, showed that BB2-50F targets the membrane-embedded c-ring of the F1Fo-ATP synthase and the catalytic subunit (substrate-binding site) of succinate dehydrogenase. Biochemical assays and metabolomic profiling showed that BB2-50F inhibits succinate oxidation, decreases the activity of the tricarboxylic acid (TCA) cycle, and results in succinate secretion from M. tuberculosis. Moreover, we show that the lethality of BB2-50F under aerobic conditions involves the accumulation of reactive oxygen species. Overall, this study identifies BB2-50F as an effective inhibitor of M. tuberculosis and highlights that targeting multiple components of the mycobacterial respiratory chain can produce fast-acting antimicrobials.
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Affiliation(s)
- Cara Adolph
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - William J Jowsey
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand
| | - Zoe C Williams
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Ashraf Aboelela
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Richard S Bujaroski
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Benjamin J Buckley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Joel D A Tyndall
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou, China
| | - Julian D Langer
- Proteomics, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Laura Preiss
- Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, UK; Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu Natal, Durban, KwaZulu, Natal, South Africa; Department of Microbiology, Centers for AIDs Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY 14853, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael J Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1042, New Zealand.
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2
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Waller NJE, Cheung CY, Cook GM, McNeil MB. The evolution of antibiotic resistance is associated with collateral drug phenotypes in Mycobacterium tuberculosis. Nat Commun 2023; 14:1517. [PMID: 36934122 PMCID: PMC10024696 DOI: 10.1038/s41467-023-37184-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
The increasing incidence of drug resistance in Mycobacterium tuberculosis has diminished the efficacy of almost all available antibiotics, complicating efforts to combat the spread of this global health burden. Alongside the development of new drugs, optimised drug combinations are needed to improve treatment success and prevent the further spread of antibiotic resistance. Typically, antibiotic resistance leads to reduced sensitivity, yet in some cases the evolution of drug resistance can lead to enhanced sensitivity to unrelated drugs. This phenomenon of collateral sensitivity is largely unexplored in M. tuberculosis but has the potential to identify alternative therapeutic strategies to combat drug-resistant strains that are unresponsive to current treatments. Here, by using drug susceptibility profiling, genomics and evolutionary studies we provide evidence for the existence of collateral drug sensitivities in an isogenic collection M. tuberculosis drug-resistant strains. Furthermore, in proof-of-concept studies, we demonstrate how collateral drug phenotypes can be exploited to select against and prevent the emergence of drug-resistant strains. This study highlights that the evolution of drug resistance in M. tuberculosis leads to collateral drug responses that can be exploited to design improved drug regimens.
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Affiliation(s)
- Natalie J E Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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3
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Berube BJ, Larsen SE, McNeil MB, Reese VA, Pecor T, Kaur S, Parish T, Baldwin SL, Coler RN. Characterizing in vivo loss of virulence of an HN878 Mycobacterium tuberculosis isolate from a genetic duplication event. Tuberculosis (Edinb) 2022; 137:102272. [PMID: 36375278 PMCID: PMC10019580 DOI: 10.1016/j.tube.2022.102272] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022]
Abstract
The increase of global cases of drug resistant (DR) Mycobacterium tuberculosis (M.tb) is a serious problem for the tuberculosis research community and the goals to END TB by 2030. Due to the need for advancing and screening next generation therapeutics and vaccines, we aimed to design preclinical DR models of Beijing lineage M.tb HN878 strain in different mouse backgrounds. We found escalating sensitivities of morbidity due to low dose aerosol challenge (50-100 bacilli) in CB6F1, C57BL/6 and SWR mice, respectively. We also observed that pulmonary bacterial burden at morbidity endpoints correlated inversely with survival over time between mouse strains. Interestingly, with in vitro passaging and in the process of selecting individual DR mutant colonies, we observed a significant decrease in in vivo HN878 strain virulence, which correlated with the acquisition of a large genetic duplication. We confirmed that low passage infection stocks with no or low prevalence of the duplication, including stocks directly acquired from the BEI resources biorepository, retained virulence, measured by morbidity over time. These data help confirm previous reports and emphasize the importance of monitoring virulence and stock fidelity.
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Affiliation(s)
- Bryan J Berube
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Sasha E Larsen
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Valerie A Reese
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Tiffany Pecor
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Suhavi Kaur
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Tanya Parish
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Susan L Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Rhea N Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA.
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4
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McNeil MB, Cheung CY, Waller NJE, Adolph C, Chapman CL, Seeto NEJ, Jowsey W, Li Z, Hameed HMA, Zhang T, Cook GM. Uncovering interactions between mycobacterial respiratory complexes to target drug-resistant Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:980844. [PMID: 36093195 PMCID: PMC9461714 DOI: 10.3389/fcimb.2022.980844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis remains a leading cause of infectious disease morbidity and mortality for which new drug combination therapies are needed. Mycobacterial bioenergetics has emerged as a promising space for the development of novel therapeutics. Further to this, unique combinations of respiratory inhibitors have been shown to have synergistic or synthetic lethal interactions, suggesting that combinations of bioenergetic inhibitors could drastically shorten treatment times. Realizing the full potential of this unique target space requires an understanding of which combinations of respiratory complexes, when inhibited, have the strongest interactions and potential in a clinical setting. In this review, we discuss (i) chemical-interaction, (ii) genetic-interaction and (iii) chemical-genetic interaction studies to explore the consequences of inhibiting multiple mycobacterial respiratory components. We provide potential mechanisms to describe the basis for the strongest interactions. Finally, whilst we place an emphasis on interactions that occur with existing bioenergetic inhibitors, by highlighting interactions that occur with alternative respiratory components we envision that this information will provide a rational to further explore alternative proteins as potential drug targets and as part of unique drug combinations.
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Affiliation(s)
- Matthew B. McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins, Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- *Correspondence: Matthew B. McNeil, ; Gregory M. Cook,
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Natalie J. E. Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Cara Adolph
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Cassandra L. Chapman
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Noon E. J. Seeto
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - William Jowsey
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou, China
| | - H. M. Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins, Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- *Correspondence: Matthew B. McNeil, ; Gregory M. Cook,
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5
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Harold LK, Jinich A, Hards K, Cordeiro A, Keighley LM, Cross A, McNeil MB, Rhee K, Cook GM. Deciphering functional redundancy and energetics of malate oxidation in mycobacteria. J Biol Chem 2022; 298:101859. [PMID: 35337802 PMCID: PMC9062433 DOI: 10.1016/j.jbc.2022.101859] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
Oxidation of malate to oxaloacetate, catalyzed by either malate dehydrogenase (Mdh) or malate quinone oxidoreductase (Mqo), is a critical step of the tricarboxylic acid cycle. Both Mqo and Mdh are found in most bacterial genomes, but the level of functional redundancy between these enzymes remains unclear. A bioinformatic survey revealed that Mqo was not as widespread as Mdh in bacteria but that it was highly conserved in mycobacteria. We therefore used mycobacteria as a model genera to study the functional role(s) of Mqo and its redundancy with Mdh. We deleted mqo from the environmental saprophyte Mycobacterium smegmatis, which lacks Mdh, and found that Mqo was essential for growth on nonfermentable carbon sources. On fermentable carbon sources, the Δmqo mutant exhibited delayed growth and lowered oxygen consumption and secreted malate and fumarate as terminal end products. Furthermore, heterologous expression of Mdh from the pathogenic species Mycobacterium tuberculosis shortened the delayed growth on fermentable carbon sources and restored growth on nonfermentable carbon sources at a reduced growth rate. In M. tuberculosis, CRISPR interference of either mdh or mqo expression resulted in a slower growth rate compared to controls, which was further inhibited when both genes were knocked down simultaneously. These data reveal that exergonic Mqo activity powers mycobacterial growth under nonenergy limiting conditions and that endergonic Mdh activity complements Mqo activity, but at an energetic cost for mycobacterial growth. We propose Mdh is maintained in slow-growing mycobacterial pathogens for use under conditions such as hypoxia that require reductive tricarboxylic acid cycle activity.
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Affiliation(s)
- Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Alexandra Cordeiro
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Laura M Keighley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alec Cross
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Kyu Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.
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6
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Hards K, Cheung CY, Waller N, Adolph C, Keighley L, Tee ZS, Harold LK, Menorca A, Bujaroski RS, Buckley BJ, Tyndall JDA, McNeil MB, Rhee KY, Opel-Reading HK, Krause K, Preiss L, Langer JD, Meier T, Hasenoehrl EJ, Berney M, Kelso MJ, Cook GM. An amiloride derivative is active against the F 1F o-ATP synthase and cytochrome bd oxidase of Mycobacterium tuberculosis. Commun Biol 2022; 5:166. [PMID: 35210534 PMCID: PMC8873251 DOI: 10.1038/s42003-022-03110-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Increasing antimicrobial resistance compels the search for next-generation inhibitors with differing or multiple molecular targets. In this regard, energy conservation in Mycobacterium tuberculosis has been clinically validated as a promising new drug target for combatting drug-resistant strains of M. tuberculosis. Here, we show that HM2-16F, a 6-substituted derivative of the FDA-approved drug amiloride, is an anti-tubercular inhibitor with bactericidal properties comparable to the FDA-approved drug bedaquiline (BDQ; Sirturo®) and inhibits the growth of bedaquiline-resistant mutants. We show that HM2-16F weakly inhibits the F1Fo-ATP synthase, depletes ATP, and affects the entry of acetyl-CoA into the Krebs cycle. HM2-16F synergizes with the cytochrome bcc-aa3 oxidase inhibitor Q203 (Telacebec) and co-administration with Q203 sterilizes in vitro cultures in 14 days. Synergy with Q203 occurs via direct inhibition of the cytochrome bd oxidase by HM2-16F. This study shows that amiloride derivatives represent a promising discovery platform for targeting energy generation in drug-resistant tuberculosis. Derivatives of the FDA-approved drug, amiloride, can eliminate drug-resistant Mycobacterium tuberculosis in vitro by interfering with bacterial energy conservation.
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Affiliation(s)
- Kiel Hards
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Otago, Dunedin, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Natalie Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Cara Adolph
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laura Keighley
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Zhi Shean Tee
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Otago, Dunedin, New Zealand
| | - Ayana Menorca
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Richard S Bujaroski
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Benjamin J Buckley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia.,Illawarra Health and Medical Research Institute, Wollongong, Australia
| | | | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Otago, Dunedin, New Zealand
| | - Kyu Y Rhee
- Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Kurt Krause
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Otago, Dunedin, New Zealand
| | - Laura Preiss
- Department of Structural Biology, Max-Planck Institute of Biophysics, Frankfurt am Main, Germany.,Octapharma Biopharmaceuticals GmbH, Heidelberg, Germany
| | - Julian D Langer
- Department of Molecular Membrane Biology, Max-Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Thomas Meier
- Department of Life Sciences, Imperial College London, London, UK.,Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Erik J Hasenoehrl
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael Berney
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA
| | - Michael J Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, Australia. .,Illawarra Health and Medical Research Institute, Wollongong, Australia.
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Otago, Dunedin, New Zealand.
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7
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Cheung CY, McNeil MB, Cook GM. Utilization of CRISPR interference to investigate the contribution of genes to pathogenesis in a macrophage model of Mycobacterium tuberculosis infection. J Antimicrob Chemother 2021; 77:615-619. [PMID: 34850009 DOI: 10.1093/jac/dkab437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES There is an urgent need for novel drugs that target unique cellular pathways to combat infections caused by Mycobacterium tuberculosis. CRISPR interference (CRISPRi)-mediated transcriptional repression has recently been developed for use in mycobacteria as a genetic tool for identifying and validating essential genes as novel drug targets. Whilst CRISPRi has been applied to extracellular bacteria, no studies to date have determined whether CRISPRi can be used in M. tuberculosis infection models. METHODS Using the human monocytic macrophage-like THP-1 cell line as a model for M. tuberculosis infection we investigated if CRISPRi can be activated within intracellular M. tuberculosis. RESULTS The transcriptional repression of two candidate M. tuberculosis genes, i.e. mmpL3 and qcrB, leads to a reduction in viable M. tuberculosis within infected THP-1 cells. The reduction in viable colonies is dependent on both the level of CRISPRi-mediated repression and the duration of repression. CONCLUSIONS These results highlight the utility of CRISPRi in exploring mycobacterial gene function and essentiality under a variety of conditions pertinent to host infection.
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Affiliation(s)
- Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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8
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McNeil MB, Keighley LM, Cook JR, Cheung CY, Cook GM. CRISPR interference identifies vulnerable cellular pathways with bactericidal phenotypes in Mycobacterium tuberculosis. Mol Microbiol 2021; 116:1033-1043. [PMID: 34346123 DOI: 10.1111/mmi.14790] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis remains a leading cause of death for which new drugs are needed. The identification of drug targets has been advanced by high-throughput and targeted genetic deletion strategies. Each though has limitations including the inability to distinguish between levels of vulnerability, lethality and scalability as a molecular tool. Using mycobacterial CRISPR interference in combination with phenotypic screening we have overcome these individual issues to investigate essentiality, vulnerability and lethality for 94 target genes from a diverse array of cellular pathways, many of which are potential antibiotic targets. Essential genes involved in cell wall synthesis and central cellular functions were equally vulnerable and often had bactericidal consequences. Conversely, essential genes involved in metabolism, oxidative phosphorylation or amino acid synthesis were less vulnerable to inhibition and frequently bacteriostatic. In conclusion, this study provides novel insights into mycobacterial genetics and biology that will help to prioritise potential drug targets.
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Affiliation(s)
- Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Otago, New Zealand.,Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Laura M Keighley
- Department of Microbiology and Immunology, University of Otago, Otago, New Zealand
| | - Josephine R Cook
- Department of Microbiology and Immunology, University of Otago, Otago, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Otago, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Otago, New Zealand.,Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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9
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Hembre E, Early JV, Odingo J, Shelton C, Anoshchenko O, Guzman J, Flint L, Dennison D, McNeil MB, Korkegian A, Ovechkina Y, Ornstein P, Masquelin T, Hipskind PA, Parish T. Novel Trifluoromethyl Pyrimidinone Compounds With Activity Against Mycobacterium tuberculosis. Front Chem 2021; 9:613349. [PMID: 33996738 PMCID: PMC8117417 DOI: 10.3389/fchem.2021.613349] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 03/05/2021] [Indexed: 11/13/2022] Open
Abstract
The identification and development of new anti-tubercular agents are a priority research area. We identified the trifluoromethyl pyrimidinone series of compounds in a whole-cell screen against Mycobacterium tuberculosis. Fifteen primary hits had minimum inhibitory concentrations (MICs) with good potency IC90 is the concentration at which M. tuberculosis growth is inhibited by 90% (IC90 < 5 μM). We conducted a structure-activity relationship investigation for this series. We designed and synthesized an additional 44 molecules and tested all analogs for activity against M. tuberculosis and cytotoxicity against the HepG2 cell line. Substitution at the 5-position of the pyrimidinone with a wide range of groups, including branched and straight chain alkyl and benzyl groups, resulted in active molecules. Trifluoromethyl was the preferred group at the 6-position, but phenyl and benzyl groups were tolerated. The 2-pyridyl group was required for activity; substitution on the 5-position of the pyridyl ring was tolerated but not on the 6-position. Active molecules from the series demonstrated low selectivity, with cytotoxicity against eukaryotic cells being an issue. However, there were active and non-cytotoxic molecules; the most promising molecule had an MIC (IC90) of 4.9 μM with no cytotoxicity (IC50 > 100 μM). The series was inactive against Gram-negative bacteria but showed good activity against Gram-positive bacteria and yeast. A representative molecule from this series showed rapid concentration-dependent bactericidal activity against replicating M. tuberculosis bacilli with ~4 log kill in <7 days. Overall the biological properties were promising, if cytotoxicity could be reduced. There is scope for further medicinal chemistry optimization to improve the properties without major change in structural features.
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Affiliation(s)
- Erik Hembre
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Julie V Early
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Joshua Odingo
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Catherine Shelton
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Olena Anoshchenko
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Junitta Guzman
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Devon Dennison
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Yulia Ovechkina
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Paul Ornstein
- Apollo Drug Discovery Consulting, LLC, Northbrook, IL, United States
| | - Thierry Masquelin
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Philip A Hipskind
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
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10
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Hards K, Adolph C, Harold LK, McNeil MB, Cheung CY, Jinich A, Rhee KY, Cook GM. Two for the price of one: Attacking the energetic-metabolic hub of mycobacteria to produce new chemotherapeutic agents. Prog Biophys Mol Biol 2019; 152:35-44. [PMID: 31733221 DOI: 10.1016/j.pbiomolbio.2019.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
Cellular bioenergetics is an area showing promise for the development of new antimicrobials, antimalarials and cancer therapy. Enzymes involved in central carbon metabolism and energy generation are essential mediators of bacterial physiology, persistence and pathogenicity, lending themselves natural interest for drug discovery. In particular, succinate and malate are two major focal points in both the central carbon metabolism and the respiratory chain of Mycobacterium tuberculosis. Both serve as direct links between the citric acid cycle and the respiratory chain due to the quinone-linked reactions of succinate dehydrogenase, fumarate reductase and malate:quinone oxidoreductase. Inhibitors against these enzymes therefore hold the promise of disrupting two distinct, but essential, cellular processes at the same time. In this review, we discuss the roles and unique adaptations of these enzymes and critically evaluate the role that future inhibitors of these complexes could play in the bioenergetics target space.
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Affiliation(s)
- Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
| | - Cara Adolph
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Liam K Harold
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand
| | - Adrian Jinich
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 9054, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1042, Auckland, New Zealand.
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11
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McNeil MB, Chettiar S, Awasthi D, Parish T. Cell wall inhibitors increase the accumulation of rifampicin in Mycobacterium tuberculosis. Access Microbiol 2019; 1:e000006. [PMID: 32974492 PMCID: PMC7470358 DOI: 10.1099/acmi.0.000006] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/16/2019] [Indexed: 11/18/2022] Open
Abstract
There is a need for new combination regimens for tuberculosis. Identifying synergistic drug combinations can avoid toxic side effects and reduce treatment times. Using a fluorescent rifampicin conjugate, we demonstrated that synergy between cell wall inhibitors and rifampicin was associated with increased accumulation of rifampicin. Increased accumulation was also associated with increased cellular permeability.
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Affiliation(s)
- Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA.,Present address: Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Divya Awasthi
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
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12
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Xia Y, Zhou Y, Carter DS, McNeil MB, Choi W, Halladay J, Berry PW, Mao W, Hernandez V, O'Malley T, Korkegian A, Sunde B, Flint L, Woolhiser LK, Scherman MS, Gruppo V, Hastings C, Robertson GT, Ioerger TR, Sacchettini J, Tonge PJ, Lenaerts AJ, Parish T, Alley M. Discovery of a cofactor-independent inhibitor of Mycobacterium tuberculosis InhA. Life Sci Alliance 2018; 1:e201800025. [PMID: 30456352 PMCID: PMC6238539 DOI: 10.26508/lsa.201800025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/12/2022] Open
Abstract
AN12855 is a novel cofactor-independent inhibitor of Mycobacterium tuberculosis InhA. AN12855 has potent activity against M. tuberculosis, good oral bioavailability, and comparable efficacy to isoniazid in infection models. New antitubercular agents are needed to combat the spread of multidrug- and extensively drug-resistant strains of Mycobacterium tuberculosis. The frontline antitubercular drug isoniazid (INH) targets the mycobacterial enoyl-ACP reductase, InhA. Resistance to INH is predominantly through mutations affecting the prodrug-activating enzyme KatG. Here, we report the identification of the diazaborines as a new class of direct InhA inhibitors. The lead compound, AN12855, exhibited in vitro bactericidal activity against replicating bacteria and was active against several drug-resistant clinical isolates. Biophysical and structural investigations revealed that AN12855 binds to and inhibits the substrate-binding site of InhA in a cofactor-independent manner. AN12855 showed good drug exposure after i.v. and oral delivery, with 53% oral bioavailability. Delivered orally, AN12855 exhibited dose-dependent efficacy in both an acute and chronic murine model of tuberculosis infection that was comparable with INH. Combined, AN12855 is a promising candidate for the development of new antitubercular agents.
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Affiliation(s)
- Yi Xia
- Anacor Pharmaceuticals, Palo Alto, CA, USA
| | | | | | - Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Wai Choi
- Anacor Pharmaceuticals, Palo Alto, CA, USA
| | | | | | - Weimin Mao
- Anacor Pharmaceuticals, Palo Alto, CA, USA
| | | | - Theresa O'Malley
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Bjorn Sunde
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Lisa K Woolhiser
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Michael S Scherman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Veronica Gruppo
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Courtney Hastings
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Gregory T Robertson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | | | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Departments of Chemistry and Radiology, Stony Brook University, Stony Brook, NY, USA
| | - Anne J Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Mrk Alley
- Anacor Pharmaceuticals, Palo Alto, CA, USA
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13
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McNeil MB, Dennison D, Shelton C, Flint L, Korkegian A, Parish T. Corrigendum to "Mechanisms of resistance against NITD-916, a direct inhibitor of Mycobacterium tuberculosis InhA" [Tuberculosis 107 (December 2017) 133-136]. Tuberculosis (Edinb) 2018; 110:123. [PMID: 29429955 DOI: 10.1016/j.tube.2018.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Devon Dennison
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Catherine Shelton
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA.
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14
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McNeil MB, Dennison D, Shelton C, Flint L, Korkegian A, Parish T. Mechanisms of resistance against NITD-916, a direct inhibitor of Mycobacterium tuberculosis InhA. Tuberculosis (Edinb) 2017; 107:133-136. [PMID: 29050761 DOI: 10.1016/j.tube.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 07/16/2017] [Revised: 09/06/2017] [Accepted: 09/10/2017] [Indexed: 11/30/2022]
Abstract
Isoniazid inhibits Mycobacterium tuberculosis InhA and is a key component of drug regimens that treat tuberculosis. However, the high rate of resistance against isoniazid is a contributing factor to the emergence of multi-drug resistance strains of M. tuberculosis. The 4-hydroxy-2-pyridine NITD-916 is a direct inhibitor of M. tuberculosis InhA that has comparable efficacy to isoniazid in mouse models of TB infection but a lower frequency of resistance. To characterize resistance mechanisms against NITD-916 we isolated resistant mutants in H37Rv (Euro-American lineage) and HN878 (East-Asian lineage) strains of M. tuberculosis. The resistance frequency was similar in both strains. Mutations were identified in residues within or near to the active of InhA or in the fabG1inhA promoter region. All mutants were resistant to NITD-916 but were not cross resistant to isoniazid, despite homology to SNPs identified in isoniazid resistant clinical isolates.
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Affiliation(s)
- Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Devon Dennison
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Catherine Shelton
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA.
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15
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McNeil MB, Dennison D, Parish T. Mutations in MmpL3 alter membrane potential, hydrophobicity and antibiotic susceptibility in Mycobacterium smegmatis. Microbiology (Reading) 2017; 163:1065-1070. [DOI: 10.1099/mic.0.000498] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Matthew B. McNeil
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA 98102, USA
| | - Devon Dennison
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA 98102, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA 98102, USA
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16
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Hampton HG, McNeil MB, Paterson TJ, Ney B, Williamson NR, Easingwood RA, Bostina M, Salmond GPC, Fineran PC. CRISPR-Cas gene-editing reveals RsmA and RsmC act through FlhDC to repress the SdhE flavinylation factor and control motility and prodigiosin production in Serratia. Microbiology (Reading) 2016; 162:1047-1058. [PMID: 27010574 PMCID: PMC5042078 DOI: 10.1099/mic.0.000283] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SdhE is required for the flavinylation and activation of succinate dehydrogenase and fumarate reductase (FRD). In addition, SdhE is conserved in proteobacteria (α, β and γ) and eukaryotes. Although the function of this recently characterized family of proteins has been determined, almost nothing is known about how their genes are regulated. Here, the RsmA (CsrA) and RsmC (HexY) post-transcriptional and post-translational regulators have been identified and shown to repress sdhEygfX expression in Serratia sp. ATCC 39006. Conversely, the flagella master regulator complex, FlhDC, activated sdhEygfX transcription. To investigate the hierarchy of control, we developed a novel approach that utilized endogenous CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated) genome-editing by a type I-F system to generate a chromosomal point mutation in flhC. Mutation of flhC alleviated the ability of RsmC to repress sdhEygfX expression, whereas RsmA acted in both an FlhDC-dependent and -independent manner to inhibit sdhEygfX. Mutation of rsmA or rsmC, or overexpression of FlhDC, led to increased prodigiosin, biosurfactant, swimming and swarming. Consistent with the modulation of sdhE by motility regulators, we have demonstrated that SdhE and FRD are required for maximal flagella-dependent swimming. Together, these results demonstrate that regulators of both metabolism and motility (RsmA, RsmC and FlhDC) control the transcription of the sdhEygfX operon.
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Affiliation(s)
- Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Thomas J Paterson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Blair Ney
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Neil R Williamson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Richard A Easingwood
- Otago Centre for Electron Microscopy, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,Otago Centre for Electron Microscopy, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - George P C Salmond
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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17
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Richter C, Dy RL, McKenzie RE, Watson BNJ, Taylor C, Chang JT, McNeil MB, Staals RHJ, Fineran PC. Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Res 2014; 42:8516-26. [PMID: 24990370 PMCID: PMC4117759 DOI: 10.1093/nar/gku527] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 12/23/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire short sequences of nucleic acids from foreign invaders and incorporate these into their CRISPR arrays as spacers. This adaptation process is the least characterized step in CRISPR-Cas immunity. Here, we used Pectobacterium atrosepticum to investigate adaptation in Type I-F CRISPR-Cas systems. Pre-existing spacers that matched plasmids stimulated hyperactive primed acquisition and resulted in the incorporation of up to nine new spacers across all three native CRISPR arrays. Endogenous expression of the cas genes was sufficient, yet required, for priming. The new spacers inhibited conjugation and transformation, and interference was enhanced with increasing numbers of new spacers. We analyzed ∼ 350 new spacers acquired in priming events and identified a 5'-protospacer-GG-3' protospacer adjacent motif. In contrast to priming in Type I-E systems, new spacers matched either plasmid strand and a biased distribution, including clustering near the primed protospacer, suggested a bi-directional translocation model for the Cas1:Cas2-3 adaptation machinery. Taken together these results indicate priming adaptation occurs in different CRISPR-Cas systems, that it can be highly active in wild-type strains and that the underlying mechanisms vary.
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Affiliation(s)
- Corinna Richter
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Ron L Dy
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Rebecca E McKenzie
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Bridget N J Watson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Corinda Taylor
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - James T Chang
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Raymond H J Staals
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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18
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McNeil MB, Hampton HG, Hards KJ, Watson BNJ, Cook GM, Fineran PC. The succinate dehydrogenase assembly factor, SdhE, is required for the flavinylation and activation of fumarate reductase in bacteria. FEBS Lett 2013; 588:414-21. [PMID: 24374335 DOI: 10.1016/j.febslet.2013.12.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/04/2013] [Accepted: 12/08/2013] [Indexed: 12/29/2022]
Abstract
The activity of the respiratory enzyme fumarate reductase (FRD) is dependent on the covalent attachment of the redox cofactor flavin adenine dinucleotide (FAD). We demonstrate that the FAD assembly factor SdhE, which flavinylates and activates the respiratory enzyme succinate dehydrogenase (SDH), is also required for the complete activation and flavinylation of FRD. SdhE interacted with, and flavinylated, the flavoprotein subunit FrdA, whilst mutations in a conserved RGxxE motif impaired the complete flavinylation and activation of FRD. These results are of widespread relevance because SDH and FRD play an important role in cellular energetics and are required for virulence in many important bacterial pathogens.
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Affiliation(s)
- Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Hannah G Hampton
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Kiel J Hards
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Bridget N J Watson
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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19
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McNeil MB, Fineran PC. The conserved RGxxE motif of the bacterial FAD assembly factor SdhE is required for succinate dehydrogenase flavinylation and activity. Biochemistry 2013; 52:7628-40. [PMID: 24070374 DOI: 10.1021/bi401006a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Succinate dehydrogenase (SDH) is an important respiratory enzyme that plays a critical role in the generation of energy in the majority of eukaryotes, bacteria, and archaea. The activity of SDH is dependent on the covalent attachment of the redox cofactor FAD to the flavoprotein subunit SdhA. In the Gram-negative bacteria Escherichia coli and Serratia sp. ATCC 39006, the covalent attachment of FAD to SdhA is dependent on the FAD assembly factor SdhE (YgfY). Although mechanisms have been proposed, experimental evidence that elucidates the molecular details of SdhE-mediated flavinylation are scarce. In this study, truncation and alanine swap mutagenesis of SdhE identified a highly conserved RGxxE motif that was important for SdhE function. Interestingly, RGxxE site-directed variants were not impaired in terms of protein folding or interactions with SdhA. Purification and analysis of SdhA from different mutant backgrounds demonstrated that SdhE interacts with and flavinylates folded SdhA without a requirement for the assembly of the entire SDH complex. SdhA was also partially active in the absence of SdhE, suggesting that SdhA is able to attach FAD through an inefficient autocatalytic mechanism. The results presented are of widespread relevance because SdhE and SDH are required for bacterial pathogenesis and mutations in the eukaryotic homologues of SdhE and SDH are associated with cancer in humans.
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Affiliation(s)
- Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago , P.O. Box 56, Dunedin 9054, New Zealand
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20
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McNeil MB, Iglesias-Cans MC, Clulow JS, Fineran PC. YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY). Microbiology (Reading) 2013; 159:1352-1365. [PMID: 23657679 DOI: 10.1099/mic.0.068510-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Serratia sp. strain ATCC 39006 produces the red-pigmented antibiotic prodigiosin. Prodigiosin biosynthesis is regulated by a complex hierarchy that includes the uncharacterized protein YgfX (DUF1434). The ygfX gene is co-transcribed with sdhE, an FAD assembly factor essential for the flavinylation and activation of the SdhA subunit of succinate dehydrogenase (SDH), a central enzyme in the tricarboxylic acid cycle and electron transport chain. The sdhEygfX operon is highly conserved within the Enterobacteriaceae, suggesting that SdhE and YgfX function together. We performed an extensive mutagenesis to gain molecular insights into the uncharacterized protein YgfX, and have investigated the relationship between YgfX and SdhE. YgfX localized to the membrane, interacted with itself, forming dimers or larger multimers, and interacted with SdhE. The transmembrane helices of YgfX were critical for protein function and the formation of YgfX multimers. Site-directed mutagenesis of residues conserved in DUF1434 proteins revealed a periplasmic tryptophan and a cytoplasmic aspartate that were crucial for YgfX activity. Both of these amino acids were required for the formation of YgfX multimers and interactions with SdhE but not membrane localization. Multiple cell division proteins were identified as putative interaction partners of YgfX and overexpression of YgfX had effects on cell morphology. These findings represent an important step in understanding the function of DUF1434 proteins. In contrast to a recent report, we found no evidence that YgfX and SdhE form a toxin-antitoxin system. In summary, YgfX functions as a multimeric membrane-bound protein that interacts with SdhE, an important FAD assembly factor that controls SDH activity.
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Affiliation(s)
- Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Marina C Iglesias-Cans
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - James S Clulow
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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McNeil MB, Clulow JS, Wilf NM, Salmond GPC, Fineran PC. SdhE is a conserved protein required for flavinylation of succinate dehydrogenase in bacteria. J Biol Chem 2012; 287:18418-28. [PMID: 22474332 DOI: 10.1074/jbc.m111.293803] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Conserved uncharacterized genes account for ~30% of genes in both eukaryotic and bacterial genomes and are predicted to encode what are often termed "conserved hypothetical proteins." Many of these proteins have a wide phylogenetic distribution and might play important roles in conserved cellular pathways. Using the bacterium Serratia as a model system, we have investigated two conserved uncharacterized proteins, YgfY (a DUF339 protein, renamed SdhE; succinate dehydrogenase protein E) and YgfX (a DUF1434 protein). SdhE was required for growth on succinate as a sole carbon source and for the function, but not stability, of succinate dehydrogenase, an important component of the electron transport chain and the tricarboxylic acid cycle. SdhE interacted with the flavoprotein SdhA, directly bound the flavin adenine dinucleotide co-factor, and was required for the flavinylation of SdhA. This is the first demonstration of a protein required for FAD incorporation in bacteria. Furthermore, the loss of SdhE was highly pleiotropic, suggesting that SdhE might flavinylate other flavoproteins. Our findings are of wide importance to central metabolism because SdhE homologues are present in α-, β-, and γ-proteobacteria and multiple eukaryotes, including humans and yeast.
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Affiliation(s)
- Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
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