1
|
Bosch B, DeJesus MA, Schnappinger D, Rock JM. Weak links: Advancing target-based drug discovery by identifying the most vulnerable targets. Ann N Y Acad Sci 2024. [PMID: 38595325 DOI: 10.1111/nyas.15139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Mycobacterium tuberculosis remains the most common infectious killer worldwide despite decades of antitubercular drug development. Effectively controlling the tuberculosis (TB) pandemic will require innovation in drug discovery. In this review, we provide a brief overview of the two main approaches to discovering new TB drugs-phenotypic screens and target-based drug discovery-and outline some of the limitations of each method. We then explore recent advances in genetic tools that aim to overcome some of these limitations. In particular, we highlight a novel metric to prioritize essential targets, termed vulnerability. Stratifying targets based on their vulnerability presents new opportunities for future target-based drug discovery campaigns.
Collapse
Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| |
Collapse
|
2
|
Krieger IV, Yalamanchili S, Dickson P, Engelhart CA, Zimmerman MD, Wood J, Clary E, Nguyen J, Thornton N, Centrella PA, Chan B, Cuozzo JW, Gengenbacher M, Guié MA, Guilinger JP, Bienstock C, Hartl H, Hupp CD, Jetson R, Satoh T, Yeoman JTS, Zhang Y, Dartois V, Schnappinger D, Keefe AD, Sacchettini JC. Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. ACS Infect Dis 2024. [PMID: 38577994 DOI: 10.1021/acsinfecdis.3c00592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.
Collapse
Affiliation(s)
- Inna V Krieger
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | | | - Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Jeremy Wood
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Ethan Clary
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Jasmine Nguyen
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Natalie Thornton
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Paolo A Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Auron Therapeutics, 55 Chapel Street, Newton, Massachusetts 02458, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Corey Bienstock
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Hajnalka Hartl
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Orogen Therapeutics, 12 Gill Street, Woburn, Massachusetts 01801, United States
| | - Christopher D Hupp
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Ipsen Bioscience Inc., 1 Main Street, Cambridge, Massachusetts 02142, United States
| | - Rachael Jetson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Valo Health, 75 Hayden Avenue, Lexington, Massachusetts 02141, United States
| | - Takashi Satoh
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- EXO Therapeutics, 150 Cambridgepark Drive, suite 300, Cambridge, Massachusetts 02140, United States
| | - John T S Yeoman
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Recludix Pharmaceuticals, 222 Third Street, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Veronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, New Jersey 07110, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, United States
| | - Anthony D Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - James C Sacchettini
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
3
|
Choudhery S, DeJesus MA, Srinivasan A, Rock J, Schnappinger D, Ioerger TR. A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens. bioRxiv 2024:2023.08.03.551759. [PMID: 37577548 PMCID: PMC10418283 DOI: 10.1101/2023.08.03.551759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.
Collapse
Affiliation(s)
- Sanjeevani Choudhery
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, United States of America
| | - Aarthi Srinivasan
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, 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
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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.
| |
Collapse
|
5
|
Xu Y, Ehrt S, Schnappinger D, Beites T. Synthetic lethality of Mycobacterium tuberculosis NADH dehydrogenases is due to impaired NADH oxidation. mBio 2023; 14:e0104523. [PMID: 38032200 PMCID: PMC10746327 DOI: 10.1128/mbio.01045-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE In 2022, it was estimated that 10.6 million people fell ill, and 1.6 million people died from tuberculosis (TB). Available treatment is lengthy and requires a multi-drug regimen, which calls for new strategies to cure Mycobacterium tuberculosis (Mtb) infections more efficiently. We have previously shown that simultaneous inactivation of type 1 (Ndh-1) and type 2 (Ndh-2) NADH dehydrogenases kills Mtb. NADH dehydrogenases play two main physiological roles: NADH oxidation and electron entry into the respiratory chain. Here, we show that this bactericidal effect is a consequence of impaired NADH oxidation. Importantly, we demonstrate that Ndh-1/Ndh-2 synthetic lethality can be achieved through simultaneous chemical inhibition, which could be exploited by TB drug development programs.
Collapse
Affiliation(s)
- Yuanyuan Xu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
| | - Tiago Beites
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, USA
| |
Collapse
|
6
|
Green SR, Wilson C, Eadsforth TC, Punekar AS, Tamaki FK, Wood G, Caldwell N, Forte B, Norcross NR, Kiczun M, Post JM, Lopez-Román EM, Engelhart CA, Lukac I, Zuccotto F, Epemolu O, Boshoff HIM, Schnappinger D, Walpole C, Gilbert IH, Read KD, Wyatt PG, Baragaña B. Identification and Optimization of Novel Inhibitors of the Polyketide Synthase 13 Thioesterase Domain with Antitubercular Activity. J Med Chem 2023; 66:15380-15408. [PMID: 37948640 PMCID: PMC10683028 DOI: 10.1021/acs.jmedchem.3c01514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
There is an urgent need for new tuberculosis (TB) treatments, with novel modes of action, to reduce the incidence/mortality of TB and to combat resistance to current treatments. Through both chemical and genetic methodologies, polyketide synthase 13 (Pks13) has been validated as essential for mycobacterial survival and as an attractive target for Mycobacterium tuberculosis growth inhibitors. A benzofuran series of inhibitors that targeted the Pks13 thioesterase domain, failed to progress to preclinical development due to concerns over cardiotoxicity. Herein, we report the identification of a novel oxadiazole series of Pks13 inhibitors, derived from a high-throughput screening hit and structure-guided optimization. This new series binds in the Pks13 thioesterase domain, with a distinct binding mode compared to the benzofuran series. Through iterative rounds of design, assisted by structural information, lead compounds were identified with improved antitubercular potencies (MIC < 1 μM) and in vitro ADMET profiles.
Collapse
Affiliation(s)
- Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Caroline Wilson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Thomas C. Eadsforth
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Avinash S. Punekar
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Fabio K. Tamaki
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Gavin Wood
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Barbara Forte
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Neil R. Norcross
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Michael Kiczun
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - John M. Post
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Eva Maria Lopez-Román
- Global
Health Medicines R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid Spain
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Iva Lukac
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Chris Walpole
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, QC H4A 3J1, Canada
| | - Ian H. Gilbert
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Beatriz Baragaña
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| |
Collapse
|
7
|
Smith AA, Su H, Wallach J, Liu Y, Maiello P, Borish HJ, Winchell C, Simonson AW, Lin PL, Rodgers M, Fillmore D, Sakal J, Lin K, Schnappinger D, Ehrt S, Flynn JL. A "suicide" BCG strain provides enhanced immunogenicity and robust protection against Mycobacterium tuberculosis in macaques. bioRxiv 2023:2023.11.22.568105. [PMID: 38045242 PMCID: PMC10690263 DOI: 10.1101/2023.11.22.568105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Intravenous (IV) BCG delivery provides robust protection against Mycobacterium tuberculosis (Mtb) in macaques but poses safety challenges. Here, we constructed two BCG strains (BCG-TetON-DL and BCG-TetOFF-DL) in which tetracyclines regulate two phage lysin operons. Once the lysins are expressed, these strains are cleared in immunocompetent and immunocompromised mice, yet induced similar immune responses and provided similar protection against Mtb challenge as wild type BCG. Lysin induction resulted in release of intracellular BCG antigens and enhanced cytokine production by macrophages. In macaques, cessation of doxycycline administration resulted in rapid elimination of BCG-TetOFF-DL. However, IV BCG-TetOFF-DL induced increased pulmonary CD4 T cell responses compared to WT BCG and provided robust protection against Mtb challenge, with sterilizing immunity in 6 of 8 macaques, compared to 2 of 8 macaques immunized with WT BCG. Thus, a "suicide" BCG strain provides an additional measure of safety when delivered intravenously and robust protection against Mtb infection.
Collapse
Affiliation(s)
- Alexander A Smith
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Hongwei Su
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
- Present address: Center for Veterinary Science, Zhejiang University, Hangzhou, China
| | - Joshua Wallach
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yao Liu
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - H Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Caylin Winchell
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Andrew W Simonson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Philana Ling Lin
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
- Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Mark Rodgers
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Daniel Fillmore
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Jennifer Sakal
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| | - Kan Lin
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh PA
| |
Collapse
|
8
|
Wang X, Su H, Wallach JB, Wagner JC, Braunecker B, Gardner M, Guinn KM, Klevorn T, Lin K, Liu YJ, Liu Y, Mugahid D, Rodgers M, Sixsmith J, Wakabayashi S, Zhu J, Zimmerman M, Dartois V, Flynn JL, Lin PL, Ehrt S, Fortune SM, Rubin EJ, Schnappinger D. Development of an Engineered Mycobacterium tuberculosis Strain for a Safe and Effective Tuberculosis Human Challenge Model. bioRxiv 2023:2023.11.19.567569. [PMID: 38014062 PMCID: PMC10680849 DOI: 10.1101/2023.11.19.567569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Human challenge experiments could greatly accelerate the development of a tuberculosis (TB) vaccine. Human challenge for tuberculosis requires a strain that can both replicate in the host and be reliably cleared. To accomplish this, we designed Mycobacterium tuberculosis (Mtb) strains featuring up to three orthogonal kill switches, tightly regulated by exogenous tetracyclines and trimethoprim. The resultant strains displayed immunogenicity and antibiotic susceptibility similar to wild-type Mtb under permissive conditions. In the absence of supplementary exogenous compounds, the strains were rapidly killed in axenic culture, mice and nonhuman primates. Notably, the strain that contained three kill switches had an escape rate of less than 10 -10 per genome per generation and displayed no relapse in a SCID mouse model. Collectively, these findings suggest that this engineered Mtb strain could be a safe and effective candidate for a human challenge model.
Collapse
|
9
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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
| |
Collapse
|
10
|
Hegde P, Orimoloye MO, Sharma S, Engelhart CA, Schnappinger D, Aldrich CC. Polyfluorinated salicylic acid analogs do not interfere with siderophore biosynthesis. Tuberculosis (Edinb) 2023; 140:102346. [PMID: 37119793 DOI: 10.1016/j.tube.2023.102346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/01/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is a leading cause of infectious disease mortality. The salicylic acid derived small molecule siderophores known as mycobactins are essential in vivo for iron acquisition of Mtb where iron is restricted in the host. Herein, we synthesize and explore the mechanism of action of polyfluorinated salicylic acid derivates, which were previously reported to possess potent antimycobacterial activity. We hypothesized fluorinated salicylic acid derivates may inhibit mycobactin biosynthesis through initial bioactivation and conversion to downstream metabolites that block late steps in assembly of the mycobactins. Enzymatic studies demonstrated that some of the fluorinated salicylic acid derivatives compounds were readily activated by the bifunctional adenylating enzyme MbtA, responsible for incorporation of salicylic acid into the mycobactin biosynthetic pathway; however, they did not inhibit mycobactin biosynthesis as confirmed by LS-MS/MS using an authentic synthetic mycobactin standard. Further mechanistic analysis of the most active derivative (Sal-4) using an MbtA-overexpressing Mtb strain as well as complementation studies with iron and salicylic acid revealed Sal-4 cannot be antagonized by overexpression of MbtA or through supplementation with iron or salicylic acid. Taken together, our results indicate the observed antimycobacterial activity of polyfluorinated salicylic acid derivative is independent of mycobactin biosynthesis.
Collapse
Affiliation(s)
- Pooja Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Moyosore O Orimoloye
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Sachin Sharma
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10021, USA.
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, MN, 55455, USA.
| |
Collapse
|
11
|
Xu Y, Ehrt S, Schnappinger D, Beites T. Synthetic lethality of Mycobacterium tuberculosis NADH dehydrogenases is due to impaired NADH oxidation. bioRxiv 2023:2023.04.10.536268. [PMID: 37090679 PMCID: PMC10120654 DOI: 10.1101/2023.04.10.536268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Type 2 NADH dehydrogenase (Ndh-2) is an oxidative phosphorylation enzyme discussed as a promising drug target in different pathogens, including Plasmodium falciparum and Mycobacterium tuberculosis (Mtb). To kill Mtb, Ndh-2 needs to be inactivated together with the alternative enzyme type 1 NADH dehydrogenase (Ndh-1), but the mechanism of this synthetic lethality remained unknown. Here, we provide insights into the biology of NADH dehydrogenases and a mechanistic explanation for Ndh-1 and Ndh-2 synthetic lethality in Mtb. NADH dehydrogenases have two main functions: maintaining an appropriate NADH/NAD+ ratio by converting NADH into NAD+ and providing electrons to the respiratory chain. Heterologous expression of a water forming NADH oxidase (Nox), which catalyzes the oxidation of NADH, allows to distinguish between these two functions and show that Nox rescues Mtb from Ndh-1/Ndh-2 synthetic lethality, indicating that NADH oxidation is the essential function of NADH dehydrogenases for Mtb viability. Quantification of intracellular levels of NADH, NAD, ATP, and oxygen consumption revealed that preventing NADH oxidation by Ndh-2 depletes NAD(H) and inhibits respiration. Finally, we show that Ndh-1/ Ndh-2 synthetic lethality can be achieved through chemical inhibition.
Collapse
Affiliation(s)
- Yuanyuan Xu
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Tiago Beites
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| |
Collapse
|
12
|
Wong AI, Beites T, Planck KA, Fieweger RA, Eckartt KA, Li S, Poulton NC, VanderVen BC, Rhee KY, Schnappinger D, Ehrt S, Rock J. Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis. eLife 2023; 12:e81177. [PMID: 36810158 PMCID: PMC9995111 DOI: 10.7554/elife.81177] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/22/2023] [Indexed: 02/24/2023] Open
Abstract
Cyclic AMP (cAMP) is a ubiquitous second messenger that transduces signals from cellular receptors to downstream effectors. Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, devotes a considerable amount of coding capacity to produce, sense, and degrade cAMP. Despite this fact, our understanding of how cAMP regulates Mtb physiology remains limited. Here, we took a genetic approach to investigate the function of the sole essential adenylate cyclase in Mtb H37Rv, Rv3645. We found that a lack of rv3645 resulted in increased sensitivity to numerous antibiotics by a mechanism independent of substantial increases in envelope permeability. We made the unexpected observation that rv3645 is conditionally essential for Mtb growth only in the presence of long-chain fatty acids, a host-relevant carbon source. A suppressor screen further identified mutations in the atypical cAMP phosphodiesterase rv1339 that suppress both fatty acid and drug sensitivity phenotypes in strains lacking rv3645. Using mass spectrometry, we found that Rv3645 is the dominant source of cAMP under standard laboratory growth conditions, that cAMP production is the essential function of Rv3645 in the presence of long-chain fatty acids, and that reduced cAMP levels result in increased long-chain fatty acid uptake and metabolism and increased antibiotic susceptibility. Our work defines rv3645 and cAMP as central mediators of intrinsic multidrug resistance and fatty acid metabolism in Mtb and highlights the potential utility of small molecule modulators of cAMP signaling.
Collapse
Affiliation(s)
- Andrew I Wong
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Tiago Beites
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
| | - Kyle A Planck
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell MedicineNew YorkUnited States
| | - Rachael A Fieweger
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Kathryn A Eckartt
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell MedicineNew YorkUnited States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell MedicineNew YorkUnited States
| | - Jeremy Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller UniversityNew YorkUnited States
| |
Collapse
|
13
|
Li S, Poulton NC, Chang JS, Azadian ZA, DeJesus MA, Ruecker N, Zimmerman MD, Eckartt KA, Bosch B, Engelhart CA, Sullivan DF, Gengenbacher M, Dartois VA, Schnappinger D, Rock JM. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat Microbiol 2022; 7:766-779. [PMID: 35637331 PMCID: PMC9159947 DOI: 10.1038/s41564-022-01130-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Mycobacterium tuberculosis (Mtb) infection is notoriously difficult to treat. Treatment efficacy is limited by Mtb's intrinsic drug resistance, as well as its ability to evolve acquired resistance to all antituberculars in clinical use. A deeper understanding of the bacterial pathways that influence drug efficacy could facilitate the development of more effective therapies, identify new mechanisms of acquired resistance, and reveal overlooked therapeutic opportunities. Here we developed a CRISPR interference chemical-genetics platform to titrate the expression of Mtb genes and quantify bacterial fitness in the presence of different drugs. We discovered diverse mechanisms of intrinsic drug resistance, unveiling hundreds of potential targets for synergistic drug combinations. Combining chemical genetics with comparative genomics of Mtb clinical isolates, we further identified several previously unknown mechanisms of acquired drug resistance, one of which is associated with a multidrug-resistant tuberculosis outbreak in South America. Lastly, we found that the intrinsic resistance factor whiB7 was inactivated in an entire Mtb sublineage endemic to Southeast Asia, presenting an opportunity to potentially repurpose the macrolide antibiotic clarithromycin to treat tuberculosis. This chemical-genetic map provides a rich resource to understand drug efficacy in Mtb and guide future tuberculosis drug development and treatment.
Collapse
Affiliation(s)
- Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Jesseon S Chang
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Kathryn A Eckartt
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Daniel F Sullivan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA
| | - Véronique A Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
14
|
Grover S, Engelhart CA, Perez‐Herran E, Tiwari D, Li W, Abrahams KA, Papavinasasundaram K, Bean JM, Sassetti CM, Mendoza‐Losana A, Besra GS, Jackson M, Aldrich C, Schnappinger D. Two‐way regulation of protein expression for identification and validation of on‐target inhibitors of
Mycobacterium tuberculosis. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l7723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shipra Grover
- Microbiology and ImmunologyWeill Cornell MedicineNew YorkNY
| | | | - Esther Perez‐Herran
- TB Research Unit, Global Health R&D, GlaxoSmithKlineGlaxoSmithKlineTres Cantos
| | - Divya Tiwari
- Centre for ImmunobiologyQueen Mary University of LondonLondon
| | - Wei Li
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsCO
| | | | | | | | | | | | - Gurdyal S. Besra
- Institute of Microbiology and InfectionUniversity of BirminghamBirmingham
| | - Mary Jackson
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsCO
| | - Courtney Aldrich
- Department of Medicinal ChemistryUniversity of MinnesotaMinneapolisMN
| | | |
Collapse
|
15
|
Govender P, Müller R, Singh K, Reddy V, Eyermann CJ, Fienberg S, Ghorpade SR, Koekemoer L, Myrick A, Schnappinger D, Engelhart C, Meshanni J, Byl JAW, Osheroff N, Singh V, Chibale K, Basarab GS. Spiropyrimidinetrione DNA Gyrase Inhibitors with Potent and Selective Antituberculosis Activity. J Med Chem 2022; 65:6903-6925. [PMID: 35500229 DOI: 10.1021/acs.jmedchem.2c00266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New antibiotics with either a novel mode of action or novel mode of inhibition are urgently needed to overcome the threat of drug-resistant tuberculosis (TB). The present study profiles new spiropyrimidinetriones (SPTs), DNA gyrase inhibitors having activity against drug-resistant Mycobacterium tuberculosis (Mtb), the causative agent of TB. While the clinical candidate zoliflodacin has progressed to phase 3 trials for the treatment of gonorrhea, compounds herein demonstrated higher inhibitory potency against Mtb DNA gyrase (e.g., compound 42 with IC50 = 2.0) and lower Mtb minimum inhibitor concentrations (0.49 μM for 42). Notably, 42 and analogues showed selective Mtb activity relative to representative Gram-positive and Gram-negative bacteria. DNA gyrase inhibition was shown to involve stabilization of double-cleaved DNA, while on-target activity was supported by hypersensitivity against a gyrA hypomorph. Finally, a docking model for SPTs with Mtb DNA gyrase was developed, and a structural hypothesis was built for structure-activity relationship expansion.
Collapse
Affiliation(s)
- Preshendren Govender
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Rudolf Müller
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Kawaljit Singh
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Virsinha Reddy
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Charles J Eyermann
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Stephen Fienberg
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Sandeep R Ghorpade
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Lizbé Koekemoer
- Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Alissa Myrick
- Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Curtis Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Jaclynn Meshanni
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Jo Ann W Byl
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Neil Osheroff
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,Department of Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.,VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D) South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
| | - Gregory S Basarab
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.,Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, Cape Town, 7935, South Africa
| |
Collapse
|
16
|
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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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.
Collapse
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.
| |
Collapse
|
17
|
Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE, Park SW, Lee HN, Kiritsy MC, Bellerose MM, Olive AJ, Murphy KC, Papavinasasundaram K, Boehm FJ, Reames CJ, Meade RK, Hampton BK, Linnertz CL, Shaw GD, Hock P, Bell TA, Ehrt S, Schnappinger D, Pardo-Manuel de Villena F, Ferris MT, Ioerger TR, Sassetti CM. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. eLife 2022; 11:74419. [PMID: 35112666 PMCID: PMC8846590 DOI: 10.7554/elife.74419] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/27/2022] [Indexed: 11/21/2022] Open
Abstract
The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen’s ability to adapt to the variable immune pressures exerted by the host. Understanding this interplay has proven difficult, largely because experimentally tractable animal models do not recapitulate the heterogeneity of tuberculosis disease. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to create a resource for associating bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and produce qualitatively distinct immune states. Global analysis of Mtb transposon mutant fitness (TnSeq) across the CC panel revealed that many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen’s genome that has been maintained to ensure fitness in a diverse population. Both immunological and bacterial traits can be associated with genetic variants distributed across the mouse genome, making the CC a unique population for identifying specific host-pathogen genetic interactions that influence pathogenesis.
Collapse
Affiliation(s)
- Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Megan K Proulx
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Bibhuti B Mishra
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Michael C Kiritsy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Michelle M Bellerose
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Andrew J Olive
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Frederick J Boehm
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Charlotte J Reames
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Morrisville, United States
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Timothy A Bell
- Department of Genetics,, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Sabine Ehrt
- 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
| | | | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| |
Collapse
|
18
|
Wilson C, Ray P, Zuccotto F, Hernandez J, Aggarwal A, Mackenzie C, Caldwell N, Taylor M, Huggett M, Mathieson M, Murugesan D, Smith A, Davis S, Cocco M, Parai MK, Acharya A, Tamaki F, Scullion P, Epemolu O, Riley J, Stojanovski L, Lopez-Román EM, Torres-Gómez PA, Toledo AM, Guijarro-Lopez L, Camino I, Engelhart CA, Schnappinger D, Massoudi LM, Lenaerts A, Robertson GT, Walpole C, Matthews D, Floyd D, Sacchettini JC, Read KD, Encinas L, Bates RH, Green SR, Wyatt PG. Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target. J Med Chem 2022; 65:409-423. [PMID: 34910486 PMCID: PMC8762665 DOI: 10.1021/acs.jmedchem.1c01586] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Indexed: 11/28/2022]
Abstract
With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran 1 was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against Mycobacterium tuberculosis, its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.
Collapse
Affiliation(s)
- Caroline Wilson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Peter Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jorge Hernandez
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Anup Aggarwal
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Claire Mackenzie
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Alasdair Smith
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Mattia Cocco
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Maloy K. Parai
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Arjun Acharya
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Fabio Tamaki
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Eva Maria Lopez-Román
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | | | - Ana Maria Toledo
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Laura Guijarro-Lopez
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Isabel Camino
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Lisa M. Massoudi
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne Lenaerts
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Chris Walpole
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Matthews
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Floyd
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - James C. Sacchettini
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lourdes Encinas
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Robert H. Bates
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| |
Collapse
|
19
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
20
|
Dutta E, DeJesus MA, Ruecker N, Zaveri A, Koh EI, Sassetti CM, Schnappinger D, Ioerger TR. An improved statistical method to identify chemical-genetic interactions by exploiting concentration-dependence. PLoS One 2021; 16:e0257911. [PMID: 34597304 PMCID: PMC8486102 DOI: 10.1371/journal.pone.0257911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Chemical-genetics (C-G) experiments can be used to identify interactions between inhibitory compounds and bacterial genes, potentially revealing the targets of drugs, or other functionally interacting genes and pathways. C-G experiments involve constructing a library of hypomorphic strains with essential genes that can be knocked-down, treating it with an inhibitory compound, and using high-throughput sequencing to quantify changes in relative abundance of individual mutants. The hypothesis is that, if the target of a drug or other genes in the same pathway are present in the library, such genes will display an excessive fitness defect due to the synergy between the dual stresses of protein depletion and antibiotic exposure. While assays at a single drug concentration are susceptible to noise and can yield false-positive interactions, improved detection can be achieved by requiring that the synergy between gene and drug be concentration-dependent. We present a novel statistical method based on Linear Mixed Models, called CGA-LMM, for analyzing C-G data. The approach is designed to capture the dependence of the abundance of each gene in the hypomorph library on increasing concentrations of drug through slope coefficients. To determine which genes represent candidate interactions, CGA-LMM uses a conservative population-based approach in which genes with negative slopes are considered significant only if they are outliers with respect to the rest of the population (assuming that most genes in the library do not interact with a given inhibitor). We applied the method to analyze 3 independent hypomorph libraries of M. tuberculosis for interactions with antibiotics with anti-tubercular activity, and we identify known target genes or expected interactions for 7 out of 9 drugs where relevant interacting genes are known.
Collapse
Affiliation(s)
- Esha Dutta
- Department of Computer Science, Texas A&M University, College Station, TX, United States of America
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, United States of America
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States of America
| | - Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States of America
| | - Eun-Ik Koh
- Department of Microbiology & Physiological Systems, University of Massachusetts Medical School, Worchester, MA, United States of America
| | - Christopher M. Sassetti
- Department of Microbiology & Physiological Systems, University of Massachusetts Medical School, Worchester, MA, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, United States of America
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX, United States of America
| |
Collapse
|
21
|
Su H, Lin K, Tiwari D, Healy C, Trujillo C, Liu Y, Ioerger TR, Schnappinger D, Ehrt S. Genetic models of latent tuberculosis in mice reveal differential influence of adaptive immunity. J Exp Med 2021; 218:e20210332. [PMID: 34269789 PMCID: PMC8289691 DOI: 10.1084/jem.20210332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/27/2021] [Accepted: 06/29/2021] [Indexed: 01/29/2023] Open
Abstract
Studying latent Mycobacterium tuberculosis (Mtb) infection has been limited by the lack of a suitable mouse model. We discovered that transient depletion of biotin protein ligase (BPL) and thioredoxin reductase (TrxB2) results in latent infections during which Mtb cannot be detected but that relapse in a subset of mice. The immune requirements for Mtb control during latency, and the frequency of relapse, were strikingly different depending on how latency was established. TrxB2 depletion resulted in a latent infection that required adaptive immunity for control and reactivated with high frequency, whereas latent infection after BPL depletion was independent of adaptive immunity and rarely reactivated. We identified immune signatures of T cells indicative of relapse and demonstrated that BCG vaccination failed to protect mice from TB relapse. These reproducible genetic latency models allow investigation of the host immunological determinants that control the latent state and offer opportunities to evaluate therapeutic strategies in settings that mimic aspects of latency and TB relapse in humans.
Collapse
Affiliation(s)
- Hongwei Su
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - Kan Lin
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - Claire Healy
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - Yao Liu
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY
| |
Collapse
|
22
|
Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell 2021; 184:4579-4592.e24. [PMID: 34297925 PMCID: PMC8382161 DOI: 10.1016/j.cell.2021.06.033] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/13/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Antibacterial agents target the products of essential genes but rarely achieve complete target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic approaches fails to discern the most attractive bacterial targets: those whose incomplete inhibition results in major fitness costs. In contrast, gene "vulnerability" is a continuous, quantifiable trait that relates the magnitude of gene inhibition to the effect on bacterial fitness. We developed a CRISPR interference-based functional genomics method to systematically titrate gene expression in Mycobacterium tuberculosis (Mtb) and monitor fitness outcomes. We identified highly vulnerable genes in various processes, including novel targets unexplored for drug discovery. Equally important, we identified invulnerable essential genes, potentially explaining failed drug discovery efforts. Comparison of vulnerability between the reference and a hypervirulent Mtb isolate revealed incomplete conservation of vulnerability and that differential vulnerability can predict differential antibacterial susceptibility. Our results quantitatively redefine essential bacterial processes and identify high-value targets for drug development.
Collapse
Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sophie Lavalette
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joshua B Wallach
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
23
|
Aldridge BB, Barros-Aguirre D, Barry CE, Bates RH, Berthel SJ, Boshoff HI, Chibale K, Chu XJ, Cooper CB, Dartois V, Duncan K, Fotouhi N, Gusovsky F, Hipskind PA, Kempf DJ, Lelièvre J, Lenaerts AJ, McNamara CW, Mizrahi V, Nathan C, Olsen DB, Parish T, Petrassi HM, Pym A, Rhee KY, Robertson GT, Rock JM, Rubin EJ, Russell B, Russell DG, Sacchettini JC, Schnappinger D, Schrimpf M, Upton AM, Warner P, Wyatt PG, Yuan Y. The Tuberculosis Drug Accelerator at year 10: what have we learned? Nat Med 2021; 27:1333-1337. [PMID: 34226736 PMCID: PMC10478072 DOI: 10.1038/s41591-021-01442-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Tuberculosis Drug Accelerator, an experiment designed to facilitate collaboration in TB drug discovery by breaking down barriers among competing labs and institutions, has reached the 10-year landmark. We review the consortium’s achievements, advantages and limitations and advocate for application of similar models to other diseases.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Xin-Jie Chu
- Global Health Drug Discovery Institute, Beijing, China
| | | | - Véronique Dartois
- Hackensack Meridian Health Center for Discovery & Innovation, Nutley, NJ, USA
| | - Ken Duncan
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Nader Fotouhi
- Global Alliance for TB Drug Development, New York, NY, USA
| | | | | | | | | | | | - Case W McNamara
- Calibr, a division of the Scripps Research Institute, La Jolla, CA, USA
| | | | | | | | - Tanya Parish
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Kyu Y Rhee
- Weill Cornell Medicine, New York, NY, USA
| | | | | | - Eric J Rubin
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Betsy Russell
- Bill & Melinda Gates Medical Research Institute, Boston, MA, USA
| | | | | | | | | | | | - Peter Warner
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Ying Yuan
- Global Health Drug Discovery Institute, Beijing, China
| |
Collapse
|
24
|
Ray P, Huggett M, Turner PA, Taylor M, Cleghorn LAT, Early J, Kumar A, Bonnett SA, Flint L, Joerss D, Johnson J, Korkegian A, Mullen S, Moure AL, Davis SH, Murugesan D, Mathieson M, Caldwell N, Engelhart CA, Schnappinger D, Epemolu O, Zuccotto F, Riley J, Scullion P, Stojanovski L, Massoudi L, Robertson GT, Lenaerts AJ, Freiberg G, Kempf DJ, Masquelin T, Hipskind PA, Odingo J, Read KD, Green SR, Wyatt PG, Parish T. Spirocycle MmpL3 Inhibitors with Improved hERG and Cytotoxicity Profiles as Inhibitors of Mycobacterium tuberculosis Growth. ACS Omega 2021; 6:2284-2311. [PMID: 33521468 PMCID: PMC7841955 DOI: 10.1021/acsomega.0c05589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 05/10/2023]
Abstract
With the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, there is a pressing need for new oral drugs with novel mechanisms of action. A number of scaffolds with potent anti-tubercular in vitro activity have been identified from phenotypic screening that appear to target MmpL3. However, the scaffolds are typically lipophilic, which facilitates partitioning into hydrophobic membranes, and several contain basic amine groups. Highly lipophilic basic amines are typically cytotoxic against mammalian cell lines and have associated off-target risks, such as inhibition of human ether-à-go-go related gene (hERG) and IKr potassium current modulation. The spirocycle compound 3 was reported to target MmpL3 and displayed promising efficacy in a murine model of acute tuberculosis (TB) infection. However, this highly lipophilic monobasic amine was cytotoxic and inhibited the hERG ion channel. Herein, the related spirocycles (1-2) are described, which were identified following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis. The novel N-alkylated pyrazole portion offered improved physicochemical properties, and optimization led to identification of a zwitterion series, exemplified by lead 29, with decreased HepG2 cytotoxicity as well as limited hERG ion channel inhibition. Strains with mutations in MmpL3 were resistant to 29, and under replicating conditions, 29 demonstrated bactericidal activity against M. tuberculosis. Unfortunately, compound 29 had no efficacy in an acute model of TB infection; this was most likely due to the in vivo exposure remaining above the minimal inhibitory concentration for only a limited time.
Collapse
Affiliation(s)
- Peter
C. Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Penelope A. Turner
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laura A. T. Cleghorn
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Julie Early
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Anuradha Kumar
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Shilah A. Bonnett
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Lindsay Flint
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Douglas Joerss
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - James Johnson
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Steven Mullen
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Abraham L. Moure
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan H. Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lisa Massoudi
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne J. Lenaerts
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gail Freiberg
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dale J. Kempf
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Thierry Masquelin
- Discovery
Chemistry Research, Eli Lilly and Company, Lilly Corporate Centre, MC/87/02/203, G17, Indianapolis, Indiana 46285, United States
| | | | - Joshua Odingo
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| |
Collapse
|
25
|
Soares de Melo C, Singh V, Myrick A, Simelane SB, Taylor D, Brunschwig C, Lawrence N, Schnappinger D, Engelhart CA, Kumar A, Parish T, Su Q, Myers TG, Boshoff HIM, Barry CE, Sirgel FA, van Helden PD, Buchanan KI, Bayliss T, Green SR, Ray PC, Wyatt PG, Basarab GS, Eyermann CJ, Chibale K, Ghorpade SR. Antitubercular 2-Pyrazolylpyrimidinones: Structure-Activity Relationship and Mode-of-Action Studies. J Med Chem 2021; 64:719-740. [PMID: 33395287 PMCID: PMC7816196 DOI: 10.1021/acs.jmedchem.0c01727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 11/30/2022]
Abstract
Phenotypic screening of a Medicines for Malaria Venture compound library against Mycobacterium tuberculosis (Mtb) identified a cluster of pan-active 2-pyrazolylpyrimidinones. The biology triage of these actives using various tool strains of Mtb suggested a novel mechanism of action. The compounds were bactericidal against replicating Mtb and retained potency against clinical isolates of Mtb. Although selected MmpL3 mutant strains of Mtb showed resistance to these compounds, there was no shift in the minimum inhibitory concentration (MIC) against a mmpL3 hypomorph, suggesting mutations in MmpL3 as a possible resistance mechanism for the compounds but not necessarily as the target. RNA transcriptional profiling and the checkerboard board 2D-MIC assay in the presence of varying concentrations of ferrous salt indicated perturbation of the Fe-homeostasis by the compounds. Structure-activity relationship studies identified potent compounds with good physicochemical properties and in vitro microsomal metabolic stability with moderate selectivity over cytotoxicity against mammalian cell lines.
Collapse
Affiliation(s)
- Candice Soares de Melo
- Drug
Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch 7701, South Africa
| | - Alissa Myrick
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa
| | - Sandile B. Simelane
- Drug
Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Dale Taylor
- Drug
Discovery and Development Centre (H3D), Division of Clinical Pharmacology,
Department of Medicine, University of Cape
Town, Observatory 7925, South Africa
| | - Christel Brunschwig
- Drug
Discovery and Development Centre (H3D), Division of Clinical Pharmacology,
Department of Medicine, University of Cape
Town, Observatory 7925, South Africa
| | - Nina Lawrence
- Drug
Discovery and Development Centre (H3D), Division of Clinical Pharmacology,
Department of Medicine, University of Cape
Town, Observatory 7925, South Africa
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Anuradha Kumar
- Infectious
Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, Washington 98102, United States
| | - Tanya Parish
- Infectious
Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, Washington 98102, United States
| | - Qin Su
- Genomic
Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Timothy G. Myers
- Genomic
Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, 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 Infectious Diseases, National Institute of Allergy and Infectious Diseases,
National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Frederick A. Sirgel
- South
African Medical Research Council Centre for Tuberculosis Research/DST/NRF
Centre of Excellence for Biomedical Tuberculosis Research, Division
of Molecular Biology and Human Genetics, Faculty of Medicine and Health
Science, Stellenbosch University, Tygerberg 7505, South Africa
| | - Paul D. van Helden
- South
African Medical Research Council Centre for Tuberculosis Research/DST/NRF
Centre of Excellence for Biomedical Tuberculosis Research, Division
of Molecular Biology and Human Genetics, Faculty of Medicine and Health
Science, Stellenbosch University, Tygerberg 7505, South Africa
| | - Kirsteen I. Buchanan
- Drug
Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Tracy Bayliss
- Drug
Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Peter C. Ray
- Drug
Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Gregory S. Basarab
- Drug
Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Drug
Discovery and Development Centre (H3D), Division of Clinical Pharmacology,
Department of Medicine, University of Cape
Town, Observatory 7925, South Africa
| | - Charles J. Eyermann
- Drug
Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, Department of Chemistry and Institute of Infectious Disease
and Molecular Medicine, University of Cape
Town, Rondebosch 7701, South Africa
| | - Sandeep R. Ghorpade
- Drug
Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| |
Collapse
|
26
|
Lee BS, Hards K, Engelhart CA, Hasenoehrl EJ, Kalia NP, Mackenzie JS, Sviriaeva E, Chong SMS, Manimekalai MSS, Koh VH, Chan J, Xu J, Alonso S, Miller MJ, Steyn AJC, Grüber G, Schnappinger D, Berney M, Cook GM, Moraski GC, Pethe K. Dual inhibition of the terminal oxidases eradicates antibiotic-tolerant Mycobacterium tuberculosis. EMBO Mol Med 2021; 13:e13207. [PMID: 33283973 PMCID: PMC7799364 DOI: 10.15252/emmm.202013207] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/09/2022] Open
Abstract
The approval of bedaquiline has placed energy metabolism in the limelight as an attractive target space for tuberculosis antibiotic development. While bedaquiline inhibits the mycobacterial F1 F0 ATP synthase, small molecules targeting other components of the oxidative phosphorylation pathway have been identified. Of particular interest is Telacebec (Q203), a phase 2 drug candidate inhibitor of the cytochrome bcc:aa3 terminal oxidase. A functional redundancy between the cytochrome bcc:aa3 and the cytochrome bd oxidase protects M. tuberculosis from Q203-induced death, highlighting the attractiveness of the bd-type terminal oxidase for drug development. Here, we employed a facile whole-cell screen approach to identify the cytochrome bd inhibitor ND-011992. Although ND-011992 is ineffective on its own, it inhibits respiration and ATP homeostasis in combination with Q203. The drug combination was bactericidal against replicating and antibiotic-tolerant, non-replicating mycobacteria, and increased efficacy relative to that of a single drug in a mouse model. These findings suggest that a cytochrome bd oxidase inhibitor will add value to a drug combination targeting oxidative phosphorylation for tuberculosis treatment.
Collapse
Affiliation(s)
- Bei Shi Lee
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Kiel Hards
- Department of Microbiology and ImmunologySchool of Biomedical SciencesUniversity of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryUniversity of AucklandAucklandNew Zealand
| | - Curtis A Engelhart
- Department of Microbiology and ImmunologyWeill Cornell Medical CollegeNew YorkNYUSA
| | - Erik J Hasenoehrl
- Department of Microbiology and ImmunologyAlbert Einstein College of MedicineBronxNYUSA
| | - Nitin P Kalia
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Ramalingaswami FellowClinical Microbiology DivisionCSIR‐IIIMJammu and KashmirIndia
| | - Jared S Mackenzie
- Africa Health Research InstituteNelson R. Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Ekaterina Sviriaeva
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Shi Min Sherilyn Chong
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Nanyang Institute of Technology in Health and MedicineInterdisciplinary Graduate SchoolNanyang Technological UniversitySingaporeSingapore
| | | | - Vanessa H Koh
- Department of MicrobiologyYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Infectious Disease ProgrammeDepartment of Microbiology and ImmunologyNational University of SingaporeSingaporeSingapore
| | - John Chan
- Department of MedicineAlbert Einstein College of MedicineBronxNYUSA
| | - Jiayong Xu
- Department of MedicineAlbert Einstein College of MedicineBronxNYUSA
| | - Sylvie Alonso
- Department of MicrobiologyYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Infectious Disease ProgrammeDepartment of Microbiology and ImmunologyNational University of SingaporeSingaporeSingapore
| | - Marvin J Miller
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameINUSA
| | - Adrie J C Steyn
- Africa Health Research InstituteNelson R. Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
- Department of MicrobiologyUniversity of AlabamaBirminghamALUSA
| | - Gerhard Grüber
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Dirk Schnappinger
- Department of Microbiology and ImmunologyWeill Cornell Medical CollegeNew YorkNYUSA
| | - Michael Berney
- Department of Microbiology and ImmunologyAlbert Einstein College of MedicineBronxNYUSA
| | - Gregory M Cook
- Department of Microbiology and ImmunologySchool of Biomedical SciencesUniversity of OtagoDunedinNew Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryUniversity of AucklandAucklandNew Zealand
| | - Garrett C Moraski
- Department of Chemistry and BiochemistryMontana State UniversityBozemanMTUSA
| | - Kevin Pethe
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
| |
Collapse
|
27
|
Grover S, Engelhart CA, Pérez-Herrán E, Li W, Abrahams KA, Papavinasasundaram K, Bean JM, Sassetti CM, Mendoza-Losana A, Besra GS, Jackson M, Schnappinger D. Two-Way Regulation of MmpL3 Expression Identifies and Validates Inhibitors of MmpL3 Function in Mycobacterium tuberculosis. ACS Infect Dis 2021; 7:141-152. [PMID: 33319550 PMCID: PMC7802072 DOI: 10.1021/acsinfecdis.0c00675] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
MmpL3,
an essential mycolate transporter in the inner membrane
of Mycobacterium tuberculosis (Mtb), has been identified as a target of multiple, chemically diverse
antitubercular drugs. However, several of these molecules seem to
have secondary targets and inhibit bacterial growth by more than one
mechanism. Here, we describe a cell-based assay that utilizes two-way
regulation of MmpL3 expression to readily identify MmpL3-specific
inhibitors. We successfully used this assay to identify a novel guanidine-based
MmpL3 inhibitor from a library of 220 compounds that inhibit growth
of Mtb by largely unknown mechanisms. We furthermore
identified inhibitors of cytochrome bc1-aa3 oxidase as one class of off-target hits in whole-cell screens for
MmpL3 inhibitors and report a novel sulfanylacetamide as a potential
QcrB inhibitor.
Collapse
Affiliation(s)
- Shipra Grover
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Curtis A. Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Esther Pérez-Herrán
- TB Research Unit, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Katherine A. Abrahams
- Institute of Microbiology and Infection, School of Biological Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - James M. Bean
- Sloan Kettering Institute, New York, New York 10065, United States
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Alfonso Mendoza-Losana
- TB Research Unit, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biological Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| |
Collapse
|
28
|
Wang H, Xu M, Engelhart CA, Zhang X, Yan B, Pan M, Xu Y, Fan S, Liu R, Xu L, Hua L, Schnappinger D, Chen S. Rediscovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis. J Biol Chem 2021; 296:100257. [PMID: 33837735 PMCID: PMC7948948 DOI: 10.1016/j.jbc.2021.100257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains the deadliest pathogenic bacteria worldwide. The search for new antibiotics to treat drug-sensitive as well as drug-resistant tuberculosis has become a priority. The essential enzyme phenylalanyl-tRNA synthetase (PheRS) is an antibacterial drug target because of the large differences between bacterial and human PheRS counterparts. In a high-throughput screening of 2148 bioactive compounds, PF-3845, which is a known inhibitor of human fatty acid amide hydrolase, was identified inhibiting Mtb PheRS at Ki ∼ 0.73 ± 0.06 μM. The inhibition mechanism was studied with enzyme kinetics, protein structural modeling, and crystallography, in comparison to a PheRS inhibitor of the noted phenyl–thiazolylurea–sulfonamide class. The 2.3-Å crystal structure of Mtb PheRS in complex with PF-3845 revealed its novel binding mode, in which a trifluoromethyl–pyridinylphenyl group occupies the phenylalanine pocket, whereas a piperidine–piperazine urea group binds into the ATP pocket through an interaction network enforced by a sulfate ion. It represents the first non-nucleoside bisubstrate competitive inhibitor of bacterial PheRS. PF-3845 inhibits the in vitro growth of Mtb H37Rv at ∼24 μM, and the potency of PF-3845 increased against an engineered strain Mtb pheS–FDAS, suggesting on target activity in mycobacterial whole cells. PF-3845 does not inhibit human cytoplasmic or mitochondrial PheRS in biochemical assay, which can be explained from the crystal structures. Further medicinal chemistry efforts focused on the piperidine–piperazine urea moiety may result in the identification of a selective antibacterial lead compound.
Collapse
Affiliation(s)
- Heng Wang
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Min Xu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Xi Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Baohua Yan
- Center of Protein Science Facility, Tsinghua University, Beijing, China
| | - Miaomiao Pan
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Yuanyuan Xu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Shilong Fan
- Center of Protein Science Facility, Tsinghua University, Beijing, China
| | - Renhe Liu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Lan Xu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Lan Hua
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Shawn Chen
- Global Health Drug Discovery Institute, Haidian, Beijing, China.
| |
Collapse
|
29
|
Wang H, Xu M, Engelhart CA, Zhang X, Yan B, Pan M, Xu Y, Fan S, Liu R, Xu L, Hua L, Schnappinger D, Chen S. Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis. J Biol Chem 2021:jbc.RA120.016477. [PMID: 33397709 DOI: 10.1074/jbc.ra120.016477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Mycobacteria tuberculosis (Mtb) remains the deadliest pathogenic bacteria worldwide. The search for new antibiotics to treat drug-sensitive as well as drug-resistant tuberculosis has become a priority. The essential enzyme phenylalanyl-tRNA synthetase (PheRS) is an antibacterial drug target because of the large differences between bacterial and human PheRS counterparts. In a high-throughput screening of 2148 bioactive compounds, PF-3845, which is a known inhibitor of human fatty acid amide hydrolase (FAAH), was identified inhibiting Mtb PheRS at Ki ~0.73 ± 0.06 µM. The inhibition mechanism was studied with enzyme kinetics, protein structural modelling and crystallography, in comparison to a PheRS inhibitor of the noted phenyl-thiazolylurea-sulfonamide class. The 2.3-Å crystal structure of Mtb PheRS in complex with PF-3845 revealed its novel binding mode, in which a trifluoromethyl-pyridinylphenyl group occupies the Phe pocket while a piperidine-piperazine urea group binds into the ATP pocket through an interaction network enforced by a sulfate ion. It represents the first non-nucleoside bi-substrate competitive inhibitor of bacterial PheRS. PF-3845 inhibits the in vitro growth of Mtb H37Rv at ~24 µM, and the potency of PF-3845 increased against Mtb pheS-FDAS, suggesting on target activity in mycobacterial whole cells. PF-3845 does not inhibit human cytoplasmic or mitochondrial PheRS in biochemical assay, which can be explained from the crystal structures. Further medicinal chemistry efforts focused on the piperidine-piperazine urea moiety may result in the identification of a selective antibacterial lead compound.
Collapse
Affiliation(s)
- Heng Wang
- Global Health Drug Discovery Institute, China
| | - Min Xu
- Global Health Drug Discovery Institute, China
| | | | - Xi Zhang
- Global Health Drug Discovery Institute, China
| | | | | | - Yuanyuan Xu
- Global Health Drug Discovery Institute, China
| | | | - Renhe Liu
- Global Health Drug Discovery Institute, China
| | - Lan Xu
- Global Health Drug Discovery Institute, China
| | - Lan Hua
- Global Health Drug Discovery Institute, China
| | | | - Shawn Chen
- Global Health Drug Discovery Institute, China
| |
Collapse
|
30
|
Zaveri A, Wang R, Botella L, Sharma R, Zhu L, Wallach JB, Song N, Jansen RS, Rhee KY, Ehrt S, Schnappinger D. Depletion of the DarG antitoxin in Mycobacterium tuberculosis triggers the DNA-damage response and leads to cell death. Mol Microbiol 2020; 114:641-652. [PMID: 32634279 PMCID: PMC7689832 DOI: 10.1111/mmi.14571] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 01/01/2023]
Abstract
Of the ~80 putative toxin-antitoxin (TA) modules encoded by the bacterial pathogen Mycobacterium tuberculosis (Mtb), three contain antitoxins essential for bacterial viability. One of these, Rv0060 (DNA ADP-ribosyl glycohydrolase, DarGMtb ), functions along with its cognate toxin Rv0059 (DNA ADP-ribosyl transferase, DarTMtb ), to mediate reversible DNA ADP-ribosylation (Jankevicius et al., 2016). We demonstrate that DarTMtb -DarGMtb form a functional TA pair and essentiality of darGMtb is dependent on the presence of darTMtb , but simultaneous deletion of both darTMtb -darGMtb does not alter viability of Mtb in vitro or in mice. The antitoxin, DarGMtb , forms a cytosolic complex with DNA-repair proteins that assembles independently of either DarTMtb or interaction with DNA. Depletion of DarGMtb alone is bactericidal, a phenotype that is rescued by expression of an orthologous antitoxin, DarGTaq , from Thermus aquaticus. Partial depletion of DarGMtb triggers a DNA-damage response and sensitizes Mtb to drugs targeting DNA metabolism and respiration. Induction of the DNA-damage response is essential for Mtb to survive partial DarGMtb -depletion and leads to a hypermutable phenotype.
Collapse
Affiliation(s)
- Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Ruojun Wang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Laure Botella
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Ritu Sharma
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Linnan Zhu
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Joshua B Wallach
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Naomi Song
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Robert S Jansen
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kyu Y Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
31
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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
| |
Collapse
|
32
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
33
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
34
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
35
|
Freire DM, Gutierrez C, Garza-Garcia A, Grabowska AD, Sala AJ, Ariyachaokun K, Panikova T, Beckham KSH, Colom A, Pogenberg V, Cianci M, Tuukkanen A, Boudehen YM, Peixoto A, Botella L, Svergun DI, Schnappinger D, Schneider TR, Genevaux P, de Carvalho LPS, Wilmanns M, Parret AHA, Neyrolles O. An NAD + Phosphorylase Toxin Triggers Mycobacterium tuberculosis Cell Death. Mol Cell 2019; 73:1282-1291.e8. [PMID: 30792174 PMCID: PMC6436930 DOI: 10.1016/j.molcel.2019.01.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/13/2018] [Accepted: 01/18/2019] [Indexed: 01/13/2023]
Abstract
Toxin-antitoxin (TA) systems regulate fundamental cellular processes in bacteria and represent potential therapeutic targets. We report a new RES-Xre TA system in multiple human pathogens, including Mycobacterium tuberculosis. The toxin, MbcT, is bactericidal unless neutralized by its antitoxin MbcA. To investigate the mechanism, we solved the 1.8 Å-resolution crystal structure of the MbcTA complex. We found that MbcT resembles secreted NAD+-dependent bacterial exotoxins, such as diphtheria toxin. Indeed, MbcT catalyzes NAD+ degradation in vitro and in vivo. Unexpectedly, the reaction is stimulated by inorganic phosphate, and our data reveal that MbcT is a NAD+ phosphorylase. In the absence of MbcA, MbcT triggers rapid M. tuberculosis cell death, which reduces mycobacterial survival in macrophages and prolongs the survival of infected mice. Our study expands the molecular activities employed by bacterial TA modules and uncovers a new class of enzymes that could be exploited to treat tuberculosis and other infectious diseases.
Collapse
Affiliation(s)
- Diana Mendes Freire
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Claude Gutierrez
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Acely Garza-Garcia
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Anna D Grabowska
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Ambre J Sala
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31400 Toulouse, France
| | - Kanchiyaphat Ariyachaokun
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Terezie Panikova
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Katherine S H Beckham
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - André Colom
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Vivian Pogenberg
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Michele Cianci
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Anne Tuukkanen
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Yves-Marie Boudehen
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Antonio Peixoto
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France
| | - Laure Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31400 Toulouse, France
| | - Luiz Pedro Sorio de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany; University Hamburg Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Annabel H A Parret
- European Molecular Biology Laboratory, Hamburg Unit, Notkestraße 85, 22607 Hamburg, Germany.
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31400 Toulouse, France.
| |
Collapse
|
36
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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).
Collapse
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
| |
Collapse
|
37
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [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.
Collapse
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
| |
Collapse
|
38
|
Bockman MR, Engelhart CA, Dawadi S, Larson P, Tiwari D, Ferguson DM, Schnappinger D, Aldrich CC. Avoiding Antibiotic Inactivation in Mycobacterium tuberculosis by Rv3406 through Strategic Nucleoside Modification. ACS Infect Dis 2018; 4:1102-1113. [PMID: 29663798 DOI: 10.1021/acsinfecdis.8b00038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
5'-[ N-(d-biotinoyl)sulfamoyl]amino-5'-deoxyadenosine (Bio-AMS, 1) possesses selective activity against Mycobacterium tuberculosis ( Mtb) and arrests fatty acid and lipid biosynthesis through inhibition of the Mycobacterium tuberculosis biotin protein ligase ( MtBPL). Mtb develops spontaneous resistance to 1 with a frequency of at least 1 × 10-7 by overexpression of Rv3406, a type II sulfatase that enzymatically inactivates 1. In an effort to circumvent this resistance mechanism, we describe herein strategic modification of the nucleoside at the 5'-position to prevent enzymatic inactivation. The new analogues retained subnanomolar potency to MtBPL ( KD = 0.66-0.97 nM), and 5' R- C-methyl derivative 6 exhibited identical antimycobacterial activity toward: Mtb H37Rv, MtBPL overexpression, and an isogenic Rv3406 overexpression strain (minimum inhibitory concentration, MIC = 1.56 μM). Moreover, 6 was not metabolized by recombinant Rv3406 and resistant mutants to 6 could not be isolated (frequency of resistance <1.4 × 10-10) demonstrating it successfully overcame Rv3406-mediated resistance.
Collapse
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
| | - Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Peter Larson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10021, United States
| | - David M. Ferguson
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, 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
| |
Collapse
|
39
|
Dawadi S, Boshoff HIM, Park SW, Schnappinger D, Aldrich CC. Conformationally Constrained Cinnolinone Nucleoside Analogues as Siderophore Biosynthesis Inhibitors for Tuberculosis. ACS Med Chem Lett 2018; 9:386-391. [PMID: 29670706 DOI: 10.1021/acsmedchemlett.8b00090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/16/2018] [Indexed: 12/25/2022] Open
Abstract
5'-O-[N-(Salicyl)sulfamoyl]adenosine (Sal-AMS, 1) is a nucleoside antibiotic that inhibits incorporation of salicylate into siderophores required for bacterial iron acquisition and has potent activity against Mycobacterium tuberculosis (Mtb). Cinnolone analogues exemplified by 5 were designed to replace the acidic acyl-sulfamate functional group of 1 (pKa = 3) by a more stable sulfonamide linkage (pKa = 6.0) in an attempt to address potential metabolic liabilities and improve membrane permeability. We showed 5 potently inhibited the mycobacterial salicylate ligase MbtA (apparent Ki = 12 nM), blocked production of the salicylate-capped siderophores in whole-cell Mtb, and exhibited excellent antimycobacterial activity under iron-deficient conditions (minimum inhibitor concentration, MIC = 2.3 μM). To provide additional confirmation of the mechanism of action, we demonstrated the whole-cell activity of 5 could be fully antagonized by the addition of exogenous salicylate to the growth medium. Although the total polar surface area (tPSA) of 5 still exceeds the nominal threshold value (140 Å) typically required for oral bioavailability, we were pleasantly surprised to observe introduction of the less acidic and conformationally constrained cinnolone moiety conferred improved drug disposition properties as evidenced by the 7-fold increase in volume of distribution in Sprague-Dawley rats.
Collapse
Affiliation(s)
- Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, United States
| | - Sae Woong Park
- 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
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
40
|
Ngadjeua F, Braud E, Saidjalolov S, Iannazzo L, Schnappinger D, Ehrt S, Hugonnet JE, Mengin-Lecreulx D, Patin D, Ethève-Quelquejeu M, Fonvielle M, Arthur M. Critical Impact of Peptidoglycan Precursor Amidation on the Activity ofl,d-Transpeptidases fromEnterococcus faeciumandMycobacterium tuberculosis. Chemistry 2018; 24:5743-5747. [DOI: 10.1002/chem.201706082] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Flora Ngadjeua
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Saidbakhrom Saidjalolov
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Dirk Schnappinger
- Department of Microbiology and Immunology; 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
| | - Jean-Emmanuel Hugonnet
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie, Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris 75005 France
- CNRS UMR 8601; Paris 75006 France
| | - Matthieu Fonvielle
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
| | - Michel Arthur
- INSERM UMRS 1138; Sorbonne Universités UPMC Univ Paris 06
- Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot
- Centre de Recherche des Cordeliers; 75006 Paris France
| |
Collapse
|
41
|
Liu F, Dawadi S, Maize KM, Dai R, Park SW, Schnappinger D, Finzel BC, Aldrich CC. Structure-Based Optimization of Pyridoxal 5'-Phosphate-Dependent Transaminase Enzyme (BioA) Inhibitors that Target Biotin Biosynthesis in Mycobacterium tuberculosis. J Med Chem 2017; 60:5507-5520. [PMID: 28594172 DOI: 10.1021/acs.jmedchem.7b00189] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pyridoxal 5'-phosphate (PLP)-dependent transaminase BioA catalyzes the second step in the biosynthesis of biotin in Mycobacterium tuberculosis (Mtb) and is an essential enzyme for bacterial survival and persistence in vivo. A promising BioA inhibitor 6 containing an N-aryl, N'-benzoylpiperazine scaffold was previously identified by target-based whole-cell screening. Here, we explore the structure-activity relationships (SAR) through the design, synthesis, and biological evaluation of a systematic series of analogues of the original hit using a structure-based drug design strategy, which was enabled by cocrystallization of several analogues with BioA. To confirm target engagement and discern analogues with off-target activity, each compound was evaluated against wild-type (WT) Mtb in biotin-free and -containing medium as well as BioA under- and overexpressing Mtb strains. Conformationally constrained derivative 36 emerged as the most potent analogue with a KD of 76 nM against BioA and a minimum inhibitory concentration of 1.7 μM (0.6 μg/mL) against Mtb in biotin-free medium.
Collapse
Affiliation(s)
- Feng Liu
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Surendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Kimberly M Maize
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Ran Dai
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College , New York, New York 10065, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College , New York, New York 10065, United States
| | - Barry C Finzel
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| |
Collapse
|
42
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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.
Collapse
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
| |
Collapse
|
43
|
Evans JC, Trujillo C, Wang Z, Eoh H, Ehrt S, Schnappinger D, Boshoff HIM, Rhee KY, Barry CE, Mizrahi V. Validation of CoaBC as a Bactericidal Target in the Coenzyme A Pathway of Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:958-968. [PMID: 27676316 PMCID: PMC5153693 DOI: 10.1021/acsinfecdis.6b00150] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Mycobacterium tuberculosis relies on its own ability to biosynthesize coenzyme A to meet the
needs of the myriad enzymatic reactions that depend on this cofactor
for activity. As such, the essential pantothenate and coenzyme A biosynthesis
pathways have attracted attention as targets for tuberculosis drug
development. To identify the optimal step for coenzyme A pathway disruption
in M. tuberculosis, we constructed
and characterized a panel of conditional knockdown mutants in coenzyme
A pathway genes. Here, we report that silencing of coaBC was bactericidal in vitro, whereas silencing of panB, panC, or coaE was bacteriostatic
over the same time course. Silencing of coaBC was
likewise bactericidal in vivo, whether initiated at infection or during
either the acute or chronic stages of infection, confirming that CoaBC
is required for M. tuberculosis to grow and persist in mice and arguing against significant CoaBC
bypass via transport and assimilation of host-derived pantetheine
in this animal model. These results provide convincing genetic validation
of CoaBC as a new bactericidal drug target.
Collapse
Affiliation(s)
- Joanna C. Evans
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Carolina Trujillo
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Zhe Wang
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Hyungjin Eoh
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Sabine Ehrt
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kyu Y. Rhee
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Clifton E. Barry
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - 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 and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| |
Collapse
|
44
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
Collapse
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)
| |
Collapse
|
45
|
Chauhan R, Ravi J, Datta P, Chen T, Schnappinger D, Bassler KE, Balázsi G, Gennaro ML. Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis. Nat Commun 2016; 7:11062. [PMID: 27029515 PMCID: PMC4821874 DOI: 10.1038/ncomms11062] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 02/15/2016] [Indexed: 01/26/2023] Open
Abstract
Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen Mycobacterium tuberculosis by an integrated approach. The approach combines identification of direct regulatory interactions between M. tuberculosis sigma factors in an E. coli model system, validation of selected links in M. tuberculosis, and extensive literature review. The resulting network comprises 41 direct interactions among all 13 sigma factors. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors. These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Moreover, the identification of overrepresented network motifs, such as autoregulation and coregulation of sigma and anti-sigma factor pairs, provides structural information that is relevant for studies of network dynamics. Sigma factors are regulatory proteins that reprogram the bacterial RNA polymerase in response to stress conditions to transcribe certain genes, including those for other sigma factors. Here, Chauhan et al. describe the complete sigma factor regulatory network of the pathogen Mycobacterium tuberculosis.
Collapse
Affiliation(s)
- Rinki Chauhan
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Janani Ravi
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Pratik Datta
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| | - Tianlong Chen
- Department of Physics, University of Houston, Houston, Texas 77204-5005, USA.,Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5002, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021, USA
| | - Kevin E Bassler
- Department of Physics, University of Houston, Houston, Texas 77204-5005, USA.,Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5002, USA.,Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Strasse 38, D-01187 Dresden, Germany
| | - Gábor Balázsi
- Laufer Center for Physical &Quantitative Biology and Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, USA
| |
Collapse
|
46
|
Abstract
Mycobacterium tuberculosis (Mtb) has evolved within the human immune system as both host and reservoir. The study of genes required for its growth and persistence in vivo thus offers linked insights into its pathogenicity and host immunity. Studies of Mtb mutants have implicated metabolic adaptation (consisting of carbon, nitrogen, vitamin, and cofactor metabolism), intrabacterial pH homeostasis, and defense against reactive oxygen and reactive nitrogen species, as key determinants of its pathogenicity. However, the mechanisms of host immunity are complex and often combinatorial. Growing evidence has thus begun to reveal that the determinants of Mtb's pathogenicity may serve a broader and more complex array of functions than the isolated experimental settings in which they were initially found. Here, we review select examples, which exemplify this complexity, highlighting the distinct phases of Mtb's life cycle and the diverse microenvironments encountered therein.
Collapse
Affiliation(s)
- Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | | | | |
Collapse
|
47
|
Bockman MR, Kalinda AS, Petrelli R, De la Mora-Rey T, Tiwari D, Liu F, Dawadi S, Nandakumar M, Rhee KY, Schnappinger D, Finzel BC, Aldrich CC. Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors. J Med Chem 2015; 58:7349-7369. [PMID: 26299766 PMCID: PMC4667793 DOI: 10.1021/acs.jmedchem.5b00719] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Mycobacterium tuberculosis (Mtb), responsible for both latent and symptomatic tuberculosis (TB), remains the second leading cause of mortality among infectious diseases worldwide. Mycobacterial biotin protein ligase (MtBPL) is an essential enzyme in Mtb and regulates lipid metabolism through the post-translational biotinylation of acyl coenzyme A carboxylases. We report the synthesis and evaluation of a systematic series of potent nucleoside-based inhibitors of MtBPL that contain modifications to the ribofuranosyl ring of the nucleoside. All compounds were characterized by isothermal titration calorimetry (ITC) and shown to bind potently with K(D)s ≤ 2 nM. Additionally, we obtained high-resolution cocrystal structures for a majority of the compounds. Despite fairly uniform biochemical potency, the whole-cell Mtb activity varied greatly with minimum inhibitory concentrations (MIC) ranging from 0.78 to >100 μM. Cellular accumulation studies showed a nearly 10-fold enhancement in accumulation of a C-2'-α analogue over the corresponding C-2'-β analogue, consistent with their differential whole-cell activity.
Collapse
Affiliation(s)
- Matthew R. Bockman
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Alvin S. Kalinda
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Riccardo Petrelli
- Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA
| | - Teresa De la Mora-Rey
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Divya Tiwari
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Feng Liu
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Surrendra Dawadi
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Madhumitha Nandakumar
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Barry C. Finzel
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA,Center for Drug Design, Academic Health Center, University of Minnesota, MN 55455 USA,Corresponding Author Footnote: To whom correspondence should be addressed. Phone 612-625-7956. Fax 612-626-3114.
| |
Collapse
|
48
|
Dai R, Geders TW, Liu F, Park SW, Schnappinger D, Aldrich CC, Finzel BC. Fragment-based exploration of binding site flexibility in Mycobacterium tuberculosis BioA. J Med Chem 2015; 58:5208-17. [PMID: 26068403 DOI: 10.1021/acs.jmedchem.5b00092] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The PLP-dependent transaminase (BioA) of Mycobacterium tuberculosis and other pathogens that catalyzes the second step of biotin biosynthesis is a now well-validated target for antibacterial development. Fragment screening by differential scanning fluorimetry has been performed to discover new chemical scaffolds and promote optimization of existing inhibitors. Calorimetry confirms binding of six molecules with high ligand efficiency. Thermodynamic data identifies which molecules bind with the enthalpy driven stabilization preferred in compounds that represent attractive starting points for future optimization. Crystallographic characterization of complexes with these molecules reveals the dynamic nature of the BioA active site. Different side chain conformational states are stabilized in response to binding by different molecules. A detailed analysis of conformational diversity in available BioA structures is presented, resulting in the identification of two states that might be targeted with molecular scaffolds incorporating well-defined conformational attributes. This new structural data can be used as part of a scaffold hopping strategy to further optimize existing inhibitors or create new small molecules with improved therapeutic potential.
Collapse
Affiliation(s)
- Ran Dai
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Todd W Geders
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Feng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Sae Woong Park
- ‡Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- ‡Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Courtney C Aldrich
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Barry C Finzel
- †Department of Medicinal Chemistry, University of Minnesota, 8-101 Weaver-Densford, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
49
|
Abstract
Very few chemically novel agents have been approved for antibacterial chemotherapies during the last 50 yr. Yet new antibacterial drugs are needed to reduce the impact on global health of an increasing number of drug-resistant infections, including highly drug-resistant forms of tuberculosis. This review discusses how genetic approaches can be used to study the mechanism of action of whole-cell screening hits and facilitate target-driven strategies for antimicrobial drug development.
Collapse
Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
| |
Collapse
|
50
|
Goodsmith N, Guo XV, Vandal OH, Vaubourgeix J, Wang R, Botella H, Song S, Bhatt K, Liba A, Salgame P, Schnappinger D, Ehrt S. Disruption of an M. tuberculosis membrane protein causes a magnesium-dependent cell division defect and failure to persist in mice. PLoS Pathog 2015; 11:e1004645. [PMID: 25658098 PMCID: PMC4450064 DOI: 10.1371/journal.ppat.1004645] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/28/2014] [Indexed: 01/17/2023] Open
Abstract
The identification of Mycobacterium tuberculosis genes necessary for persistence in vivo provides insight into bacterial biology as well as host defense strategies. We show that disruption of M. tuberculosis membrane protein PerM (Rv0955) resulted in an IFN-γ-dependent persistence defect in chronic mouse infection despite the mutant's near normal growth during acute infection. The perM mutant required increased magnesium for replication and survival; incubation in low magnesium media resulted in cell elongation and lysis. Transcriptome analysis of the perM mutant grown in reduced magnesium revealed upregulation of cell division and cell wall biosynthesis genes, and live cell imaging showed PerM accumulation at the division septa in M. smegmatis. The mutant was acutely sensitive to β-lactam antibiotics, including specific inhibitors of cell division-associated peptidoglycan transpeptidase FtsI. Together, these data implicate PerM as a novel player in mycobacterial cell division and pathogenesis, and are consistent with the hypothesis that immune activation deprives M. tuberculosis of magnesium.
Collapse
Affiliation(s)
- Nichole Goodsmith
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Xinzheng V. Guo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Omar H. Vandal
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Julien Vaubourgeix
- 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
| | - Hélène Botella
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Shuang Song
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Kamlesh Bhatt
- Department of Medicine, Center for Emerging Pathogens, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Amir Liba
- Agilent Technologies, Wilmington, Delaware, United States of America
| | - Padmini Salgame
- Department of Medicine, Center for Emerging Pathogens, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
| |
Collapse
|