Synergistic Lethality of a Binary Inhibitor of <named-content content-type="genus-species">Mycobacterium tuberculosis</named-content> KasA

Pradeep Kumar; Glenn C. Capodagli; Divya Awasthi; Riju Shrestha; Karishma Maharaja; Paridhi Sukheja; Shao-Gang Li; Daigo Inoyama; Matthew Zimmerman; Hsin Pin Ho Liang; Jansy Sarathy; Marizel Mina; George Rasic; Riccardo Russo; Alexander L. Perryman; Todd Richmann; Aditi Gupta; Eric Singleton; Sheetal Verma; Seema Husain; Patricia Soteropoulos; Zhe Wang; Roxanne Morris; Gene Porter; Gautam Agnihotri; Padmini Salgame; Sean Ekins; Kyu Y. Rhee; Nancy Connell; Véronique Dartois; Matthew B. Neiditch; Joel S. Freundlich; David Alland

doi:10.1128/mBio.02101-17

mBio (Dec 2018)

Synergistic Lethality of a Binary Inhibitor of <named-content content-type="genus-species">Mycobacterium tuberculosis</named-content> KasA

Pradeep Kumar,
Glenn C. Capodagli,
Divya Awasthi,
Riju Shrestha,
Karishma Maharaja,
Paridhi Sukheja,
Shao-Gang Li,
Daigo Inoyama,
Matthew Zimmerman,
Hsin Pin Ho Liang,
Jansy Sarathy,
Marizel Mina,
George Rasic,
Riccardo Russo,
Alexander L. Perryman,
Todd Richmann,
Aditi Gupta,
Eric Singleton,
Sheetal Verma,
Seema Husain,
Patricia Soteropoulos,
Zhe Wang,
Roxanne Morris,
Gene Porter,
Gautam Agnihotri,
Padmini Salgame,
Sean Ekins,
Kyu Y. Rhee,
Nancy Connell,
Véronique Dartois,
Matthew B. Neiditch,
Joel S. Freundlich,
David Alland

Affiliations

Pradeep Kumar: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Glenn C. Capodagli: Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, USA
Divya Awasthi: Department of Pharmacology, Physiology & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Riju Shrestha: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Karishma Maharaja: Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, USA
Paridhi Sukheja: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Shao-Gang Li: Department of Pharmacology, Physiology & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Daigo Inoyama: Department of Pharmacology, Physiology & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Matthew Zimmerman: Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Hsin Pin Ho Liang: Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Jansy Sarathy: Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Marizel Mina: Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
George Rasic: Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Riccardo Russo: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Alexander L. Perryman: Department of Pharmacology, Physiology & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Todd Richmann: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Aditi Gupta: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Eric Singleton: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Sheetal Verma: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Seema Husain: Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, USA
Patricia Soteropoulos: Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, USA
Zhe Wang: Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
Roxanne Morris: Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
Gene Porter: WuXi AppTec, Plainsboro, New Jersey, USA
Gautam Agnihotri: WuXi AppTec, Plainsboro, New Jersey, USA
Padmini Salgame: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Sean Ekins: Collaborations Pharmaceuticals, Inc., Raleigh, North Carolina, USA
Kyu Y. Rhee: Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
Nancy Connell: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Véronique Dartois: Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
Matthew B. Neiditch: Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, USA
Joel S. Freundlich: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
David Alland: Division of Infectious Disease, Department of Medicine, and the Ruy V. Lourenco Center for the Study of Emerging and Reemerging Pathogens, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA

DOI: https://doi.org/10.1128/mBio.02101-17
Journal volume & issue: Vol. 9, no. 6

Abstract

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ABSTRACT We report GSK3011724A (DG167) as a binary inhibitor of β-ketoacyl-ACP synthase (KasA) in Mycobacterium tuberculosis. Genetic and biochemical studies established KasA as the primary target. The X-ray crystal structure of the KasA-DG167 complex refined to 2.0-Å resolution revealed two interacting DG167 molecules occupying nonidentical sites in the substrate-binding channel of KasA. The binding affinities of KasA to DG167 and its analog, 5g, which binds only once in the substrate-binding channel, were determined, along with the KasA-5g X-ray crystal structure. DG167 strongly augmented the in vitro activity of isoniazid (INH), leading to synergistic lethality, and also synergized in an acute mouse model of M. tuberculosis infection. Synergistic lethality correlated with a unique transcriptional signature, including upregulation of oxidoreductases and downregulation of molecular chaperones. The lead structure-activity relationships (SAR), pharmacokinetic profile, and detailed interactions with the KasA protein that we describe may be applied to evolve a next-generation therapeutic strategy for tuberculosis (TB). IMPORTANCE Cell wall biosynthesis inhibitors have proven highly effective for treating tuberculosis (TB). We discovered and validated members of the indazole sulfonamide class of small molecules as inhibitors of Mycobacterium tuberculosis KasA—a key component for biosynthesis of the mycolic acid layer of the bacterium’s cell wall and the same pathway as that inhibited by the first-line antitubercular drug isoniazid (INH). One lead compound, DG167, demonstrated synergistic lethality in combination with INH and a transcriptional pattern consistent with bactericidality and loss of persisters. Our results also detail a novel dual-binding mechanism for this compound as well as substantial structure-activity relationships (SAR) that may help in lead optimization activities. Together, these results suggest that KasA inhibition, specifically, that shown by the DG167 series, may be developed into a potent therapy that can synergize with existing antituberculars.

Published in mBio

ISSN: 2161-2129 (Print); 2150-7511 (Online)
Publisher: American Society for Microbiology
Country of publisher: United States
LCC subjects: Science: Microbiology
Website: https://journals.asm.org/journal/mbio

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