Synergistic lethality of a binary inhibitor of mycobacterium tuberculosis 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 & 13 others 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

Research output: Contribution to journalArticle

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 sulfon-amide 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, spe-cifically, that shown by the DG167 series, may be developed into a potent therapy that can synergize with existing antituberculars.

Original languageEnglish (US)
Article numbere02101-17
JournalmBio
Volume9
Issue number6
DOIs
StatePublished - Nov 1 2018
Externally publishedYes

Fingerprint

Mycobacterium tuberculosis
Isoniazid
Structure-Activity Relationship
Cell Wall
Tuberculosis
Indazoles
X-Rays
Mycolic Acids
Antitubercular Agents
Mycobacterium Infections
Molecular Chaperones
Amides
Molecular Biology
Oxidoreductases
Up-Regulation
Down-Regulation
Pharmacokinetics
Therapeutics
Lead
Proteins

Keywords

  • Antitubercular
  • DG167
  • Drug development
  • Isoniazid
  • KasA
  • Mycobacterium tuberculosis
  • Mycolic acid biosynthesis
  • Synergistic lethality

ASJC Scopus subject areas

  • Microbiology
  • Virology

Cite this

Kumar, P., Capodagli, G. C., Awasthi, D., Shrestha, R., Maharaja, K., Sukheja, P., ... Alland, D. (2018). Synergistic lethality of a binary inhibitor of mycobacterium tuberculosis kasA. mBio, 9(6), [e02101-17]. https://doi.org/10.1128/mBio.02101-17

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

In: mBio, Vol. 9, No. 6, e02101-17, 01.11.2018.

Research output: Contribution to journalArticle

Kumar, P, Capodagli, GC, Awasthi, D, Shrestha, R, Maharaja, K, Sukheja, P, Li, SG, Inoyama, D, Zimmerman, M, Liang, HPH, Sarathy, J, Mina, M, Rasic, G, Russo, R, Perryman, AL, Richmann, T, Gupta, A, Singleton, E, Verma, S, Husain, S, Soteropoulos, P, Wang, Z, Morris, R, Porter, G, Agnihotri, G, Salgame, P, Ekins, S, Rhee, KY, Connell, N, Dartois, V, Neiditch, MB, Freundlich, JS & Alland, D 2018, 'Synergistic lethality of a binary inhibitor of mycobacterium tuberculosis kasA', mBio, vol. 9, no. 6, e02101-17. https://doi.org/10.1128/mBio.02101-17
Kumar P, Capodagli GC, Awasthi D, Shrestha R, Maharaja K, Sukheja P et al. Synergistic lethality of a binary inhibitor of mycobacterium tuberculosis kasA. mBio. 2018 Nov 1;9(6). e02101-17. https://doi.org/10.1128/mBio.02101-17
Kumar, Pradeep ; Capodagli, Glenn C. ; Awasthi, Divya ; Shrestha, Riju ; Maharaja, Karishma ; Sukheja, Paridhi ; Li, Shao Gang ; Inoyama, Daigo ; Zimmerman, Matthew ; Liang, Hsin Pin Ho ; Sarathy, Jansy ; Mina, Marizel ; Rasic, George ; Russo, Riccardo ; Perryman, Alexander L. ; Richmann, Todd ; Gupta, Aditi ; Singleton, Eric ; Verma, Sheetal ; Husain, Seema ; Soteropoulos, Patricia ; Wang, Zhe ; Morris, Roxanne ; Porter, Gene ; Agnihotri, Gautam ; Salgame, Padmini ; Ekins, Sean ; Rhee, Kyu Y. ; Connell, Nancy ; Dartois, Véronique ; Neiditch, Matthew B. ; Freundlich, Joel S. ; Alland, David. / Synergistic lethality of a binary inhibitor of mycobacterium tuberculosis kasA. In: mBio. 2018 ; Vol. 9, No. 6.
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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-{\AA} 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 sulfon-amide 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, spe-cifically, that shown by the DG167 series, may be developed into a potent therapy that can synergize with existing antituberculars.",
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AU - Kumar, Pradeep

AU - Capodagli, Glenn C.

AU - Awasthi, Divya

AU - Shrestha, Riju

AU - Maharaja, Karishma

AU - Sukheja, Paridhi

AU - Li, Shao Gang

AU - Inoyama, Daigo

AU - Zimmerman, Matthew

AU - Liang, Hsin Pin Ho

AU - Sarathy, Jansy

AU - Mina, Marizel

AU - Rasic, George

AU - Russo, Riccardo

AU - Perryman, Alexander L.

AU - Richmann, Todd

AU - Gupta, Aditi

AU - Singleton, Eric

AU - Verma, Sheetal

AU - Husain, Seema

AU - Soteropoulos, Patricia

AU - Wang, Zhe

AU - Morris, Roxanne

AU - Porter, Gene

AU - Agnihotri, Gautam

AU - Salgame, Padmini

AU - Ekins, Sean

AU - Rhee, Kyu Y.

AU - Connell, Nancy

AU - Dartois, Véronique

AU - Neiditch, Matthew B.

AU - Freundlich, Joel S.

AU - Alland, David

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N2 - 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 sulfon-amide 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, spe-cifically, that shown by the DG167 series, may be developed into a potent therapy that can synergize with existing antituberculars.

AB - 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 sulfon-amide 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, spe-cifically, that shown by the DG167 series, may be developed into a potent therapy that can synergize with existing antituberculars.

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KW - DG167

KW - Drug development

KW - Isoniazid

KW - KasA

KW - Mycobacterium tuberculosis

KW - Mycolic acid biosynthesis

KW - Synergistic lethality

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