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Park Y, Pacitto A, Bayliss T, Cleghorn LAT, Wang Z, Hartman T, Arora K, Ioerger TR, Sacchettini J, Rizzi M, Donini S, Blundell TL, Ascher DB, Rhee K, Breda A, Zhou N, Dartois V, Jonnala SR, Via LE, Mizrahi V, Epemolu O, Stojanovski L, Simeons F, Osuna-Cabello M, Ellis L, MacKenzie CJ, Smith ARC, Davis SH, Murugesan D, Buchanan KI, Turner PA, Huggett M, Zuccotto F, Rebollo-Lopez MJ, Lafuente-Monasterio MJ, Sanz O, Diaz GS, Lelièvre J, Ballell L, Selenski C, Axtman M, Ghidelli-Disse S, Pflaumer H, Bösche M, Drewes G, Freiberg GM, Kurnick MD, Srikumaran M, Kempf DJ, Green SR, Ray PC, Read K, Wyatt P, Barry CE, Boshoff HI. Essential but Not Vulnerable: Indazole Sulfonamides Targeting Inosine Monophosphate Dehydrogenase as Potential Leads against Mycobacterium tuberculosis. ACS Infect Dis 2017; 3:18-33. [PMID: 27704782 DOI: 10.1021/acsinfecdis.6b00103] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A potent, noncytotoxic indazole sulfonamide was identified by high-throughput screening of >100,000 synthetic compounds for activity against Mycobacterium tuberculosis (Mtb). This noncytotoxic compound did not directly inhibit cell wall biogenesis but triggered a slow lysis of Mtb cells as measured by release of intracellular green fluorescent protein (GFP). Isolation of resistant mutants followed by whole-genome sequencing showed an unusual gene amplification of a 40 gene region spanning from Rv3371 to Rv3411c and in one case a potential promoter mutation upstream of guaB2 (Rv3411c) encoding inosine monophosphate dehydrogenase (IMPDH). Subsequent biochemical validation confirmed direct inhibition of IMPDH by an uncompetitive mode of inhibition, and growth inhibition could be rescued by supplementation with guanine, a bypass mechanism for the IMPDH pathway. Beads containing immobilized indazole sulfonamides specifically interacted with IMPDH in cell lysates. X-ray crystallography of the IMPDH-IMP-inhibitor complex revealed that the primary interactions of these compounds with IMPDH were direct pi-pi interactions with the IMP substrate. Advanced lead compounds in this series with acceptable pharmacokinetic properties failed to show efficacy in acute or chronic murine models of tuberculosis (TB). Time-kill experiments in vitro suggest that sustained exposure to drug concentrations above the minimum inhibitory concentration (MIC) for 24 h were required for a cidal effect, levels that have been difficult to achieve in vivo. Direct measurement of guanine levels in resected lung tissue from tuberculosis-infected animals and patients revealed 0.5-2 mM concentrations in caseum and normal lung tissue. The high lesional levels of guanine and the slow lytic, growth-rate-dependent effect of IMPDH inhibition pose challenges to developing drugs against this target for use in treating TB.
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Affiliation(s)
- Yumi Park
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
| | - Angela Pacitto
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Tracy Bayliss
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Laura A. T. Cleghorn
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Zhe Wang
- Division
of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Travis Hartman
- Division
of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Kriti Arora
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, 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 Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Menico Rizzi
- Dipartimento
di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio
6, 28100 Novara, Italy
| | - Stefano Donini
- Dipartimento
di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio
6, 28100 Novara, Italy
| | - Tom L. Blundell
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - David B. Ascher
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Kyu Rhee
- Division
of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Ardala Breda
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Nian Zhou
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Veronique Dartois
- Public
Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey 07103, United States
| | - Surendranadha Reddy Jonnala
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
| | - Laura E. Via
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit, Institute of Infectious
Disease and Molecular Medicine, University of Cape Town, Rondebosch 7700, South Africa
| | - Valerie Mizrahi
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit, Institute of Infectious
Disease and Molecular Medicine, University of Cape Town, Rondebosch 7700, South Africa
| | - Ola Epemolu
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Laste Stojanovski
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Fred Simeons
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Maria Osuna-Cabello
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Lucy Ellis
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Claire J. MacKenzie
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Alasdair R. C. Smith
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Susan H. Davis
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Dinakaran Murugesan
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kirsteen I. Buchanan
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Penelope A. Turner
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Margaret Huggett
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Fabio Zuccotto
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Maria Jose Rebollo-Lopez
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | | | - Olalla Sanz
- Diseases
of the Developing World, GlaxoSmithKline, Calle Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Gracia Santos Diaz
- 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
| | - Carolyn Selenski
- GlaxoSmithKline, 5 Crescent Drive, Philadelphia, Pennsylvania 19112, United States
| | - Matthew Axtman
- GlaxoSmithKline, 5 Crescent Drive, Philadelphia, Pennsylvania 19112, United States
| | - Sonja Ghidelli-Disse
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Hannah Pflaumer
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Bösche
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gerard Drewes
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gail M. Freiberg
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Matthew D. Kurnick
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Myron Srikumaran
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dale J. Kempf
- AbbVie Molecular Characterization, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Simon R. Green
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Peter C. Ray
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kevin Read
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Paul Wyatt
- Drug
Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Clifton E. Barry
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
- MRC/NHLS/UCT
Molecular Mycobacteriology Research Unit, Institute of Infectious
Disease and Molecular Medicine, University of Cape Town, Rondebosch 7700, South Africa
| | - Helena I. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-3206, United States
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