1
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Yadav V, Boshoff HI, Trifonov L, Roma JSO, Ioerger TR, Barry CE, Oh S. Synthesis and Structure-Activity Relationships of a New Class of Oxadiazoles Targeting DprE1 as Antitubercular Agents. ACS Med Chem Lett 2023; 14:1275-1283. [PMID: 37736177 PMCID: PMC10510505 DOI: 10.1021/acsmedchemlett.3c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/09/2023] [Indexed: 09/23/2023] Open
Abstract
The continuing prevalence of drug-resistant tuberculosis threatens global TB control programs, highlighting the need to discover new drug candidates to feed the drug development pipeline. In this study, we describe a high-throughput screening hit (4-benzylpiperidin-1-yl)(1-(5-phenyl-1,3,4-oxadiazol-2-yl)piperidin-4-yl)methanone (P1) as a potent antitubercular agent. Structure-activity guided synthesis led to the discovery of several analogs with high in vitro potency. P1 was found to have promising potency against many drug-resistant strains, as well as drug-susceptible clinical isolates. It also showed cidality against Mtb growing in host macrophages. Whole genome sequencing of genomic DNA from resistant mutants raised to P1 revealed mutations in decaprenylphosphoryl-β-d-ribose 2'-oxidase (DprE1). This novel oxadiazole scaffold expands the set of chemical tools for targeting a well-validated pathway to treat tuberculosis.
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Affiliation(s)
- Veena
D. Yadav
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
(NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
| | - Helena I. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
(NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
| | - Lena Trifonov
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
(NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
| | - Jose Santinni O. Roma
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
(NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
| | - Thomas R. Ioerger
- Department
of Computer Science and Engineering, Texas
A&M University, College
Station, Texas 77843, United States
| | - Clifton E. Barry
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
(NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
| | - Sangmi Oh
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
(NIAID), National Institutes of Health (NIH), Bethesda, Maryland 20892, United States
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2
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Singh V, Grzegorzewicz AE, Fienberg S, Müller R, Khonde LP, Sanz O, Alfonso S, Urones B, Drewes G, Bantscheff M, Ghidelli-Disse S, Ioerger TR, Angala B, Liu J, Lee RE, Sacchettini JC, Krieger IV, Jackson M, Chibale K, Ghorpade SR. 1,3-Diarylpyrazolyl-acylsulfonamides Target HadAB/BC Complex in Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:2315-2326. [PMID: 36325756 PMCID: PMC9673142 DOI: 10.1021/acsinfecdis.2c00392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Indexed: 11/05/2022]
Abstract
Alternative mode-of-inhibition of clinically validated targets is an effective strategy for circumventing existing clinical drug resistance. Herein, we report 1,3-diarylpyrazolyl-acylsulfonamides as potent inhibitors of HadAB/BC, a 3-hydroxyl-ACP dehydratase complex required to iteratively elongate the meromycolate chain of mycolic acids in Mycobacterium tuberculosis (Mtb). Mutations in compound 1-resistant Mtb mutants mapped to HadC (Rv0637; K157R), while chemoproteomics confirmed the compound's binding to HadA (Rv0635), HadB (Rv0636), and HadC. The compounds effectively inhibited the HadAB and HadBC enzyme activities and affected mycolic acid biosynthesis in Mtb, in a concentration-dependent manner. Unlike known 3-hydroxyl-ACP dehydratase complex inhibitors of clinical significance, isoxyl and thioacetazone, 1,3-diarylpyrazolyl-acylsulfonamides did not require activation by EthA and thus are not liable to EthA-mediated resistance. Further, the crystal structure of a key compound in a complex with Mtb HadAB revealed unique binding interactions within the active site of HadAB, providing a useful tool for further structure-based optimization of the series.
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Affiliation(s)
- Vinayak Singh
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, 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, Rondebosch7701, South Africa
| | - Anna E. Grzegorzewicz
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Stephen Fienberg
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Rudolf Müller
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Lutete Peguy Khonde
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
| | - Olalla Sanz
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Salvatore Alfonso
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Beatriz Urones
- Global
Health Pharma Research Unit, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid28760, Spain
| | - Gerard Drewes
- Cellzome
GmbH · A GSK Company, Meyerhofstrasse 1, Heidelberg69117, Germany
| | - Marcus Bantscheff
- Cellzome
GmbH · A GSK Company, Meyerhofstrasse 1, Heidelberg69117, Germany
| | | | - Thomas R. Ioerger
- Department
of Computer Science and Engineering, Texas
A&M University, College
Station, Texas77843, United States
| | - Bhanupriya Angala
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Jiuyu Liu
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee38105, United States
| | - Richard E. Lee
- Department
of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee38105, United States
| | - James C. Sacchettini
- Texas A&M
University, Department of Biochemistry and
Biophysics, ILSB 2138,
301 Old Main Dr, College Station, Texas77843-3474, United States
| | - Inna V. Krieger
- Texas A&M
University, Department of Biochemistry and
Biophysics, ILSB 2138,
301 Old Main Dr, College Station, Texas77843-3474, United States
| | - Mary Jackson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology and
Pathology, Colorado State University, Fort Collins, Colorado80523-1682, United States
| | - Kelly Chibale
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, 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, Rondebosch7701, South Africa
| | - Sandeep R. Ghorpade
- Drug
Discovery and Development Centre (H3D), University of Cape Town, Rondebosch7701, South Africa
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3
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Dasmahapatra U, Chanda K. Synthetic approaches to potent heterocyclic inhibitors of tuberculosis: A decade review. Front Pharmacol 2022; 13:1021216. [DOI: 10.3389/fphar.2022.1021216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant global health concern with about 1.5 million deaths annually. Despite efforts to develop more efficient vaccines, reliable diagnostics, and chemotherapeutics, tuberculosis has become a concern to world health due to HIV, the rapid growth of bacteria that are resistant to treatment, and the recently introduced COVID-19 pandemic. As is well known, advances in synthetic organic chemistry have historically enabled the production of important life-saving medications that have had a tremendous impact on patients’ lives and health all over the world. Small-molecule research as a novel chemical entity for a specific disease target offers in-depth knowledge and potential therapeutic targets. In this viewpoint, we concentrated on the synthesis of a number of heterocycles reported in the previous decade and the screening of their inhibitory action against diverse strains of Mycobacterium tuberculosis. These findings offer specific details on the structure-based activity of several heterocyclic scaffolds backed by their in vitro tests as a promising class of antitubercular medicines, which will be further useful to build effective treatments to prevent this terrible illness.
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4
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Roubert C, Fontaine E, Upton AM. “Upcycling” known molecules and targets for drug-resistant TB. Front Cell Infect Microbiol 2022; 12:1029044. [PMID: 36275029 PMCID: PMC9582839 DOI: 10.3389/fcimb.2022.1029044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Despite reinvigorated efforts in Tuberculosis (TB) drug discovery over the past 20 years, relatively few new drugs and candidates have emerged with clear utility against drug resistant TB. Over the same period, significant technological advances and learnings around target value have taken place. This has offered opportunities to re-assess the potential for optimization of previously discovered chemical matter against Mycobacterium tuberculosis (M.tb) and for reconsideration of clinically validated targets encumbered by drug resistance. A re-assessment of discarded compounds and programs from the “golden age of antibiotics” has yielded new scaffolds and targets against TB and uncovered classes, for example beta-lactams, with previously unappreciated utility for TB. Leveraging validated classes and targets has also met with success: booster technologies and efforts to thwart efflux have improved the potential of ethionamide and spectinomycin classes. Multiple programs to rescue high value targets while avoiding cross-resistance are making progress. These attempts to make the most of known classes, drugs and targets complement efforts to discover new chemical matter against novel targets, enhancing the chances of success of discovering effective novel regimens against drug-resistant TB.
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5
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Chengalroyen MD, Mason MK, Borsellini A, Tassoni R, Abrahams GL, Lynch S, Ahn YM, Ambler J, Young K, Crowley BM, Olsen DB, Warner DF, Barry III CE, Boshoff HIM, Lamers MH, Mizrahi V. DNA-Dependent Binding of Nargenicin to DnaE1 Inhibits Replication in Mycobacterium tuberculosis. ACS Infect Dis 2022; 8:612-625. [PMID: 35143160 PMCID: PMC8922275 DOI: 10.1021/acsinfecdis.1c00643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Natural products
provide a rich source of potential antimicrobials
for treating infectious diseases for which drug resistance has emerged.
Foremost among these diseases is tuberculosis. Assessment of the antimycobacterial
activity of nargenicin, a natural product that targets the replicative
DNA polymerase of Staphylococcus aureus, revealed that it is a bactericidal genotoxin that induces a DNA
damage response in Mycobacterium tuberculosis (Mtb) and inhibits growth by blocking the replicative
DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding
of nargenicin to Mtb DnaE1 requires the DNA substrate
such that nargenicin is wedged between the terminal base pair and
the polymerase and occupies the position of both the incoming nucleotide
and templating base. Comparative analysis across three bacterial species
suggests that the activity of nargenicin is partly attributable to
the DNA binding affinity of the replicative polymerase. This work
has laid the foundation for target-led drug discovery efforts focused
on Mtb DnaE1.
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Affiliation(s)
- Melissa D. Chengalroyen
- SAMRC/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
| | - Mandy K. Mason
- SAMRC/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
| | - Alessandro Borsellini
- Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Raffaella Tassoni
- Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Garth L. Abrahams
- SAMRC/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 Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Sasha Lynch
- SAMRC/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
| | - Yong-Mo Ahn
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Jon Ambler
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Katherine Young
- Infectious Disease, Merck & Co. Inc., West Point, Pennsylvania 19446, United States
| | - Brendan M. Crowley
- Discovery Chemistry, Merck & Co. Inc., West Point, Pennsylvania 19446, United States
| | - David B. Olsen
- Infectious Disease, Merck & Co. Inc., West Point, Pennsylvania 19446, United States
| | - Digby F. Warner
- SAMRC/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
| | - Clifton E. Barry III
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Meindert H. Lamers
- Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Valerie Mizrahi
- SAMRC/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
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6
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Spiropyrimidinetriones: a Class of DNA Gyrase Inhibitors with Activity against Mycobacterium tuberculosis and without Cross-Resistance to Fluoroquinolones. Antimicrob Agents Chemother 2022; 66:e0219221. [PMID: 35266826 PMCID: PMC9017349 DOI: 10.1128/aac.02192-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Described here is a series of spiropyrimidinetrione (SPT) compounds with activity against Mycobacterium tuberculosis through inhibition of DNA gyrase. The SPT class operates via a novel mode of inhibition, which involves Mg2+-independent stabilization of the DNA cleavage complex with DNA gyrase and is thereby not cross-resistant with other DNA gyrase-inhibiting antibacterials, including fluoroquinolones. Compound 22 from the series was profiled broadly and showed in vitro cidality as well as intracellular activity against M. tuberculosis in macrophages. Evidence for the DNA gyrase mode of action was supported by inhibition of the target in a DNA supercoiling assay and elicitation of an SOS response seen in a recA reporter strain of M. tuberculosis. Pharmacokinetic properties of 22 supported evaluation of efficacy in an acute model of M. tuberculosis infection, where modest reduction in CFU numbers was seen. This work offers promise for deriving a novel drug class of tuberculosis agent without preexisting clinical resistance.
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7
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Khonde LP, Müller R, Boyle GA, Reddy V, Nchinda AT, Eyermann CJ, Fienberg S, Singh V, Myrick A, Abay E, Njoroge M, Lawrence N, Su Q, Myers TG, Boshoff HIM, Barry CE, Sirgel FA, van Helden PD, Massoudi LM, Robertson GT, Lenaerts AJ, Basarab GS, Ghorpade SR, Chibale K. 1,3-Diarylpyrazolyl-acylsulfonamides as Potent Anti-tuberculosis Agents Targeting Cell Wall Biosynthesis in Mycobacterium tuberculosis. J Med Chem 2021; 64:12790-12807. [PMID: 34414766 PMCID: PMC10500703 DOI: 10.1021/acs.jmedchem.1c00837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenotypic whole cell high-throughput screening of a ∼150,000 diverse set of compounds against Mycobacterium tuberculosis (Mtb) in cholesterol-containing media identified 1,3-diarylpyrazolyl-acylsulfonamide 1 as a moderately active hit. Structure-activity relationship (SAR) studies demonstrated a clear scope to improve whole cell potency to MIC values of <0.5 μM, and a plausible pharmacophore model was developed to describe the chemical space of active compounds. Compounds are bactericidal in vitro against replicating Mtb and retained activity against multidrug-resistant clinical isolates. Initial biology triage assays indicated cell wall biosynthesis as a plausible mode-of-action for the series. However, no cross-resistance with known cell wall targets such as MmpL3, DprE1, InhA, and EthA was detected, suggesting a potentially novel mode-of-action or inhibition. The in vitro and in vivo drug metabolism and pharmacokinetics profiles of several active compounds from the series were established leading to the identification of a compound for in vivo efficacy proof-of-concept studies.
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Affiliation(s)
- Lutete Peguy Khonde
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Rudolf Müller
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Grant A. Boyle
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Virsinha Reddy
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Aloysius T. Nchinda
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Charles J. Eyermann
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Stephen Fienberg
- 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), Institute of Infectious Disease and Molecular Medicine, 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), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Efrem Abay
- Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, 7925, South Africa
| | - Mathew Njoroge
- 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
| | - 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, Cape Town, 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, Cape Town, 7505, South Africa
| | - Lisa M. Massoudi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Gregory T. Robertson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Anne J. Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - 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
| | - Sandeep R. Ghorpade
- 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
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8
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In Vitro Profiling of Antitubercular Compounds by Rapid, Efficient, and Nondestructive Assays Using Autoluminescent Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:e0028221. [PMID: 34097493 PMCID: PMC8284454 DOI: 10.1128/aac.00282-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anti-infective drug discovery is greatly facilitated by the availability of in vitro assays that are more proficient at predicting the preclinical success of screening hits. Tuberculosis (TB) drug discovery is hindered by the relatively slow growth rate of Mycobacterium tuberculosis and the use of whole-cell-based in vitro assays that are inherently time-consuming, and for these reasons, rapid, noninvasive bioluminescence-based assays have been widely used in anti-TB drug discovery and development. In this study, in vitro assays that employ autoluminescent M. tuberculosis were optimized to determine MIC, minimum bactericidal concentration (MBC), time-kill curves, activity against macrophage internalized M. tuberculosis (90% effective concentration [EC90]), and postantibiotic effect (PAE) to provide rapid and dynamic biological information. Standardization of the luminescence-based MIC, MBC, time-kill, EC90, and PAE assays was accomplished by comparing results of established TB drugs and two ClpC1-targeting TB leads, ecumicin and rufomycin, to those obtained from conventional assays and/or to previous studies. Cumulatively, the use of the various streamlined luminescence-based in vitro assays has reduced the time for comprehensive in vitro profiling (MIC, MBC, time-kill, EC90, and PAE) by 2 months. The luminescence-based in vitro MBC and EC90 assays yield time and concentration-dependent kill information that can be used for pharmacokinetic-pharmacodynamic (PK-PD) modeling. The MBC and EC90 time-kill graphs revealed a significantly more rapid bactericidal activity for ecumicin than rufomycin. The PAEs of both ecumicin and rufomycin were comparable to that of the first-line TB drug rifampin. The optimization of several nondestructive, luminescence-based TB assays facilitates the in vitro profiling of TB drug leads in an efficient manner.
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9
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Abstract
New, more-effective drugs for the treatment of lung disease caused by nontuberculous mycobacteria (NTM) are needed. Among NTM opportunistic pathogens, Mycobacterium abscessus is the most difficult to cure and intrinsically multidrug resistant. In a whole-cell screen of a compound collection active against Mycobacterium tuberculosis, we previously identified the piperidine-4-carboxamide (P4C) MMV688844 (844) as a hit against M. abscessus. Here, we identified a more potent analog of 844 and showed that both the parent and improved analog retain activity against strains representing all three subspecies of the M. abscessus complex. Furthermore, P4Cs showed bactericidal and antibiofilm activity. Spontaneous resistance against the P4Cs emerged at a frequency of 10−8/CFU and mapped to gyrA and gyrB encoding the subunits of DNA gyrase. Biochemical studies with recombinant M. abscessus DNA gyrase showed that P4Cs inhibit the wild-type enzyme but not the P4C-resistant mutant. P4C-resistant strains showed limited cross-resistance to the fluoroquinolone moxifloxacin, which is in clinical use for the treatment of macrolide-resistant M. abscessus disease, and no cross-resistance to the benzimidazole SPR719, a novel DNA gyrase inhibitor in clinical development for the treatment of mycobacterial diseases. Analyses of P4Cs in recA promoter-based DNA damage reporter strains showed induction of recA promoter activity in the wild type but not in the P4C-resistant mutant background. This indicates that P4Cs, similar to fluoroquinolones, cause DNA gyrase-mediated DNA damage. Together, our results show that P4Cs present a novel class of mycobacterial DNA gyrase inhibitors with attractive antimicrobial activities against the M. abscessus complex.
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10
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Erasmus C, Aucamp J, Smit FJ, Seldon R, Jordaan A, Warner DF, N'Da DD. Synthesis and comparison of in vitro dual anti-infective activities of novel naphthoquinone hybrids and atovaquone. Bioorg Chem 2021; 114:105118. [PMID: 34216896 DOI: 10.1016/j.bioorg.2021.105118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 05/11/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022]
Abstract
A principal factor that contributes towards the failure to eradicate leishmaniasis and tuberculosis infections is the reduced efficacy of existing chemotherapies, owing to a continuous increase in multidrug-resistant strains of the causative pathogens. This accentuates the dire need to develop new and effective drugs against both plights. A series of naphthoquinone-triazole hybrids was synthesized and evaluated in vitro against Leishmania (L.) and Mycobacterium tuberculosis (Mtb) strains. Their cytotoxicities were also evaluated, using the human embryonic kidney cell line (HEK-293). The hybrids were found to be non-toxic towards human cells and had demonstrated micromolar cellular antileishmanial and antimycobacterial potencies. Hybrid 13, i.e. 2-{[1-(4-methylbenzyl)-1H-1,2,3-triazol-4-yl]methoxy}naphthalene-1,4-dione was the most active of all. It was found with MIC90 0.5 µM potency against Mtb in a protein free medium, and with half-maxima inhibitory concentrations (IC50) of 0.81 µM and 1.48 µM against the infective promastigote parasites of L. donavani and L. major, respectively, with good selectivity towards these pathogens (SI 22 - 65). Comparatively, the clinical naphthoquinone, atovaquone, although less cytotoxic, was found to be two-fold less antimycobacterial potent, and six- to twelve-fold less active against leishmania. Hybrid 13 may therefore stand as a potential anti-infective hit for further development in the search for new antitubercular and antileishmanial drugs. Elucidation of its exact mechanism of action and molecular targets will constitute future endeavour.
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Affiliation(s)
- Chané Erasmus
- Pharmaceutical Chemistry, School of Pharmacy, North-West University, Potchefstroom 2520, South Africa
| | - Janine Aucamp
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Frans J Smit
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Ronnett Seldon
- SAMRC Drug Discovery and Development Research Unit, University of Cape Town, Cape Town 7700, South Africa
| | - Audrey Jordaan
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925, South Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925, South Africa; Wellcome Centre for Clinical Infectious Diseases Research in Africa, University of Cape Town, Cape Town 7925, South Africa
| | - David D N'Da
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa.
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11
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Antimycobacterial Activity, Synergism, and Mechanism of Action Evaluation of Novel Polycyclic Amines against Mycobacterium tuberculosis. Adv Pharmacol Pharm Sci 2021; 2021:5583342. [PMID: 34240057 PMCID: PMC8238621 DOI: 10.1155/2021/5583342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/24/2021] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis has developed extensive resistance to numerous antimycobacterial agents used in the treatment of tuberculosis. Insufficient intracellular accumulation of active moieties allows for selective survival of mycobacteria with drug resistance mutations and accordingly promotes the development of microbial drug resistance. Discovery of compounds with new mechanisms of action and physicochemical properties that promote intracellular accumulation, or compounds that act synergistically with other antimycobacterial drugs, has the potential to reduce and prevent further drug resistance. To this end, antimycobacterial activity, mechanism of action, and synergism in combination therapy were investigated for a series of polycyclic amine derivatives. Compound selection was based on the presence of moieties with possible antimycobacterial activity, the inclusion of bulky lipophilic carriers to promote intracellular accumulation, and previously demonstrated bioactivity that potentially support inhibition of efflux pump activity. The most potent antimycobacterial demonstrated a minimum inhibitory concentration (MIC99) of 9.6 μM against Mycobacterium tuberculosis H37Rv. Genotoxicity and inhibition of the cytochrome bc1 respiratory complex were excluded as mechanisms of action for all compounds. Inhibition of cell wall synthesis was identified as a likely mechanism of action for the two most active compounds (14 and 15). Compounds 5 and 6 demonstrated synergistic activity with the known Rv1258c efflux pump substrate, spectinomycin, pointing to possible efflux pump inhibition. For this series, the nature of the side chain, rather than the type of polycyclic carrier, seems to play a determining role in the antimycobacterial activity and cytotoxicity of the compounds. Contrariwise, the nature of the polycyclic carrier, particularly the azapentacycloundecane cage, appears to promote synergistic activity. Results point to the possibility of combining an azapentacycloundecane carrier with a side chain that promotes antimycobacterial activity to develop dual acting molecules for the treatment of Mycobacterium tuberculosis.
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12
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Yuan T, Werman JM, Sampson NS. The pursuit of mechanism of action: uncovering drug complexity in TB drug discovery. RSC Chem Biol 2021; 2:423-440. [PMID: 33928253 PMCID: PMC8081351 DOI: 10.1039/d0cb00226g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
Whole cell-based phenotypic screens have become the primary mode of hit generation in tuberculosis (TB) drug discovery during the last two decades. Different drug screening models have been developed to mirror the complexity of TB disease in the laboratory. As these culture conditions are becoming more and more sophisticated, unraveling the drug target and the identification of the mechanism of action (MOA) of compounds of interest have additionally become more challenging. A good understanding of MOA is essential for the successful delivery of drug candidates for TB treatment due to the high level of complexity in the interactions between Mycobacterium tuberculosis (Mtb) and the TB drug used to treat the disease. There is no single "standard" protocol to follow and no single approach that is sufficient to fully investigate how a drug restrains Mtb. However, with the recent advancements in -omics technologies, there are multiple strategies that have been developed generally in the field of drug discovery that have been adapted to comprehensively characterize the MOAs of TB drugs in the laboratory. These approaches have led to the successful development of preclinical TB drug candidates, and to a better understanding of the pathogenesis of Mtb infection. In this review, we describe a plethora of efforts based upon genetic, metabolomic, biochemical, and computational approaches to investigate TB drug MOAs. We assess these different platforms for their strengths and limitations in TB drug MOA elucidation in the context of Mtb pathogenesis. With an emphasis on the essentiality of MOA identification, we outline the unmet needs in delivering TB drug candidates and provide direction for further TB drug discovery.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Joshua M. Werman
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook UniversityStony BrookNY 11794-3400USA+1-631-632-5738+1-631-632-7952
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13
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Oh S, Libardo MDJ, Azeeza S, Pauly GT, Roma JSO, Sajid A, Tateishi Y, Duncombe C, Goodwin M, Ioerger TR, Wyatt PG, Ray PC, Gray DW, Boshoff HIM, Barry CE. Structure-Activity Relationships of Pyrazolo[1,5- a]pyrimidin-7(4 H)-ones as Antitubercular Agents. ACS Infect Dis 2021; 7:479-492. [PMID: 33405882 PMCID: PMC7887755 DOI: 10.1021/acsinfecdis.0c00851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Pyrazolo[1,5-a]pyrimidin-7(4H)-one was identified through high-throughput whole-cell
screening
as a potential antituberculosis lead. The core of this scaffold has
been identified several times previously and has been associated with
various modes of action against Mycobacterium tuberculosis (Mtb). We explored this scaffold through the synthesis
of a focused library of analogues and identified key features of the
pharmacophore while achieving substantial improvements in antitubercular
activity. Our best hits had low cytotoxicity and showed promising
activity against Mtb within macrophages. The mechanism
of action of these compounds was not related to cell-wall biosynthesis,
isoprene biosynthesis, or iron uptake as has been found for other
compounds sharing this core structure. Resistance to these compounds
was conferred by mutation of a flavin adenine dinucleotide (FAD)-dependent
hydroxylase (Rv1751) that promoted compound catabolism by hydroxylation
from molecular oxygen. Our results highlight the risks of chemical
clustering without establishing mechanistic similarity of chemically
related growth inhibitors.
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Affiliation(s)
- Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - M. Daben J. Libardo
- 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
| | - Shaik Azeeza
- 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
| | - Gary T. Pauly
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Jose Santinni O. Roma
- 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
| | - Andaleeb Sajid
- 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
| | - Yoshitaka Tateishi
- 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
| | - Caroline Duncombe
- 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
| | - 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
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Paul G. Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Peter C. Ray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David W. Gray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
- Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7935, South Africa
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14
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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] [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.
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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
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15
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Chengalroyen MD, Jordaan A, Seldon R, Ioerger T, Franzblau SG, Nasr M, Warner DF, Mizrahi V. Biological Profiling Enables Rapid Mechanistic Classification of Phenotypic Screening Hits and Identification of KatG Activation-Dependent Pyridine Carboxamide Prodrugs With Activity Against Mycobacterium tuberculosis. Front Cell Infect Microbiol 2020; 10:582416. [PMID: 33282750 PMCID: PMC7691319 DOI: 10.3389/fcimb.2020.582416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/20/2020] [Indexed: 01/22/2023] Open
Abstract
Compounds with novel modes of action are urgently needed to develop effective combination therapies for the treatment of tuberculosis. In this study, a series of compounds was evaluated for activity against replicating Mycobacterium tuberculosis and Vero cell line toxicity. Fourteen of the compounds with in vitro activities in the low micrometer range and a favorable selectivity index were classified using reporter strains of M. tuberculosis which showed that six interfered with cell wall metabolism and one disrupted DNA metabolism. Counter-screening against strains carrying mutations in promiscuous drug targets argued against DprE1 and MmpL3 as hits of any of the cell wall actives and eliminated the cytochrome bc1 complex as a target of any of the compounds. Instead, whole-genome sequencing of spontaneous resistant mutants and/or counter-screening against common isoniazid-resistant mutants of M. tuberculosis revealed that four of the six cell wall-active compounds, all pyridine carboxamide analogues, were metabolized by KatG to form InhA inhibitors. Resistance to two of these compounds was associated with mutations in katG that did not confer cross-resistance to isoniazid. Of the remaining seven compounds, low-level resistance to one was associated with an inactivating mutation in Rv0678, the regulator of the MmpS5-MmpL5 system, which has been implicated in non-specific efflux of multiple chemotypes. Another mapped to the mycothiol-dependent reductase, Rv2466c, suggesting a prodrug mechanism of action in that case. The inability to isolate spontaneous resistant mutants to the seven remaining compounds suggests that they act via mechanisms which have yet to be elucidated.
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Affiliation(s)
- Melissa D Chengalroyen
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Audrey Jordaan
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ronnett Seldon
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa.,H3D Drug Discovery and Development Centre, Department of Chemistry, University of Cape Town, Cape Town, South Africa
| | - Thomas Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, United States
| | - Scott G Franzblau
- Institute for Tuberculosis Research, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, United States
| | - Mohamed Nasr
- Division of AIDS, NIAID, National Institutes of Health, Bethesda, MD, United States
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town, Cape Town, South Africa.,Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
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16
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de Wet TJ, Winkler KR, Mhlanga M, Mizrahi V, Warner DF. Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes. eLife 2020; 9:e60083. [PMID: 33155979 PMCID: PMC7647400 DOI: 10.7554/elife.60083] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium tuberculosis possesses a large number of genes of unknown or predicted function, undermining fundamental understanding of pathogenicity and drug susceptibility. To address this challenge, we developed a high-throughput functional genomics approach combining inducible CRISPR-interference and image-based analyses of morphological features and sub-cellular chromosomal localizations in the related non-pathogen, M. smegmatis. Applying automated imaging and analysis to 263 essential gene knockdown mutants in an arrayed library, we derive robust, quantitative descriptions of bacillary morphologies consequent on gene silencing. Leveraging statistical-learning, we demonstrate that functionally related genes cluster by morphotypic similarity and that this information can be used to inform investigations of gene function. Exploiting this observation, we infer the existence of a mycobacterial restriction-modification system, and identify filamentation as a defining mycobacterial response to histidine starvation. Our results support the application of large-scale image-based analyses for mycobacterial functional genomics, simultaneously establishing the utility of this approach for drug mechanism-of-action studies.
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Affiliation(s)
- Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Kristy R Winkler
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Musa Mhlanga
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Department of Integrative Biomedical Sciences, University of Cape TownCape TownSouth Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
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17
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Schäfer AB, Wenzel M. A How-To Guide for Mode of Action Analysis of Antimicrobial Peptides. Front Cell Infect Microbiol 2020; 10:540898. [PMID: 33194788 PMCID: PMC7604286 DOI: 10.3389/fcimb.2020.540898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a promising alternative to classical antibiotics in the fight against multi-resistant bacteria. They are produced by organisms from all domains of life and constitute a nearly universal defense mechanism against infectious agents. No drug can be approved without information about its mechanism of action. In order to use them in a clinical setting, it is pivotal to understand how AMPs work. While many pore-forming AMPs are well-characterized in model membrane systems, non-pore-forming peptides are often poorly understood. Moreover, there is evidence that pore formation may not happen or not play a role in vivo. It is therefore imperative to study how AMPs interact with their targets in vivo and consequently kill microorganisms. This has been difficult in the past, since established methods did not provide much mechanistic detail. Especially, methods to study membrane-active compounds have been scarce. Recent advances, in particular in microscopy technology and cell biological labeling techniques, now allow studying mechanisms of AMPs in unprecedented detail. This review gives an overview of available in vivo methods to investigate the antibacterial mechanisms of AMPs. In addition to classical mode of action classification assays, we discuss global profiling techniques, such as genomic and proteomic approaches, as well as bacterial cytological profiling and other cell biological assays. We cover approaches to determine the effects of AMPs on cell morphology, outer membrane, cell wall, and inner membrane properties, cellular macromolecules, and protein targets. We particularly expand on methods to examine cytoplasmic membrane parameters, such as composition, thickness, organization, fluidity, potential, and the functionality of membrane-associated processes. This review aims to provide a guide for researchers, who seek a broad overview of the available methodology to study the mechanisms of AMPs in living bacteria.
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Affiliation(s)
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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18
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Burke C, Jankute M, Moynihan P, Gonzalez Del Rio R, Li X, Esquivias J, Lelièvre J, Cox JAG, Sacchettini J, Besra GS. Development of a novel secondary phenotypic screen to identify hits within the mycobacterial protein synthesis pipeline. FASEB Bioadv 2020; 2:600-612. [PMID: 33089076 PMCID: PMC7566049 DOI: 10.1096/fba.2020-00022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/17/2020] [Accepted: 07/31/2020] [Indexed: 12/03/2022] Open
Abstract
Background Whole‐cell phenotypic screening is the driving force behind modern anti‐tubercular drug discovery efforts. Focus has shifted from screening for bactericidal scaffolds to screens incorporating target deconvolution. Target‐based screening aims to direct drug discovery toward known effective targets and avoid investing resources into unproductive lines of enquiry. The protein synthesis pipeline, including RNA polymerase and the ribosome, is a clinically proven target in Mycobacterium tuberculosis. Screening for new hits of this effective target pathway is an invaluable tool in the drug discovery arsenal. Methods Using M. tuberculosis H37Rv augmented with anhydrotetracycline‐inducible expression of mCherry, a phenotypic screen was developed for the identification of protein synthesis inhibitors in a medium throughput screening format. Results The assay was validated using known inhibitors of protein synthesis to show a dose‐dependent reduction in mCherry fluorescence. This was expanded to a proprietary screen of hypothetical protein synthesis hits and modified to include quantitative viability measurement of cells using resazurin. Conclusion Following the success of the proprietary screen, a larger scale screen of the GlaxoSmithKline anti‐tubercular library containing 2799 compounds was conducted. Combined single shot and dose‐response screening yielded 18 hits, 0.64% of all screened compounds.
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Affiliation(s)
- Christopher Burke
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
| | - Monika Jankute
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
| | - Patrick Moynihan
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
| | | | - Xiaojun Li
- Department of Biochemistry and Biophysics Texas A&M University College Station Texas United States
| | - Jorge Esquivias
- Diseases of the Developing World GlaxoSmithKline Tres Cantos Madrid Spain
| | - Joël Lelièvre
- Diseases of the Developing World GlaxoSmithKline Tres Cantos Madrid Spain
| | | | - James Sacchettini
- Department of Biochemistry and Biophysics Texas A&M University College Station Texas United States
| | - Gurdyal S Besra
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
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19
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Smith TC, Pullen KM, Olson MC, McNellis ME, Richardson I, Hu S, Larkins-Ford J, Wang X, Freundlich JS, Ando DM, Aldridge BB. Morphological profiling of tubercle bacilli identifies drug pathways of action. Proc Natl Acad Sci U S A 2020; 117:18744-18753. [PMID: 32680963 PMCID: PMC7414088 DOI: 10.1073/pnas.2002738117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Morphological profiling is a method to classify target pathways of antibacterials based on how bacteria respond to treatment through changes to cellular shape and spatial organization. Here we utilized the cell-to-cell variation in morphological features of Mycobacterium tuberculosis bacilli to develop a rapid profiling platform called Morphological Evaluation and Understanding of Stress (MorphEUS). MorphEUS classified 94% of tested drugs correctly into broad categories according to modes of action previously identified in the literature. In the other 6%, MorphEUS pointed to key off-target activities. We observed cell wall damage induced by bedaquiline and moxifloxacin through secondary effects downstream from their main target pathways. We implemented MorphEUS to correctly classify three compounds in a blinded study and identified an off-target effect for one compound that was not readily apparent in previous studies. We anticipate that the ability of MorphEUS to rapidly identify pathways of drug action and the proximal cause of cellular damage in tubercle bacilli will make it applicable to other pathogens and cell types where morphological responses are subtle and heterogeneous.
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Affiliation(s)
- Trever C Smith
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA 02111
| | - Krista M Pullen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michaela C Olson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
| | - Morgan E McNellis
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
| | - Ian Richardson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Roxbury Latin School, West Roxbury, MA 02132
| | - Sophia Hu
- Department of Bioinformatics and Computational Biology, University of Maryland, Baltimore County, Baltimore, MD 21250
| | - Jonah Larkins-Ford
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Tufts University School of Graduate Biomedical Sciences, Boston, MA 02111
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Xin Wang
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ 07103
| | - Joel S Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ 07103
- Division of Infectious Disease, Department of Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103
- Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ 07103
| | - D Michael Ando
- Applied Science Team, Google Research, Mountain View, CA 94043
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111;
- Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA 02111
- Tufts University School of Graduate Biomedical Sciences, Boston, MA 02111
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA 02155
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20
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Yang Z, Cui Q, Zhang M, Li Z, Wang M, Xu H. A lux-based Staphylococcus aureus bioluminescence screening assay for the detection/identification of antibiotics and prediction of antibiotic mechanisms. J Antibiot (Tokyo) 2020; 73:828-836. [PMID: 32678336 DOI: 10.1038/s41429-020-0349-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 06/09/2020] [Accepted: 06/30/2020] [Indexed: 11/09/2022]
Abstract
The need for the discovery of new antibiotics and solving the antibiotic resistance problem requires rapid detection of antibiotics, identification of known antibiotics, and prediction of antibiotic mechanisms. The bacterial lux genes encode proteins that convert chemical energy into photonic energy and lead to bioluminescence. Exploiting this phenomenon, we constructed a lux-based bioluminescence system in Staphylococcus aureus by expressing lux genes under the control of stress-inducible chaperon promoters. When experiencing antibiotic stress, these constructed reporter strains showed clear bioluminescence response. Therefore, this bioluminescence screening system can be used for the detection of antibiotics in unknown chemical mixtures. Further analysis of bioluminescence response patterns showed that: (1) these bioluminescence response patterns are highly antibiotic specific and therefore can be used for rapid and cheap identification of antibiotics; and that (2) antibiotics having the same mechanism of action have similar bioluminescence patterns and therefore these patterns can be used for the prediction of mechanism for an unknown antibiotic with good sensitivity and specificity. With this bioluminescence screening assay, the discovery and analysis of new antibiotics can be promoted, which benefits in solving the antibiotic resistance problem.
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Affiliation(s)
- Zhongjun Yang
- State Key Laboratory of Microbial Technology, Qilu Hospital, Shandong University, Qingdao, 266237, Shandong, China
| | - Qingyu Cui
- State Key Laboratory of Microbial Technology, Qilu Hospital, Shandong University, Qingdao, 266237, Shandong, China
| | - Mengge Zhang
- State Key Laboratory of Microbial Technology, Qilu Hospital, Shandong University, Qingdao, 266237, Shandong, China
| | - Zhiqiang Li
- Center for Optics Research and Engineering, Shandong University, Qingdao, 266237, Shandong, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Qilu Hospital, Shandong University, Qingdao, 266237, Shandong, China.
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Qilu Hospital, Shandong University, Qingdao, 266237, Shandong, China.
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21
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Akester JN, Njaria P, Nchinda A, Le Manach C, Myrick A, Singh V, Lawrence N, Njoroge M, Taylor D, Moosa A, Smith AJ, Brooks EJ, Lenaerts AJ, Robertson GT, Ioerger TR, Mueller R, Chibale K. Synthesis, Structure-Activity Relationship, and Mechanistic Studies of Aminoquinazolinones Displaying Antimycobacterial Activity. ACS Infect Dis 2020; 6:1951-1964. [PMID: 32470286 PMCID: PMC7359024 DOI: 10.1021/acsinfecdis.0c00252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Phenotypic whole-cell screening against Mycobacterium tuberculosis (Mtb) in glycerol–alanine–salts
supplemented with Tween 80 and iron (GASTE-Fe) media led to the identification
of a 2-aminoquinazolinone hit compound, sulfone 1 which
was optimized for solubility by replacing the sulfone moiety with
a sulfoxide 2. The synthesis and structure–activity
relationship (SAR) studies identified several compounds with potent
antimycobacterial activity, which were metabolically stable and noncytotoxic.
Compound 2 displayed favorable in vitro properties and was therefore selected for in vivo pharmacokinetic (PK) studies where it was found to be extensively
metabolized to the sulfone 1. Both derivatives exhibited
promising PK parameters; however, when 2 was evaluated
for in vivo efficacy in an acute TB infection mouse
model, it was found to be inactive. In order to understand the in vitro and in vivo discrepancy, compound 2 was subsequently retested in vitro using
different Mtb strains cultured in different media.
This revealed that activity was only observed in media containing
glycerol and led to the hypothesis that glycerol was not used as a
primary carbon source by Mtb in the mouse lungs,
as has previously been observed. Support for this hypothesis was provided
by spontaneous-resistant mutant generation and whole genome sequencing
studies, which revealed mutations mapping to glycerol metabolizing
genes indicating that the 2-aminoquinazolinones kill Mtb in
vitro via a glycerol-dependent mechanism of action.
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Affiliation(s)
- Jessica N. Akester
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Paul Njaria
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Aloysius Nchinda
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Claire Le Manach
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Alissa Myrick
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Nina Lawrence
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Mathew Njoroge
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Dale Taylor
- H3D, Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Atica Moosa
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape Town, Rondebosch 7701, South Africa
| | - Anthony J. Smith
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, 200 West Lake Street, Fort Collins, Colorado 80523, United States
| | - Elizabeth J. Brooks
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, 200 West Lake Street, Fort Collins, Colorado 80523, United States
| | - Anne J. Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, 200 West Lake Street, Fort Collins, Colorado 80523, United States
| | - Gregory T. Robertson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, 200 West Lake Street, Fort Collins, Colorado 80523, United States
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A&M University, College Station, Texas 77843-3112, United States
| | - Rudolf Mueller
- 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
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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22
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Zuma NH, Smit FJ, Seldon R, Aucamp J, Jordaan A, Warner DF, N'Da DD. Single-step synthesis and in vitro anti-mycobacterial activity of novel nitrofurantoin analogues. Bioorg Chem 2020; 96:103587. [PMID: 32044516 DOI: 10.1016/j.bioorg.2020.103587] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/06/2019] [Accepted: 01/13/2020] [Indexed: 01/26/2023]
Abstract
The emergence of drug-resistant tuberculosis (DR-TB) as well as the requirement for long, expensive and toxic drug regimens impede efforts to control and eliminate TB. Therefore, there's a need for effective and affordable anti-mycobacterial agents which can shorten the duration of therapy and are active against Mycobacterium tuberculosis (Mtb) in both active and latent phases. Nitrofurantoin (NFT) is a hypoxic agent with activity against a myriad of anaerobic pathogens and, like the first-line TB drug, rifampicin (RIF), kills non-replicating bacilli. However, the poor ability of NFT to cross host cell membranes and penetrate tissue means that it does not reach therapeutic concentrations. To improve TB efficacy of NFT, a series of NFT analogues was synthesized and evaluated in vitro for anti-mycobacterial activity against the laboratory strain, Mtb H37Rv, and for potential cytotoxicity using human embryonic kidney (HEK-293) and Chinese hamster ovarian (CHO) cells. The NFT analogues showed good safety profiles, enhanced anti-mycobacterial potency, improved lipophilicity, as well as reduced protein binding affinity. Analogue 9 which contains an eight carbon aliphatic chain was the most active, equipotent to isoniazid (INH), a major front-line agent, with MIC90 = 0.5 μM, 30-fold more potency than the parent drug, nitrofurantoin (MIC90 = 15 μM), and 100-fold more selective towards mycobacteria. Therefore, 9 was identified as a validated hit for further investigation in the urgent search for new, safe and affordable TB drugs.
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Affiliation(s)
- Nonkululeko H Zuma
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Frans J Smit
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Ronnett Seldon
- SAMRC Drug Discovery and Development Research Unit, University of Cape Town, Cape Town 7700, South Africa
| | - Janine Aucamp
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Audrey Jordaan
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925, South Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7925, South Africa; Wellcome Centre for Clinical Infectious Diseases Research in Africa, University of Cape Town, Cape Town 7925, South Africa
| | - David D N'Da
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa.
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23
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In Vitro Efficacies, ADME, and Pharmacokinetic Properties of Phenoxazine Derivatives Active against Mycobacterium tuberculosis. Antimicrob Agents Chemother 2019; 63:AAC.01010-19. [PMID: 31427302 DOI: 10.1128/aac.01010-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a leading infectious killer globally, demanding the urgent development of faster-acting drugs with novel mechanisms of action. Riminophenazines such as clofazimine are clinically efficacious against both drug-susceptible and drug-resistant strains of M. tuberculosis We determined the in vitro anti-M. tuberculosis activities, absorption, distribution, metabolism, and excretion properties, and in vivo mouse pharmacokinetics of a series of structurally related phenoxazines. One of these, PhX1, displayed promising drug-like properties and potent in vitro efficacy, supporting its further investigation in an M. tuberculosis-infected animal model.
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24
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Oh S, Park Y, Engelhart CA, Wallach JB, Schnappinger D, Arora K, Manikkam M, Gac B, Wang H, Murgolo N, Olsen DB, Goodwin M, Sutphin M, Weiner DM, Via LE, Boshoff HIM, Barry CE. Discovery and Structure-Activity-Relationship Study of N-Alkyl-5-hydroxypyrimidinone Carboxamides as Novel Antitubercular Agents Targeting Decaprenylphosphoryl-β-d-ribose 2'-Oxidase. J Med Chem 2018; 61:9952-9965. [PMID: 30350998 PMCID: PMC6257622 DOI: 10.1021/acs.jmedchem.8b00883] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Magnesium plays an important role
in infection with Mycobacterium
tuberculosis (Mtb) as a signal of the extracellular
environment, as a cofactor for many enzymes, and as a structural element
in important macromolecules. Raltegravir, an antiretroviral drug that
inhibits HIV-1 integrase is known to derive its potency from selective
sequestration of active-site magnesium ions in addition to binding
to a hydrophobic pocket. In order to determine if essential Mtb-related phosphoryl transfers could be disrupted in a
similar manner, a directed screen of known molecules with integrase
inhibitor-like pharmacophores (N-alkyl-5-hydroxypyrimidinone
carboxamides) was performed. Initial hits afforded compounds with
low-micromolar potency against Mtb, acceptable cytotoxicity
and PK characteristics, and robust SAR. Elucidation of the target
of these compounds revealed that they lacked magnesium dependence
and instead disappointingly inhibited a known promiscuous target in Mtb, decaprenylphosphoryl-β-d-ribose 2′-oxidase
(DprE1, Rv3790).
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Affiliation(s)
- Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Yumi Park
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Curtis A Engelhart
- Department of Microbiology and Immunology , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Joshua B Wallach
- Department of Microbiology and Immunology , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology , Weill Cornell Medical College , New York , New York 10021 , United States
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Michelle Manikkam
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Brian Gac
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Hongwu Wang
- Discovery Research , Merck & Company, Inc. , 770 Sumneytown Pike , West Point , Pennsylvania 19486 , United States
| | - Nicholas Murgolo
- Discovery Research , Merck & Company, Inc. , 770 Sumneytown Pike , West Point , Pennsylvania 19486 , United States
| | - David B Olsen
- Discovery Research , Merck & Company, Inc. , 770 Sumneytown Pike , West Point , Pennsylvania 19486 , United States
| | - Michael Goodwin
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Michelle Sutphin
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Danielle M Weiner
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Laura E Via
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Institute for Infectious Disease and Molecular Medicine , University of Cape Town , Cape Town 7935 , South Africa
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Institute for Infectious Disease and Molecular Medicine , University of Cape Town , Cape Town 7935 , South Africa
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25
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Beteck RM, Seldon R, Coertzen D, van der Watt ME, Reader J, Mackenzie JS, Lamprecht DA, Abraham M, Eribez K, Müller J, Rui F, Zhu G, de Grano RV, Williams ID, Smit FJ, Steyn AJC, Winzeler EA, Hemphill A, Birkholtz LM, Warner DF, N’Da DD, Haynes RK. Accessible and distinct decoquinate derivatives active against Mycobacterium tuberculosis and apicomplexan parasites. Commun Chem 2018. [DOI: 10.1038/s42004-018-0062-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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26
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Abramovitch RB. Mycobacterium tuberculosis Reporter Strains as Tools for Drug Discovery and Development. IUBMB Life 2018; 70:818-825. [PMID: 29707888 DOI: 10.1002/iub.1862] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/08/2018] [Indexed: 11/11/2022]
Abstract
Reporter strains have proven to be powerful tools to study Mycobacterium tuberculosis (Mtb) physiology. Transcriptional and translational reporter strains are engineered by fusing a readout gene, encoding a fluorescent, luminescent or enzymatic protein, downstream of a promoter or in-frame with a gene of interest. When the reporter is expressed, it generates a signal that acts as a synthetic phenotype, enabling the study of physiologies that might have otherwise been hidden. This review will discuss approaches for generating reporter strains in Mtb and how they can be used as tools for high-throughput genetic and small molecule screening and as biomarkers for examining Mtb responses to drug or immune stresses during animal infections. Fluorescent reporter strains have an added benefit in that they can be used for single-cell studies both in vitro and in vivo, thus enabling the study of mechanisms underlying phenotypic heterogeneity. Recent examples of the use of Mtb reporter strains will be presented with a focus on how they can be used as tools for drug discovery and development. © 2018 IUBMB Life, 70(9):818-825, 2018.
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Affiliation(s)
- Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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27
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J Libardo MD, Boshoff HI, Barry CE. The present state of the tuberculosis drug development pipeline. Curr Opin Pharmacol 2018; 42:81-94. [PMID: 30144650 DOI: 10.1016/j.coph.2018.08.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 10/28/2022]
Abstract
Tuberculosis now ranks as the leading cause of death in the world due to a single infectious agent. Current standard of care treatment can achieve very high cure rates for drug-sensitive disease but requires a 6-month duration of chemotherapy. Drug-resistant disease requires significantly longer treatment durations with drugs associated with a higher risk of adverse events. Thus, there is a pressing need for a drug regimen that is safer, shorter in duration and superior to current front-line chemotherapy in terms of efficacy. The TB drug pipeline contains several candidates that address one or more of the required attributes of chemotherapeutic regimens that may redefine the standard of care of this disease. Several new drugs have been reported and novel targets have been identified allowing regimens containing new compounds to trickle into clinical studies. Furthermore, a recent paradigm-shift in understanding the pharmacokinetics of anti-tubercular drugs is revolutionizing the way we select compounds for clinical progression.
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Affiliation(s)
- M Daben J Libardo
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Helena Im Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 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, MD 20892, United States.
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28
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Lee BS, Pethe K. Therapeutic potential of promiscuous targets in Mycobacterium tuberculosis. Curr Opin Pharmacol 2018; 42:22-26. [PMID: 30015177 DOI: 10.1016/j.coph.2018.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/31/2018] [Accepted: 06/20/2018] [Indexed: 11/16/2022]
Abstract
In the field of tuberculosis drug development, the term 'promiscuous' was coined to collectively describe targets that repeatedly show up in whole-cell screenings. With the current climate leaning towards the exclusion of these targets in future drug screens, this review discusses and clarifies misconceptions surrounding this classification, the prospects of developing compounds targeting promiscuous targets, and their potential impact on tuberculosis drug development. The dominance of these targets in cell-based screens reflect not only bias introduced by experimental setup, but also some of the pathogen's greatest vulnerabilities. Coupled with favourable predictions of their in vivo efficacies and synergism with other TB drugs, these targets open opportunities to be explored for the development of rational drug combination for tuberculosis.
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Affiliation(s)
- Bei Shi Lee
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kevin Pethe
- School of Biological Sciences, Nanyang Technological University, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Experimental Medicine Building, Singapore.
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Accelerating Early Antituberculosis Drug Discovery by Creating Mycobacterial Indicator Strains That Predict Mode of Action. Antimicrob Agents Chemother 2018; 62:AAC.00083-18. [PMID: 29661879 DOI: 10.1128/aac.00083-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Due to the rise of drug-resistant forms of tuberculosis, there is an urgent need for novel antibiotics to effectively combat these cases and shorten treatment regimens. Recently, drug screens using whole-cell analyses have been shown to be successful. However, current high-throughput screens focus mostly on stricto sensu life/death screening that give little qualitative information. In doing so, promising compound scaffolds or nonoptimized compounds that fail to reach inhibitory concentrations are missed. To accelerate early tuberculosis (TB) drug discovery, we performed RNA sequencing on Mycobacterium tuberculosis and Mycobacterium marinum to map the stress responses that follow upon exposure to subinhibitory concentrations of antibiotics with known targets, ciprofloxacin, ethambutol, isoniazid, streptomycin, and rifampin. The resulting data set comprises the first overview of transcriptional stress responses of mycobacteria to different antibiotics. We show that antibiotics can be distinguished based on their specific transcriptional stress fingerprint. Notably, this fingerprint was more distinctive in M. marinum We decided to use this to our advantage and continue with this model organism. A selection of diverse antibiotic stress genes was used to construct stress reporters. In total, three functional reporters were constructed to respond to DNA damage, cell wall damage, and ribosomal inhibition. Subsequently, these reporter strains were used to screen a small anti-TB compound library to predict the mode of action. In doing so, we identified the putative modes of action for three novel compounds, which confirms the utility of our approach.
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30
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Murugesan D, Ray PC, Bayliss T, Prosser GA, Harrison JR, Green K, Soares de Melo C, Feng TS, Street LJ, Chibale K, Warner DF, Mizrahi V, Epemolu O, Scullion P, Ellis L, Riley J, Shishikura Y, Ferguson L, Osuna-Cabello M, Read KD, Green SR, Lamprecht DA, Finin PM, Steyn AJC, Ioerger TR, Sacchettini J, Rhee KY, Arora K, Barry CE, Wyatt PG, Boshoff HIM. 2-Mercapto-Quinazolinones as Inhibitors of Type II NADH Dehydrogenase and Mycobacterium tuberculosis: Structure-Activity Relationships, Mechanism of Action and Absorption, Distribution, Metabolism, and Excretion Characterization. ACS Infect Dis 2018. [PMID: 29522317 PMCID: PMC5996347 DOI: 10.1021/acsinfecdis.7b00275] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Mycobacterium tuberculosis (MTb) possesses
two nonproton pumping type II NADH dehydrogenase (NDH-2)
enzymes which are predicted to be jointly essential for respiratory
metabolism. Furthermore, the structure of a closely related bacterial
NDH-2 has been reported recently, allowing for the structure-based
design of small-molecule inhibitors. Herein, we disclose MTb whole-cell structure–activity relationships (SARs) for a series of 2-mercapto-quinazolinones which target the ndh encoded NDH-2 with nanomolar potencies. The compounds were inactivated by glutathione-dependent adduct formation as well as quinazolinone oxidation in microsomes. Pharmacokinetic studies demonstrated modest bioavailability and compound exposures. Resistance to the compounds in MTb was conferred by promoter mutations in the alternative nonessential NDH-2 encoded by ndhA in MTb. Bioenergetic analyses revealed a decrease in oxygen consumption rates in response to inhibitor in cells in which membrane potential was uncoupled from ATP production, while inverted membrane vesicles showed mercapto-quinazolinone-dependent inhibition of ATP production when NADH was the electron donor to the respiratory chain. Enzyme kinetic studies further demonstrated noncompetitive inhibition, suggesting binding of this scaffold to an allosteric site. In summary, while the initial MTb SAR showed limited improvement in potency, these results, combined with structural information on the bacterial protein, will aid in the future discovery of new and improved NDH-2 inhibitors.
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Affiliation(s)
- Dinakaran Murugesan
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Peter C. Ray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Tracy Bayliss
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Gareth A. Prosser
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Justin R. Harrison
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Kirsteen Green
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Candice Soares de Melo
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Tzu-Shean Feng
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Leslie J. Street
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kelly Chibale
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
- 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, University of Cape Town, Rondebosch, 7701, South Africa
| | - Digby F. Warner
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Valerie Mizrahi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Paul Scullion
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Lucy Ellis
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Yoko Shishikura
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Liam Ferguson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Maria Osuna-Cabello
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Kevin D. Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Simon R. Green
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Dirk A. Lamprecht
- Africa Health Research Institute (AHRI), K-RITH Tower Building Level 3, 719 Umbilo Road, Durban, 4001, South Africa
| | - Peter M. Finin
- Africa Health Research Institute (AHRI), K-RITH Tower Building Level 3, 719 Umbilo Road, Durban, 4001, South Africa
| | - Adrie J. C. Steyn
- Africa Health Research Institute (AHRI), K-RITH Tower Building Level 3, 719 Umbilo Road, Durban, 4001, South Africa
- Department of Microbiology, University of Alabama at Birmingham, 1720 Second Avenue South, Birmingham, Alabama 35294-2170, United States
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Jim Sacchettini
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Kyu Y. Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
| | - Paul G. Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
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31
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Yu M, Ohmiya Y, Naumov P, Liu YJ. Theoretical Insight into the Emission Properties of the Luciferin and Oxyluciferin of Latia. Photochem Photobiol 2018; 94:540-544. [PMID: 29253310 DOI: 10.1111/php.12876] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/27/2017] [Indexed: 11/27/2022]
Abstract
Latia neritoides is a small limpet-like snail that produces a bright green bioluminescence (BL) via a unique light-emitting system. The process, mechanism, and even light emitter of its light emission remain unknown, although this BL has been known for decades. Unlike the other BL systems, neither the luciferin (Luc) nor the oxyluciferin (OxyLuc) of Latia is fluorescent according to the previous experiments. To help to identify its bioluminophore, we studied the geometrical and electronic structures and absorption and fluorescence spectra of Latia Luc and its six analogs as well as its OxyLuc in the gas phase and in water. The calculated results provide clear evidence of the lack of fluorescence in the Luc and OxyLuc of Latia. For the analogs of Latia Luc, the electron-withdrawing or electron-donating ability of the substituted group affects the fluorescence. The results shed new light on the BL mechanism and will likely aid the understanding of Latia BL.
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Affiliation(s)
- Mohan Yu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | | | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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32
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Wilson CR, Gessner RK, Moosa A, Seldon R, Warner DF, Mizrahi V, Soares de Melo C, Simelane SB, Nchinda A, Abay E, Taylor D, Njoroge M, Brunschwig C, Lawrence N, Boshoff HIM, Barry CE, Sirgel FA, van Helden P, Harris CJ, Gordon R, Ghidelli-Disse S, Pflaumer H, Boesche M, Drewes G, Sanz O, Santos G, Rebollo-Lopez MJ, Urones B, Selenski C, Lafuente-Monasterio MJ, Axtman M, Lelièvre J, Ballell L, Mueller R, Street LJ, Ghorpade SR, Chibale K. Novel Antitubercular 6-Dialkylaminopyrimidine Carboxamides from Phenotypic Whole-Cell High Throughput Screening of a SoftFocus Library: Structure-Activity Relationship and Target Identification Studies. J Med Chem 2017; 60:10118-10134. [PMID: 29148755 PMCID: PMC5748279 DOI: 10.1021/acs.jmedchem.7b01347] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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A BioFocus
DPI SoftFocus library of ∼35 000 compounds was screened
against Mycobacterium tuberculosis (Mtb) in order
to identify novel hits with antitubercular activity. The hits were
evaluated in biology triage assays to exclude compounds suggested to function via frequently encountered promiscuous mechanisms of action including inhibition of the QcrB subunit of the cytochrome bc1 complex, disruption of cell–wall homeostasis, and DNA damage. Among the hits that passed this screening cascade, a 6-dialkylaminopyrimidine carboxamide series was prioritized for hit to lead optimization. Compounds from this series were active against clinical Mtb strains, while no cross-resistance to conventional antituberculosis drugs was observed. This suggested a novel mechanism of action, which was confirmed by chemoproteomic analysis leading to the identification of BCG_3193 and BCG_3827 as putative targets of the series with unknown function. Initial structure–activity relationship studies have resulted in compounds with moderate to potent antitubercular activity and improved physicochemical properties.
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Affiliation(s)
- Colin R Wilson
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Richard K Gessner
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Atica Moosa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape Town , Rondebosch 7701, South Africa
| | - Ronnett Seldon
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Rondebosch 7701, South Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape Town , Rondebosch 7701, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Rondebosch 7701, South Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape Town , Rondebosch 7701, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Rondebosch 7701, South Africa
| | - Candice Soares de Melo
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Sandile B Simelane
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Aloysius Nchinda
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Efrem Abay
- Department of Medicine, Division of Clinical Pharmacology, Drug Discovery and Development Centre (H3D), University of Cape Town , Observatory, 7925, South Africa
| | - Dale Taylor
- Department of Medicine, Division of Clinical Pharmacology, Drug Discovery and Development Centre (H3D), University of Cape Town , Observatory, 7925, South Africa
| | - Mathew Njoroge
- Department of Medicine, Division of Clinical Pharmacology, Drug Discovery and Development Centre (H3D), University of Cape Town , Observatory, 7925, South Africa
| | - Christel Brunschwig
- Department of Medicine, Division of Clinical Pharmacology, Drug Discovery and Development Centre (H3D), University of Cape Town , Observatory, 7925, South Africa
| | - Nina Lawrence
- Department of Medicine, Division of Clinical Pharmacology, Drug Discovery and Development Centre (H3D), University of Cape Town , Observatory, 7925, South Africa
| | - 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
- DST/NRF Centre of Excellence for Biomedical TB Research, SA MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University , 7505 Tygerberg, South Africa
| | - Paul van Helden
- DST/NRF Centre of Excellence for Biomedical TB Research, SA MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University , 7505 Tygerberg, South Africa
| | - C John Harris
- CJH Consultants , Ford Cottage, South Weirs, Brockenhurst, Hampshire SO42 7UQ, U.K
| | - Richard Gordon
- Strategic Health Innovation Partnerships (SHIP), South African Medical Research Council , Parow Valley, Cape Town, South Africa
| | - Sonja Ghidelli-Disse
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline , Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Hannah Pflaumer
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline , Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Markus Boesche
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline , Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline , Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Olalla Sanz
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Gracia Santos
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Maria José Rebollo-Lopez
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Beatriz Urones
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Carolyn Selenski
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | | | - Matthew Axtman
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Joël Lelièvre
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Lluis Ballell
- Diseases of the Developing World, GlaxoSmithKline , Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Rudolf Mueller
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Leslie J Street
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Sandeep R Ghorpade
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa
| | - Kelly Chibale
- Department of Chemistry, Drug Discovery and Development Centre (H3D), University of Cape Town , Rondebosch 7701, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Rondebosch 7701, South Africa.,South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry, University of Cape Town , Rondebosch 7701, South Africa
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33
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Mukherjee R, Chandra Pal A, Banerjee M. Enabling faster Go/No-Go decisions through secondary screens in anti-mycobacterial drug discovery. Tuberculosis (Edinb) 2017; 106:44-52. [PMID: 28802404 DOI: 10.1016/j.tube.2017.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/30/2017] [Accepted: 06/28/2017] [Indexed: 10/19/2022]
Abstract
Management of tuberculosis, already a global health emergency, is becoming increasingly challenging with extensive misuse of second line drugs and their inaccessibility to eighty percent of the eligible patients. Rising statistics of antimicrobial resistance underscores the need for a set of completely new and more effective class of compounds with novel mechanisms of action that can be administered in combination to replace and shorten the present intensive six months regimen. In this review, we stress on the importance and the successes of phenotypic screening for discovery of anti-mycobacterial compound and discuss the importance of performing secondary screens and counter screens to get early estimate on compound's potentials for a successful development. We also highlight the recent advances and the related caveats in the assays that have been developed and discuss new screening modalities that can be incorporated during hit-selection to gain a quick insight into the mechanism of action, thus enabling quicker decisions in a hit triage.
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Affiliation(s)
- Raju Mukherjee
- Division of Biology, Indian Institute of Science Education and Research, Karakambadi Road, Tirupati, 517507, India.
| | - Anup Chandra Pal
- Division of Biology, Indian Institute of Science Education and Research, Karakambadi Road, Tirupati, 517507, India
| | - Mousumi Banerjee
- Indian Institute of Technology, Tirupati, Renigunta Road, Tirupati, 517506, India
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