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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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