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Zhao H, Li J, Feng S, Xu L, Yan B, Li C, Li M, Wang Y, Li Y, Liang L, Zhou D, Wan J, Wang W, Tian GB, Gu B, Huang X. High-throughput mutagenesis and screening approach for the identification of drug-resistant mutations in the rifampicin resistance-determining region of mycobacteria. Int J Antimicrob Agents 2024; 63:107158. [PMID: 38537722 DOI: 10.1016/j.ijantimicag.2024.107158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/05/2024] [Accepted: 03/22/2024] [Indexed: 05/31/2024]
Abstract
Rifampicin is the most powerful first-line antibiotic for tuberculosis, which is caused by Mycobacterium tuberculosis. Although accumulating evidence from sequencing data of clinical M. tuberculosis isolates suggested that mutations in the rifampicin-resistance-determining region (RRDR) are strongly associated with rifampicin resistance, the comprehensive characterisation of RRDR polymorphisms that confer this resistance remains challenging. By incorporating I-SceI sites for I-SceI-based integrant removal and utilizing an L5 swap strategy, we efficiently replaced the integrated plasmid with alternative alleles, making mass allelic exchange feasible in mycobacteria. Using this method to establish a fitness-related gain-of function screen, we generated a mutant library that included all single-amino-acid mutations in the RRDR, and identified the important positions corresponding to some well-known rifampicin-resistance mutations (Q513, D516, S522, H525, R529, S531). We also detected a novel two-point mutation located in the RRDR confers a fitness advantage to M. smegmatis in the presence or absence of rifampicin. Our method provides a comprehensive insight into the growth phenotypes of RRDR mutants and should facilitate the development of anti-tuberculosis drugs.
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Affiliation(s)
- Hui Zhao
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510000, China; Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510000, China
| | - Jiachen Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Siyuan Feng
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Lin Xu
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Bin Yan
- Department of Neonatal Surgery, Guangzhou Women and Children's Medical Center, Guangzhou 510080, China
| | - Chengjuan Li
- School of Basic Medical Sciences, Xizang Minzu University, Xianyang, 712082, China
| | - Meisong Li
- Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yaxuan Wang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yaxin Li
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Lujie Liang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Dianrong Zhou
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Jia Wan
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Wenli Wang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Guo-Bao Tian
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Department of Immunology, School of Medicine, Sun Yat-Sen University, Shenzhen 518107, China; State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, 510080, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
| | - Bing Gu
- Department of Clinical Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510000, China.
| | - Xi Huang
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China.
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2
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Grigsby SJ, Prasad GVRK, Wallach JB, Mittal E, Hsu FF, Schnappinger D, Philips JA. CpsA mediates infection of recruited lung myeloid cells by Mycobacterium tuberculosis. Cell Rep 2024; 43:113607. [PMID: 38127624 PMCID: PMC10900767 DOI: 10.1016/j.celrep.2023.113607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/27/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) possesses an arsenal of virulence factors to evade host immunity. Previously, we showed that the Mtb protein CpsA, which protects Mtb against the host NADPH oxidase, is required in mice during the first 3 weeks of infection but is thereafter dispensable for full virulence. Using flow cytometry, we find that ΔcpsA Mtb is retained in alveolar macrophages, impaired in recruiting and disseminating into monocyte-derived cells, and more likely to be localized in airway cells than wild-type Mtb. The lungs of ΔcpsA-infected mice also have markedly fewer antigen-specific T cells, indicating a delay in adaptive immunity. Thus, we conclude that CpsA promotes dissemination of Mtb from alveolar macrophages and the airways and generation of an adaptive immune response. Our studies of ΔcpsA Mtb show that a more effective innate immune response against Mtb can be undermined by a corresponding delay in the adaptive immune response.
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Affiliation(s)
- Steven J Grigsby
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - G V R Krishna Prasad
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua B Wallach
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York City, NY, USA
| | - Ekansh Mittal
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism, & Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York City, NY, USA
| | - Jennifer A Philips
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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3
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Sharma R, Hartman TE, Beites T, Kim JH, Eoh H, Engelhart CA, Zhu L, Wilson DJ, Aldrich CC, Ehrt S, Rhee KY, Schnappinger D. Metabolically distinct roles of NAD synthetase and NAD kinase define the essentiality of NAD and NADP in Mycobacterium tuberculosis. mBio 2023; 14:e0034023. [PMID: 37350592 PMCID: PMC10470730 DOI: 10.1128/mbio.00340-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/01/2023] [Indexed: 06/24/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) and its phosphorylated derivative (NADP) are essential cofactors that participate in hundreds of biochemical reactions and have emerged as therapeutic targets in cancer, metabolic disorders, neurodegenerative diseases, and infections, including tuberculosis. The biological basis for the essentiality of NAD(P) in most settings, however, remains experimentally unexplained. Here, we report that inactivation of the terminal enzyme of NAD synthesis, NAD synthetase (NadE), elicits markedly different metabolic and microbiologic effects than those of the terminal enzyme of NADP biosynthesis, NAD kinase (PpnK), in Mycobacterium tuberculosis (Mtb). Inactivation of NadE led to parallel reductions of both NAD and NADP pools and Mtb viability, while inactivation of PpnK selectively depleted NADP pools but only arrested growth. Inactivation of each enzyme was accompanied by metabolic changes that were specific for the affected enzyme and associated microbiological phenotype. Bacteriostatic levels of NAD depletion caused a compensatory remodeling of NAD-dependent metabolic pathways in the absence of an impact on NADH/NAD ratios, while bactericidal levels of NAD depletion resulted in a disruption of NADH/NAD ratios and inhibition of oxygen respiration. These findings reveal a previously unrecognized physiologic specificity associated with the essentiality of two evolutionarily ubiquitous cofactors. IMPORTANCE The current course for cure of Mycobacterium tuberculosis (Mtb)-the etiologic agent of tuberculosis (TB)-infections is lengthy and requires multiple antibiotics. The development of shorter, simpler treatment regimens is, therefore, critical to the goal of eradicating TB. NadE, an enzyme required for the synthesis of the ubiquitous cofactor NAD, is essential for survival of Mtb and regarded as a promising drug target. However, the basis of this essentiality was not clear due to its role in the synthesis of both NAD and NADP. Here, we resolve this ambiguity through a combination of gene silencing and metabolomics. We specifically show that NADP deficiency is bacteriostatic, while NAD deficiency is bactericidal due to its role in Mtb's respiratory capacity. These results argue for a prioritization of NAD biosynthesis inhibitors in anti-TB drug development.
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Affiliation(s)
- Ritu Sharma
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Travis E. Hartman
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Tiago Beites
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Jee-Hyun Kim
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Hyungjin Eoh
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Curtis A. Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Linnan Zhu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Daniel J. Wilson
- Center for Drug Design, Nils Hasselmo Hall, Minneapolis, Minnesota, USA
| | | | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Kyu Young Rhee
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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4
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Kumar S, Sau S, Agnivesh PK, Roy A, Kalia NP. Role of transcription termination factor Rho in anti-tuberculosis drug discovery. Drug Discov Today 2023; 28:103490. [PMID: 36638880 DOI: 10.1016/j.drudis.2023.103490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/26/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Mycobacterial infections, including multidrug and extreme drug-resistant (MDR and XDR) infections, are a severe challenge and create a virtual antibiotic-deficient era. Bacterial transcription is an established antimicrobial drug target. In mycobacteria, efficient transcription termination relies on the ATP-dependent RNA helicase factor Rho. Rho factor is essential for Mycobacterium tuberculosis (Mtb) survival, and is a valid antibacterial drug target with no homolog in eukaryotes. Rho maintains genomic stability and virulence and prevents pervasive transcription in Mtb. In this review, we provide an overview of the essentiality of Rho in Mtb, which makes it an attractive drug target for inhibitor discovery.
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Affiliation(s)
- Sunil Kumar
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana 500 037, India
| | - Shashikanta Sau
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana 500 037, India
| | - Puja Kumari Agnivesh
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana 500 037, India
| | - Arnab Roy
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana 500 037, India
| | - Nitin Pal Kalia
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana 500 037, India.
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5
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Kreutzfeldt KM, Jansen RS, Hartman TE, Gouzy A, Wang R, Krieger IV, Zimmerman MD, Gengenbacher M, Sarathy JP, Xie M, Dartois V, Sacchettini JC, Rhee KY, Schnappinger D, Ehrt S. CinA mediates multidrug tolerance in Mycobacterium tuberculosis. Nat Commun 2022; 13:2203. [PMID: 35459278 PMCID: PMC9033802 DOI: 10.1038/s41467-022-29832-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/31/2022] [Indexed: 12/23/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to resist and tolerate antibiotics complicates the development of improved tuberculosis (TB) chemotherapies. Here we define the Mtb protein CinA as a major determinant of drug tolerance and as a potential target to shorten TB chemotherapy. By reducing the fraction of drug-tolerant persisters, genetic inactivation of cinA accelerated killing of Mtb by four antibiotics in clinical use: isoniazid, ethionamide, delamanid and pretomanid. Mtb ΔcinA was killed rapidly in conditions known to impede the efficacy of isoniazid, such as during nutrient starvation, during persistence in a caseum mimetic, in activated macrophages and during chronic mouse infection. Deletion of CinA also increased in vivo killing of Mtb by BPaL, a combination of pretomanid, bedaquiline and linezolid that is used to treat highly drug-resistant TB. Genetic and drug metabolism studies suggest that CinA mediates drug tolerance via cleavage of NAD-drug adducts.
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Affiliation(s)
- Kaj M Kreutzfeldt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Robert S Jansen
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
- Department of Microbiology, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Travis E Hartman
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alexandre Gouzy
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08540, USA
| | - Inna V Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Jansy P Sarathy
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Min Xie
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, 07110, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.
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6
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Ottavi S, Scarry SM, Mosior J, Ling Y, Roberts J, Singh A, Zhang D, Goullieux L, Roubert C, Bacqué E, Lagiakos HR, Vendome J, Moraca F, Li K, Perkowski AJ, Ramesh R, Bowler MM, Tracy W, Feher VA, Sacchettini JC, Gold BS, Nathan CF, Aubé J. In Vitro and In Vivo Inhibition of the Mycobacterium tuberculosis Phosphopantetheinyl Transferase PptT by Amidinoureas. J Med Chem 2022; 65:1996-2022. [PMID: 35044775 PMCID: PMC8842310 DOI: 10.1021/acs.jmedchem.1c01565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A newly validated target for tuberculosis treatment is phosphopantetheinyl transferase, an essential enzyme that plays a critical role in the biosynthesis of cellular lipids and virulence factors in Mycobacterium tuberculosis. The structure-activity relationships of a recently disclosed inhibitor, amidinourea (AU) 8918 (1), were explored, focusing on the biochemical potency, determination of whole-cell on-target activity for active compounds, and profiling of selective active congeners. These studies show that the AU moiety in AU 8918 is largely optimized and that potency enhancements are obtained in analogues containing a para-substituted aromatic ring. Preliminary data reveal that while some analogues, including 1, have demonstrated cardiotoxicity (e.g., changes in cardiomyocyte beat rate, amplitude, and peak width) and inhibit Cav1.2 and Nav1.5 ion channels (although not hERG channels), inhibition of the ion channels is largely diminished for some of the para-substituted analogues, such as 5k (p-benzamide) and 5n (p-phenylsulfonamide).
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Affiliation(s)
- Samantha Ottavi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Sarah M Scarry
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - John Mosior
- Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, Texas 77843, United States
| | - Yan Ling
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Julia Roberts
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Amrita Singh
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - David Zhang
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | | | | | - Eric Bacqué
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | - H Rachel Lagiakos
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - Jeremie Vendome
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - Francesca Moraca
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Andrew J Perkowski
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Remya Ramesh
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew M Bowler
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - William Tracy
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Feher
- Schrödinger, Inc., 120 W. 45 Street, New York, New York 10036, United States
| | - James C Sacchettini
- Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, Texas 77843, United States
| | - Ben S Gold
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Carl F Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York 10065, United States.,Department of Medicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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7
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Bastos RG, Alzan HF, Rathinasamy VA, Cooke BM, Dellagostin OA, Barletta RG, Suarez CE. Harnessing Mycobacterium bovis BCG Trained Immunity to Control Human and Bovine Babesiosis. Vaccines (Basel) 2022; 10:vaccines10010123. [PMID: 35062784 PMCID: PMC8781211 DOI: 10.3390/vaccines10010123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 01/02/2023] Open
Abstract
Babesiosis is a disease caused by tickborne hemoprotozoan apicomplexan parasites of the genus Babesia that negatively impacts public health and food security worldwide. Development of effective and sustainable vaccines against babesiosis is currently hindered in part by the absence of definitive host correlates of protection. Despite that, studies in Babesia microti and Babesia bovis, major causative agents of human and bovine babesiosis, respectively, suggest that early activation of innate immune responses is crucial for vertebrates to survive acute infection. Trained immunity (TI) is defined as the development of memory in vertebrate innate immune cells, allowing more efficient responses to subsequent specific and non-specific challenges. Considering that Mycobacterium bovis bacillus Calmette-Guerin (BCG), a widely used anti-tuberculosis attenuated vaccine, induces strong TI pro-inflammatory responses, we hypothesize that BCG TI may protect vertebrates against acute babesiosis. This premise is supported by early investigations demonstrating that BCG inoculation protects mice against experimental B. microti infection and recent observations that BCG vaccination decreases the severity of malaria in children infected with Plasmodium falciparum, a Babesia-related parasite. We also discuss the potential use of TI in conjunction with recombinant BCG vaccines expressing Babesia immunogens. In conclusion, by concentrating on human and bovine babesiosis, herein we intend to raise awareness of BCG TI as a strategy to efficiently control Babesia infection.
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Affiliation(s)
- Reginaldo G. Bastos
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7040, USA;
- Correspondence: (R.G.B.); (C.E.S.)
| | - Heba F. Alzan
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-7040, USA;
- Parasitology and Animal Diseases Department, Veterinary Research Institute, National Research Center, Giza 12622, Egypt
| | - Vignesh A. Rathinasamy
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4870, Australia; (V.A.R.); (B.M.C.)
| | - Brian M. Cooke
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4870, Australia; (V.A.R.); (B.M.C.)
| | - Odir A. Dellagostin
- Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas 96010-900, Rio Grande Do Sul, Brazil;
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0905, USA;
| | - Carlos E. Suarez
- Animal Disease Research Unit, United States Department of Agriculture-Agricultural Research Service, Pullman, WA 99164-7040, USA
- Correspondence: (R.G.B.); (C.E.S.)
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8
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Beites T, Jansen RS, Wang R, Jinich A, Rhee KY, Schnappinger D, Ehrt S. Multiple acyl-CoA dehydrogenase deficiency kills Mycobacterium tuberculosis in vitro and during infection. Nat Commun 2021; 12:6593. [PMID: 34782606 PMCID: PMC8593149 DOI: 10.1038/s41467-021-26941-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/26/2021] [Indexed: 11/14/2022] Open
Abstract
The human pathogen Mycobacterium tuberculosis depends on host fatty acids as a carbon source. However, fatty acid β-oxidation is mediated by redundant enzymes, which hampers the development of antitubercular drugs targeting this pathway. Here, we show that rv0338c, which we refer to as etfD, encodes a membrane oxidoreductase essential for β-oxidation in M. tuberculosis. An etfD deletion mutant is incapable of growing on fatty acids or cholesterol, with long-chain fatty acids being bactericidal, and fails to grow and survive in mice. Analysis of the mutant’s metabolome reveals a block in β-oxidation at the step catalyzed by acyl-CoA dehydrogenases (ACADs), which in other organisms are functionally dependent on an electron transfer flavoprotein (ETF) and its cognate oxidoreductase. We use immunoprecipitation to show that M. tuberculosis EtfD interacts with FixA (EtfB), a protein that is homologous to the human ETF subunit β and is encoded in an operon with fixB, encoding a homologue of human ETF subunit α. We thus refer to FixA and FixB as EtfB and EtfA, respectively. Our results indicate that EtfBA and EtfD (which is not homologous to human EtfD) function as the ETF and oxidoreductase for β-oxidation in M. tuberculosis and support this pathway as a potential target for tuberculosis drug development. The pathogen Mycobacterium tuberculosis depends on host fatty acids and cholesterol as carbon sources. Here, Beites et al. identify a protein complex that is essential for fatty acid and cholesterol utilization and thus for survival of M. tuberculosis during infection, supporting this pathway as a potential target for tuberculosis drug development.
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Affiliation(s)
- Tiago Beites
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Robert S Jansen
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Department of Microbiology, Radboud University, 6525 AJ, Nijmegen, The Netherlands
| | - Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08540, USA
| | - Adrian Jinich
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA.
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9
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Schrader SM, Botella H, Jansen R, Ehrt S, Rhee K, Nathan C, Vaubourgeix J. Multiform antimicrobial resistance from a metabolic mutation. SCIENCE ADVANCES 2021; 7:7/35/eabh2037. [PMID: 34452915 PMCID: PMC8397267 DOI: 10.1126/sciadv.abh2037] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/08/2021] [Indexed: 05/07/2023]
Abstract
A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of an essential biosynthetic pathway (arginine biosynthesis) in a mycobacterium generated three distinct forms of resistance to diverse antibiotics, each mediated by induction of WhiB7: high persistence and tolerance to kanamycin, high survival upon exposure to rifampicin, and minimum inhibitory concentration-shifted resistance to clarithromycin. As little as one base change in a gene that encodes, a metabolic pathway component conferred multiple forms of resistance to multiple antibiotics with different targets. This extraordinary resilience may help explain how substerilizing exposure to one antibiotic in a regimen can induce resistance to others and invites development of drugs targeting the mediator of multiform resistance, WhiB7.
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Affiliation(s)
- Sarah M Schrader
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Hélène Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Robert Jansen
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Kyu Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
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10
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Phosphorylation on PstP Regulates Cell Wall Metabolism and Antibiotic Tolerance in Mycobacterium smegmatis. J Bacteriol 2021; 203:JB.00563-20. [PMID: 33257524 DOI: 10.1128/jb.00563-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium tuberculosis and its relatives, like many bacteria, have dynamic cell walls that respond to environmental stresses. Modulation of cell wall metabolism in stress is thought to be responsible for decreased permeability and increased tolerance to antibiotics. The signaling systems that control cell wall metabolism under stress, however, are poorly understood. Here, we examine the cell wall regulatory function of a key cell wall regulator, the serine/threonine phosphatase PstP, in the model organism Mycobacterium smegmatis We show that the peptidoglycan regulator CwlM is a substrate of PstP. We find that a phosphomimetic mutation, pstP T171E, slows growth, misregulates both mycolic acid and peptidoglycan metabolism in different conditions, and interferes with antibiotic tolerance. These data suggest that phosphorylation on PstP affects its activity against various substrates and is important in the transition between growth and stasis.IMPORTANCE Regulation of cell wall assembly is essential for bacterial survival and contributes to pathogenesis and antibiotic tolerance in mycobacteria, including pathogens such as Mycobacterium tuberculosis However, little is known about how the cell wall is regulated in stress. We describe a pathway of cell wall modulation in Mycobacterium smegmatis through the only essential Ser/Thr phosphatase, PstP. We showed that phosphorylation on PstP is important in regulating peptidoglycan metabolism in the transition to stasis and mycolic acid metabolism in growth. This regulation also affects antibiotic tolerance in growth and stasis. This work helps us to better understand the phosphorylation-mediated cell wall regulation circuitry in Mycobacteria.
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11
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Lu J, Wei N, Cao J, Zhou Y, Gong H, Zhang H, Zhou J. Evaluation of enzymatic activity of Babesia microti thioredoxin reductase (Bmi TrxR)-mutants and screening of its potential inhibitors. Ticks Tick Borne Dis 2020; 12:101623. [PMID: 33418338 DOI: 10.1016/j.ttbdis.2020.101623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 01/25/2023]
Abstract
Babesia microti is a zoonotic pathogen that mainly parasitizes mammalian erythrocytes. Oxidative stress can induce gene mutation, protein denaturation and lipid peroxidation, such as reactive oxygen species (ROS) induced by hypoxic environment and the host immune system. An antioxidase, B. microti thioredoxin reductase (Bmi TrxR), has been identified in B. microti. We used a combination of homology modeling and domain prediction to explore the functional sites of Bmi TrxR and found that TrxR has three domains. Constructed a mutant pool which His-tag were at the N-terminus (TrxR-Nhis, C105-Nhis, C110-Nhis, C105110-Nhis, C547-Nhis, C552-Nhis, C547552-Nhis) and the His tag were at the N- and C-terminus (TrxR-NChis, C547-NChis, C552-NChis, C547552-NChis). The proteins were expressed as His-tagged fusion proteins in Escherichia coli. The His-tag of TrxR C-terminus were affected the reaction with Trx. The inhibitory efficiency of DNCB was decreased for mutant C547, compared with recombinant TrxR, indicating that the action site of DNCB might be cysteine at position 547. These results indicate that the N-terminal active site of Bmi TrxR plays an important role in accepting electrons and promotes electron transfer. The C-terminus His tag of Bmi TrxR affected the electron transfer and the reducing activity of Bmi TrxR. Reduce reactive oxygen produced in oxidative stress was reduced by Bmi TrxR, which is beneficial to Babesia survival. Therefore, reduction site of TrxR may become a potential target for Babesia microti treatment.
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Affiliation(s)
- Jinmiao Lu
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Nana Wei
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jie Cao
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yongzhi Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Haiyan Gong
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Houshuang Zhang
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Jinlin Zhou
- Key Laboratory of Animal Parasitology of Ministry of Agriculture, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
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12
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Host-Derived Lipids from Tuberculous Pleurisy Impair Macrophage Microbicidal-Associated Metabolic Activity. Cell Rep 2020; 33:108547. [PMID: 33378679 DOI: 10.1016/j.celrep.2020.108547] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/18/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) regulates the macrophage metabolic state to thrive in the host, yet the responsible mechanisms remain elusive. Macrophage activation toward the microbicidal (M1) program depends on the HIF-1α-mediated metabolic shift from oxidative phosphorylation (OXPHOS) toward glycolysis. Here, we ask whether a tuberculosis (TB) microenvironment changes the M1 macrophage metabolic state. We expose M1 macrophages to the acellular fraction of tuberculous pleural effusions (TB-PEs) and find lower glycolytic activity, accompanied by elevated levels of OXPHOS and bacillary load, compared to controls. The eicosanoid fraction of TB-PE drives these metabolic alterations. HIF-1α stabilization reverts the effect of TB-PE by restoring M1 metabolism. Furthermore, Mtb-infected mice with stabilized HIF-1α display lower bacillary loads and a pronounced M1-like metabolic profile in alveolar macrophages (AMs). Collectively, we demonstrate that lipids from a TB-associated microenvironment alter the M1 macrophage metabolic reprogramming by hampering HIF-1α functions, thereby impairing control of Mtb infection.
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13
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Bockman MR, Mishra N, Aldrich CC. The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents. Curr Med Chem 2020; 27:4194-4232. [PMID: 30663561 DOI: 10.2174/0929867326666190119161551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/14/2018] [Accepted: 01/12/2019] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.
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Affiliation(s)
- Matthew R Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, United States
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14
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Wang R, Kreutzfeldt K, Botella H, Vaubourgeix J, Schnappinger D, Ehrt S. Persistent Mycobacterium tuberculosis infection in mice requires PerM for successful cell division. eLife 2019; 8:49570. [PMID: 31751212 PMCID: PMC6872210 DOI: 10.7554/elife.49570] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/11/2019] [Indexed: 01/09/2023] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to persist in its host is central to the pathogenesis of tuberculosis, yet the underlying mechanisms remain incompletely defined. PerM, an integral membrane protein, is required for persistence of Mtb in mice. Here, we show that perM deletion caused a cell division defect specifically during the chronic phase of mouse infection, but did not affect Mtb’s cell replication during acute infection. We further demonstrate that PerM is required for cell division in chronically infected mice and in vitro under host-relevant stresses because it is part of the mycobacterial divisome and stabilizes the essential divisome protein FtsB. These data highlight the importance of sustained cell division for Mtb persistence, define condition-specific requirements for cell division and reveal that survival of Mtb during chronic infection depends on a persistence divisome.
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Affiliation(s)
- Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Kaj Kreutzfeldt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Helene Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
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15
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Plasticity of the Mycobacterium tuberculosis respiratory chain and its impact on tuberculosis drug development. Nat Commun 2019; 10:4970. [PMID: 31672993 PMCID: PMC6823465 DOI: 10.1038/s41467-019-12956-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022] Open
Abstract
The viability of Mycobacterium tuberculosis (Mtb) depends on energy generated by its respiratory chain. Cytochrome bc1-aa3 oxidase and type-2 NADH dehydrogenase (NDH-2) are respiratory chain components predicted to be essential, and are currently targeted for drug development. Here we demonstrate that an Mtb cytochrome bc1-aa3 oxidase deletion mutant is viable and only partially attenuated in mice. Moreover, treatment of Mtb-infected marmosets with a cytochrome bc1-aa3 oxidase inhibitor controls disease progression and reduces lesion-associated inflammation, but most lesions become cavitary. Deletion of both NDH-2 encoding genes (Δndh-2 mutant) reveals that the essentiality of NDH-2 as shown in standard growth media is due to the presence of fatty acids. The Δndh-2 mutant is only mildly attenuated in mice and not differently susceptible to clofazimine, a drug in clinical use proposed to engage NDH-2. These results demonstrate the intrinsic plasticity of Mtb's respiratory chain, and highlight the challenges associated with targeting the pathogen's respiratory enzymes for tuberculosis drug development.
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16
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Tiwari D, Park SW, Essawy MM, Dawadi S, Mason A, Nandakumar M, Zimmerman M, Mina M, Ho HP, Engelhart CA, Ioerger T, Sacchettini JC, Rhee K, Ehrt S, Aldrich CC, Dartois V, Schnappinger D. Targeting protein biotinylation enhances tuberculosis chemotherapy. Sci Transl Med 2019; 10:10/438/eaal1803. [PMID: 29695454 PMCID: PMC6151865 DOI: 10.1126/scitranslmed.aal1803] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 07/28/2017] [Accepted: 10/03/2017] [Indexed: 12/28/2022]
Abstract
Successful drug treatment for tuberculosis (TB) depends on the unique contributions of its component drugs. Drug resistance poses a threat to the efficacy of individual drugs and the regimens to which they contribute. Biologically and chemically validated targets capable of replacing individual components of current TB chemotherapy are a major unmet need in TB drug development. We demonstrate that chemical inhibition of the bacterial biotin protein ligase (BPL) with the inhibitor Bio-AMS (5'-[N-(d-biotinoyl)sulfamoyl]amino-5'-deoxyadenosine) killed Mycobacterium tuberculosis (Mtb), the bacterial pathogen causing TB. We also show that genetic silencing of BPL eliminated the pathogen efficiently from mice during acute and chronic infection with Mtb Partial chemical inactivation of BPL increased the potency of two first-line drugs, rifampicin and ethambutol, and genetic interference with protein biotinylation accelerated clearance of Mtb from mouse lungs and spleens by rifampicin. These studies validate BPL as a potential drug target that could serve as an alternate frontline target in the development of new drugs against Mtb.
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Affiliation(s)
- Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Maram M Essawy
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, 8-174 WDH, Minneapolis, MN 55455, USA
| | - Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, 8-174 WDH, Minneapolis, MN 55455, USA
| | - Alan Mason
- Public Health Research Institute, New Jersey Medical School, Rutgers, State University of New Jersey, Newark, NJ 07103, USA
| | - Madhumitha Nandakumar
- Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Matthew Zimmerman
- Public Health Research Institute, New Jersey Medical School, Rutgers, State University of New Jersey, Newark, NJ 07103, USA
| | - Marizel Mina
- Public Health Research Institute, New Jersey Medical School, Rutgers, State University of New Jersey, Newark, NJ 07103, USA
| | - Hsin Pin Ho
- Public Health Research Institute, New Jersey Medical School, Rutgers, State University of New Jersey, Newark, NJ 07103, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Thomas Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Kyu Rhee
- Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, 8-174 WDH, Minneapolis, MN 55455, USA
| | - Véronique Dartois
- Public Health Research Institute, New Jersey Medical School, Rutgers, State University of New Jersey, Newark, NJ 07103, USA. .,Department of Medicine, New Jersey Medical School, Rutgers, State University of New Jersey, Newark, NJ 07103, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA.
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17
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Derailing the aspartate pathway of Mycobacterium tuberculosis to eradicate persistent infection. Nat Commun 2019; 10:4215. [PMID: 31527595 PMCID: PMC6746716 DOI: 10.1038/s41467-019-12224-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 08/28/2019] [Indexed: 11/17/2022] Open
Abstract
A major constraint for developing new anti-tuberculosis drugs is the limited number of validated targets that allow eradication of persistent infections. Here, we uncover a vulnerable component of Mycobacterium tuberculosis (Mtb) persistence metabolism, the aspartate pathway. Rapid death of threonine and homoserine auxotrophs points to a distinct susceptibility of Mtb to inhibition of this pathway. Combinatorial metabolomic and transcriptomic analysis reveals that inability to produce threonine leads to deregulation of aspartate kinase, causing flux imbalance and lysine and DAP accumulation. Mtb’s adaptive response to this metabolic stress involves a relief valve-like mechanism combining lysine export and catabolism via aminoadipate. We present evidence that inhibition of the aspartate pathway at different branch-point enzymes leads to clearance of chronic infections. Together these findings demonstrate that the aspartate pathway in Mtb relies on a combination of metabolic control mechanisms, is required for persistence, and represents a target space for anti-tuberculosis drug development. Amino acid biosynthetic pathways are an attractive alternative to treat chronic infections such as Mycobacterium tuberculosis (Mtb). Here, the authors investigate the metabolic response to disruption of the aspartate pathway in persistent Mtb and identify essential enzymes as potential new targets for drug development.
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18
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Ballinger E, Mosior J, Hartman T, Burns-Huang K, Gold B, Morris R, Goullieux L, Blanc I, Vaubourgeix J, Lagrange S, Fraisse L, Sans S, Couturier C, Bacqué E, Rhee K, Scarry SM, Aubé J, Yang G, Ouerfelli O, Schnappinger D, Ioerger TR, Engelhart CA, McConnell JA, McAulay K, Fay A, Roubert C, Sacchettini J, Nathan C. Opposing reactions in coenzyme A metabolism sensitize Mycobacterium tuberculosis to enzyme inhibition. Science 2019; 363:363/6426/eaau8959. [PMID: 30705156 DOI: 10.1126/science.aau8959] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/21/2018] [Indexed: 12/27/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the leading infectious cause of death in humans. Synthesis of lipids critical for Mtb's cell wall and virulence depends on phosphopantetheinyl transferase (PptT), an enzyme that transfers 4'-phosphopantetheine (Ppt) from coenzyme A (CoA) to diverse acyl carrier proteins. We identified a compound that kills Mtb by binding and partially inhibiting PptT. Killing of Mtb by the compound is potentiated by another enzyme encoded in the same operon, Ppt hydrolase (PptH), that undoes the PptT reaction. Thus, loss-of-function mutants of PptH displayed antimicrobial resistance. Our PptT-inhibitor cocrystal structure may aid further development of antimycobacterial agents against this long-sought target. The opposing reactions of PptT and PptH uncover a regulatory pathway in CoA physiology.
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Affiliation(s)
- Elaine Ballinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - John Mosior
- Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA
| | - Travis Hartman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kristin Burns-Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Roxanne Morris
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Laurent Goullieux
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - Isabelle Blanc
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Sophie Lagrange
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - Laurent Fraisse
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - Stéphanie Sans
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - Cedric Couturier
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - Eric Bacqué
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sarah M Scarry
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Guangbin Yang
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Thomas R Ioerger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Jennifer A McConnell
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Kathrine McAulay
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine Roubert
- Infectious Diseases Therapeutic Area, Sanofi, Marcy-l'Étoile, France
| | - James Sacchettini
- Departments of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX, USA.
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA.
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19
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Bockman MR, Engelhart CA, Cramer JD, Howe MD, Mishra NK, Zimmerman M, Larson P, Alvarez-Cabrera N, Park SW, Boshoff HIM, Bean JM, Young VG, Ferguson DM, Dartois V, Jarrett JT, Schnappinger D, Aldrich CC. Investigation of ( S)-(-)-Acidomycin: A Selective Antimycobacterial Natural Product That Inhibits Biotin Synthase. ACS Infect Dis 2019; 5:598-617. [PMID: 30652474 DOI: 10.1021/acsinfecdis.8b00345] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthesis, absolute stereochemical configuration, complete biological characterization, mechanism of action and resistance, and pharmacokinetic properties of ( S)-(-)-acidomycin are described. Acidomycin possesses promising antitubercular activity against a series of contemporary drug susceptible and drug-resistant M. tuberculosis strains (minimum inhibitory concentrations (MICs) = 0.096-6.2 μM) but is inactive against nontuberculosis mycobacteria and Gram-positive and Gram-negative pathogens (MICs > 1000 μM). Complementation studies with biotin biosynthetic pathway intermediates and subsequent biochemical studies confirmed acidomycin inhibits biotin synthesis with a Ki of approximately 1 μM through the competitive inhibition of biotin synthase (BioB) and also stimulates unproductive cleavage of S-adenosyl-l-methionine (SAM) to generate the toxic metabolite 5'-deoxyadenosine. Cell studies demonstrate acidomycin selectively accumulates in M. tuberculosis providing a mechanistic basis for the observed antibacterial activity. The development of spontaneous resistance by M. tuberculosis to acidomycin was difficult, and only low-level resistance to acidomycin was observed by overexpression of BioB. Collectively, the results provide a foundation to advance acidomycin and highlight BioB as a promising target.
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Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Curtis A. Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - Julia D. Cramer
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Michael D. Howe
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Neeraj K. Mishra
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Matthew Zimmerman
- Public Health Research Institute, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Peter Larson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Nadine Alvarez-Cabrera
- Public Health Research Institute, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, 5601 Fishers Lane, Bethesda, Maryland 20892, United States
| | - James M. Bean
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, United States
| | - Victor G. Young
- X-Ray Crystallographic Laboratory, LeClaire-Dow Chemical Instrumentation Facility, Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - David M. Ferguson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Veronique Dartois
- Public Health Research Institute, Rutgers, The State University of New Jersey, 225 Warren Street, Newark, New Jersey 07103, United States
| | - Joseph T. Jarrett
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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20
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Oh S, Park Y, Engelhart CA, Wallach JB, Schnappinger D, Arora K, Manikkam M, Gac B, Wang H, Murgolo N, Olsen DB, Goodwin M, Sutphin M, Weiner DM, Via LE, Boshoff HIM, Barry CE. Discovery and Structure-Activity-Relationship Study of N-Alkyl-5-hydroxypyrimidinone Carboxamides as Novel Antitubercular Agents Targeting Decaprenylphosphoryl-β-d-ribose 2'-Oxidase. J Med Chem 2018; 61:9952-9965. [PMID: 30350998 PMCID: PMC6257622 DOI: 10.1021/acs.jmedchem.8b00883] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Magnesium plays an important role
in infection with Mycobacterium
tuberculosis (Mtb) as a signal of the extracellular
environment, as a cofactor for many enzymes, and as a structural element
in important macromolecules. Raltegravir, an antiretroviral drug that
inhibits HIV-1 integrase is known to derive its potency from selective
sequestration of active-site magnesium ions in addition to binding
to a hydrophobic pocket. In order to determine if essential Mtb-related phosphoryl transfers could be disrupted in a
similar manner, a directed screen of known molecules with integrase
inhibitor-like pharmacophores (N-alkyl-5-hydroxypyrimidinone
carboxamides) was performed. Initial hits afforded compounds with
low-micromolar potency against Mtb, acceptable cytotoxicity
and PK characteristics, and robust SAR. Elucidation of the target
of these compounds revealed that they lacked magnesium dependence
and instead disappointingly inhibited a known promiscuous target in Mtb, decaprenylphosphoryl-β-d-ribose 2′-oxidase
(DprE1, Rv3790).
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Affiliation(s)
- Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Yumi Park
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Curtis A Engelhart
- Department of Microbiology and Immunology , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Joshua B Wallach
- Department of Microbiology and Immunology , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Michelle Manikkam
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Brian Gac
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Hongwu Wang
- Discovery Research , Merck & Company, Inc. , 770 Sumneytown Pike , West Point , Pennsylvania 19486 , United States
| | - Nicholas Murgolo
- Discovery Research , Merck & Company, Inc. , 770 Sumneytown Pike , West Point , Pennsylvania 19486 , United States
| | - David B Olsen
- Discovery Research , Merck & Company, Inc. , 770 Sumneytown Pike , West Point , Pennsylvania 19486 , United States
| | - Michael Goodwin
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Michelle Sutphin
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Danielle M Weiner
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Laura E Via
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Institute for Infectious Disease and Molecular Medicine , University of Cape Town , Cape Town 7935 , South Africa
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Institute for Infectious Disease and Molecular Medicine , University of Cape Town , Cape Town 7935 , South Africa
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21
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Wescott HH, Zuniga ES, Bajpai A, Trujillo C, Ehrt S, Schnappinger D, Roberts DM, Parish T. Identification of Enolase as the Target of 2-Aminothiazoles in Mycobacterium tuberculosis. Front Microbiol 2018; 9:2542. [PMID: 30416491 PMCID: PMC6213970 DOI: 10.3389/fmicb.2018.02542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/04/2018] [Indexed: 01/26/2023] Open
Abstract
Tuberculosis is a massive global burden and Mycobacterium tuberculosis is increasingly resistant to first- and second-line drugs. There is an acute need for new anti-mycobacterial drugs with novel targets. We previously evaluated a series of 2-aminothiazoles with activity against Mycobacterium tuberculosis. In this study, we identify the glycolytic enzyme enolase as the target of these molecules using pull down studies. We demonstrate that modulation of the level of enolase expression affects sensitivity to 2-aminothiazoles; increased expression leads to resistance while decreased protein levels increase sensitivity. Exposure to 2-aminothiazoles results in increased levels of metabolites preceding the action of enolase in the glycolytic pathway and decreased ATP levels. We demonstrate that 2-aminothiazoles inhibit the activity of the human α-enolase, which could also account for the cytotoxicity of some of those molecules. If selectivity for the bacterial enzyme over the human enzyme could be achieved, enolase would represent an attractive target for M. tuberculosis drug discovery and development efforts.
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Affiliation(s)
- Heather H Wescott
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Edison S Zuniga
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Anumita Bajpai
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States
| | - David M Roberts
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, United States
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22
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A useful gene cassette for conditional knock-down of essential genes by targeted promoter replacement in Mycobacteria. Biotechniques 2018; 65:159-162. [PMID: 30227740 DOI: 10.2144/btn-2018-0074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A direct method to study essential genes is to construct conditional knock-down mutants by replacement of their native promoter by an inducible one. In Mycobacteria, replacement of an essential gene promoter with an anhydrotetracycline inducible one was successfully used but required a multi-step approach. In this work, we describe a gene cassette for the engineering of a conditional knock-down mutant, which allows the one-step targeted replacement of mycobacterial promoters by an anhydrotetracycline-inducible promoter. The functionality of this cassette was successfully tested by engineering conditional clpP and SecA1 mutants of Mycobacterium smegmatis.
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23
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Mycobacterium tuberculosis Pst/SenX3-RegX3 Regulates Membrane Vesicle Production Independently of ESX-5 Activity. mBio 2018; 9:mBio.00778-18. [PMID: 29895636 PMCID: PMC6016242 DOI: 10.1128/mbio.00778-18] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium tuberculosis releases membrane vesicles (MV) that modulate host immune responses and aid in iron acquisition, although they may have additional unappreciated functions. MV production appears to be a regulated process, but virR remains the only characterized genetic regulator of vesiculogenesis. Here, we present data supporting a role for the M. tuberculosis Pst/SenX3-RegX3 signal transduction system in regulating MV production. Deletion of pstA1, which encodes a transmembrane component of the phosphate-specific transport (Pst) system, causes constitutive activation of the SenX3-RegX3 two-component system, leading to increased protein secretion via the specialized ESX-5 type VII secretion system. Using proteomic mass spectrometry, we identified several additional proteins hyper-secreted by the ΔpstA1 mutant, including LpqH, an MV-associated lipoprotein. Nanoparticle tracking analysis revealed a 15-fold increase in MV production by the ΔpstA1 mutant. Both hyper-secretion of LpqH and increased MV release required RegX3 but were independent of VirR, suggesting that Pst/SenX3-RegX3 controls MV release by a novel mechanism. Prior proteomic analysis identified ESX-5 substrates associated with MV. We therefore hypothesized that MV release requires ESX-5 activity. We constructed strains that conditionally express eccD5, which encodes the predicted ESX-5 transmembrane channel. Upon EccD5 depletion, we observed reduced secretion of the ESX-5 substrates EsxN and PPE41, but MV release was unaffected. Our data suggest that ESX-5 does not affect vesicle production and imply that further characterization of the Pst/SenX3-RegX3 regulon might reveal novel mechanisms of M. tuberculosis vesicle biogenesis. In Gram-negative bacteria, MV derived from the outer membrane have diverse functions in bacterial physiology and pathogenesis, and several factors regulating their production have been identified. Though Gram-positive bacteria and mycobacteria that lack an outer membrane also produce vesicles with described roles in pathogenesis, the mechanisms of MV biogenesis in these organisms remain poorly characterized. Defining mechanisms of MV biogenesis might yield significant insights into the importance of MV production during infection. In M. tuberculosis, only a single genetic element, virR, is known to regulate MV production. Our work reveals that the Pst/SenX3-RegX3 signal transduction system is a novel regulator of MV biogenesis that controls MV production by a mechanism that is independent of both VirR and activation of the specialized ESX-5 protein secretion system. Understanding which genes in the RegX3 regulon cause increased MV production might reveal novel molecular mechanisms of MV release.
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24
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Abstract
After decades of relative inactivity, a large increase in efforts to discover antitubercular therapeutics has brought insights into the biology of Mycobacterium tuberculosis (Mtb) and promising new drugs such as bedaquiline, which inhibits ATP synthase, and the nitroimidazoles delamanid and pretomanid, which inhibit both mycolic acid synthesis and energy production. Despite these advances, the drug discovery pipeline remains underpopulated. The field desperately needs compounds with novel mechanisms of action capable of inhibiting multi- and extensively drug -resistant Mtb (M/XDR-TB) and, potentially, nonreplicating Mtb with the hope of shortening the duration of required therapy. New knowledge about Mtb, along with new methods and technologies, has driven exploration into novel target areas, such as energy production and central metabolism, that diverge from the classical targets in macromolecular synthesis. Here, we review new small molecule drug candidates that act on these novel targets to highlight the methods and perspectives advancing the field. These new targets bring with them the aspiration of shortening treatment duration as well as a pipeline of effective regimens against XDR-TB, positioning Mtb drug discovery to become a model for anti-infective discovery.
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Affiliation(s)
- Samantha Wellington
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
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25
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Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation. PLoS Pathog 2017; 13:e1006752. [PMID: 29176894 PMCID: PMC5720804 DOI: 10.1371/journal.ppat.1006752] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/07/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Abstract
The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen. Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), can persist for years and even decades in the lungs of its human host. Here we report that a unique M. tuberculosis gene cluster involved in the synthesis of the molybdenum cofactor, a cofactor for several oxidoreductases including the nitrate reductase, allows this major pathogen to respire nitrate and to persist in a dormant state under hypoxia, a stress condition encountered in lung TB lesions. Strikingly the M. tuberculosis ancestor, which most likely was an environmental harmless bacterium, acquired this gene cluster, together with its hypoxia-responsive transcriptional regulator, horizontally from neighboring bacteria. Our results uncover a key step in M. tuberculosis evolution towards pathogenicity.
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26
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Botella L, Vaubourgeix J, Livny J, Schnappinger D. Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death. Nat Commun 2017; 8:14731. [PMID: 28348398 PMCID: PMC5379054 DOI: 10.1038/ncomms14731] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/26/2017] [Indexed: 12/30/2022] Open
Abstract
Rifampicin, which inhibits bacterial RNA polymerase, provides one of the most effective treatments for tuberculosis. Inhibition of the transcription termination factor Rho is used to treat some bacterial infections, but its importance varies across bacteria. Here we show that Rho of Mycobacterium tuberculosis functions to both define the 3' ends of mRNAs and silence substantial fragments of the genome. Brief inactivation of Rho affects over 500 transcripts enriched for genes of foreign DNA elements and bacterial virulence factors. Prolonged inactivation of Rho causes extensive pervasive transcription, a genome-wide increase in antisense transcripts, and a rapid loss of viability of replicating and non-replicating M. tuberculosis in vitro and during acute and chronic infection in mice. Collectively, these data suggest that inhibition of Rho may provide an alternative strategy to treat tuberculosis with an efficacy similar to inhibition of RNA polymerase.
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Affiliation(s)
- Laure Botella
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413E 69th Street, New York, New York 10021, USA
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413E 69th Street, New York, New York 10021, USA
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413E 69th Street, New York, New York 10021, USA
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27
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Singh V, Mizrahi V. Identification and validation of novel drug targets in Mycobacterium tuberculosis. Drug Discov Today 2016; 22:503-509. [PMID: 27649943 DOI: 10.1016/j.drudis.2016.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/28/2016] [Accepted: 09/12/2016] [Indexed: 10/21/2022]
Abstract
Tuberculosis (TB) is a global epidemic associated increasingly with resistance to first- and second-line antitubercular drugs. The magnitude of this global health threat underscores the urgent need to discover new antimycobacterial agents that have novel mechanisms of action (MOA). In this review, we highlight some of the key advances that have enabled the strengths of target-led and phenotypic approaches to TB drug discovery to be harnessed both independently and in combination. Critically, these promise to fuel the front-end of the TB drug pipeline with new, pharmacologically validated drug targets together with lead compounds that act on these targets.
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Affiliation(s)
- Vinayak Singh
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory 7925, South Africa.
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Anzio Road, Observatory 7925, South Africa
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28
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Prigozhin DM, Papavinasasundaram KG, Baer CE, Murphy KC, Moskaleva A, Chen TY, Alber T, Sassetti CM. Structural and Genetic Analyses of the Mycobacterium tuberculosis Protein Kinase B Sensor Domain Identify a Potential Ligand-binding Site. J Biol Chem 2016; 291:22961-22969. [PMID: 27601474 DOI: 10.1074/jbc.m116.731760] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 11/06/2022] Open
Abstract
Monitoring the environment with serine/threonine protein kinases is critical for growth and survival of Mycobacterium tuberculosis, a devastating human pathogen. Protein kinase B (PknB) is a transmembrane serine/threonine protein kinase that acts as an essential regulator of mycobacterial growth and division. The PknB extracellular domain (ECD) consists of four repeats homologous to penicillin-binding protein and serine/threonine kinase associated (PASTA) domains, and binds fragments of peptidoglycan. These properties suggest that PknB activity is modulated by ECD binding to peptidoglycan substructures, however, the molecular mechanisms underpinning PknB regulation remain unclear. In this study, we report structural and genetic characterization of the PknB ECD. We determined the crystal structures of overlapping ECD fragments at near atomic resolution, built a model of the full ECD, and discovered a region on the C-terminal PASTA domain that has the properties of a ligand-binding site. Hydrophobic interaction between this surface and a bound molecule of citrate was observed in a crystal structure. Our genetic analyses in M. tuberculosis showed that nonfunctional alleles were produced either by deletion of any of single PASTA domain or by mutation of individual conserved residues lining the putative ligand-binding surface of the C-terminal PASTA repeat. These results define two distinct structural features necessary for PknB signal transduction, a fully extended ECD and a conserved, membrane-distal putative ligand-binding site.
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Affiliation(s)
- Daniil M Prigozhin
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Kadamba G Papavinasasundaram
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Christina E Baer
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Kenan C Murphy
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Alisa Moskaleva
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Tony Y Chen
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Tom Alber
- From the Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, California 94720-3220 and
| | - Christopher M Sassetti
- the Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655
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29
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Therapeutic Potential of the Mycobacterium tuberculosis Mycolic Acid Transporter, MmpL3. Antimicrob Agents Chemother 2016; 60:5198-207. [PMID: 27297488 DOI: 10.1128/aac.00826-16] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/08/2016] [Indexed: 11/20/2022] Open
Abstract
In recent years, whole-cell-based screens for novel small molecule inhibitors active against Mycobacterium tuberculosis in culture followed by the whole-genome sequencing of spontaneous resistant mutants have identified multiple chemical scaffolds thought to kill the bacterium through the inactivation of the mycolic acid transporter, MmpL3. Consistent with the fact that MmpL3 is required for the formation of the mycobacterial outer membrane, we have conclusively shown in this study, using conditionally regulated knockdown mutants, that mmpL3 is required for the replication and viability of M. tuberculosis, both under standard laboratory growth conditions and during the acute and chronic phases of infection in mice. Speaking for the vulnerability of this target, silencing mmpL3 had a rapid bactericidal effect on actively replicating cells in vitro and reduced by 3 to 5 logs in less than 4 weeks the bacterial loads of acutely and chronically infected mouse lungs, respectively. Depletion of MmpL3 further rendered M. tuberculosis hypersusceptible to MmpL3 inhibitors. The exquisite vulnerability of MmpL3 at all stages of the infection establishes this transporter as an attractive new target with the potential to improve and shorten current drug-susceptible and drug-resistant tuberculosis chemotherapies.
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30
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Hoagland DT, Liu J, Lee RB, Lee RE. New agents for the treatment of drug-resistant Mycobacterium tuberculosis. Adv Drug Deliv Rev 2016; 102:55-72. [PMID: 27151308 PMCID: PMC4903924 DOI: 10.1016/j.addr.2016.04.026] [Citation(s) in RCA: 230] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 02/06/2023]
Abstract
Inadequate dosing and incomplete treatment regimens, coupled with the ability of the tuberculosis bacilli to cause latent infections that are tolerant of currently used drugs, have fueled the rise of multidrug-resistant tuberculosis (MDR-TB). Treatment of MDR-TB infections is a major clinical challenge that has few viable or effective solutions; therefore patients face a poor prognosis and years of treatment. This review focuses on emerging drug classes that have the potential for treating MDR-TB and highlights their particular strengths as leads including their mode of action, in vivo efficacy, and key medicinal chemistry properties. Examples include the newly approved drugs bedaquiline and delaminid, and other agents in clinical and late preclinical development pipeline for the treatment of MDR-TB. Herein, we discuss the challenges to developing drugs to treat tuberculosis and how the field has adapted to these difficulties, with an emphasis on drug discovery approaches that might produce more effective agents and treatment regimens.
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Affiliation(s)
- Daniel T Hoagland
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Pharmaceutical Sciences Graduate Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jiuyu Liu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robin B Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Lin K, O'Brien KM, Trujillo C, Wang R, Wallach JB, Schnappinger D, Ehrt S. Mycobacterium tuberculosis Thioredoxin Reductase Is Essential for Thiol Redox Homeostasis but Plays a Minor Role in Antioxidant Defense. PLoS Pathog 2016; 12:e1005675. [PMID: 27249779 PMCID: PMC4889078 DOI: 10.1371/journal.ppat.1005675] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/12/2016] [Indexed: 02/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) must cope with exogenous oxidative stress imposed by the host. Unlike other antioxidant enzymes, Mtb's thioredoxin reductase TrxB2 has been predicted to be essential not only to fight host defenses but also for in vitro growth. However, the specific physiological role of TrxB2 and its importance for Mtb pathogenesis remain undefined. Here we show that genetic inactivation of thioredoxin reductase perturbed several growth-essential processes, including sulfur and DNA metabolism and rapidly killed and lysed Mtb. Death was due to cidal thiol-specific oxidizing stress and prevented by a disulfide reductant. In contrast, thioredoxin reductase deficiency did not significantly increase susceptibility to oxidative and nitrosative stress. In vivo targeting TrxB2 eradicated Mtb during both acute and chronic phases of mouse infection. Deliberately leaky knockdown mutants identified the specificity of TrxB2 inhibitors and showed that partial inactivation of TrxB2 increased Mtb's susceptibility to rifampicin. These studies reveal TrxB2 as essential thiol-reducing enzyme in Mtb in vitro and during infection, establish the value of targeting TrxB2, and provide tools to accelerate the development of TrxB2 inhibitors.
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Affiliation(s)
- Kan Lin
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
| | - Kathryn M. O'Brien
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
| | - Joshua B. Wallach
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (DS); (SE)
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, New York, United States of America
- * E-mail: (DS); (SE)
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