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
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.
