Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis

Ankita Punetha; Huy X. Ngo; Selina Y.L. Holbrook; Keith D. Green; Melisa J. Willby; Shilah A. Bonnett; Kyle Krieger; Kyle Krieger; Emily K. Dennis; James E. Posey; Tanya Parish; Tanya Parish; Oleg V. Tsodikov; Oleg V. Tsodikov; Sylvie Garneau-Tsodikova; Sylvie Garneau-Tsodikova

doi:10.1021/acschembio.0c00184

Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis

Ankita Punetha, Huy X. Ngo, Selina Y.L. Holbrook, Keith D. Green, Melisa J. Willby, Shilah A. Bonnett, Kyle Krieger, Kyle Krieger, Emily K. Dennis, James E. Posey, Tanya Parish, Tanya Parish, Oleg V. Tsodikov, Oleg V. Tsodikov, Sylvie Garneau-Tsodikova, Sylvie Garneau-Tsodikova

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Abstract

The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis (Mtb) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb, we designed and optimized structurally unique thieno[2,3-d]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-d]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro. This study showcases how structural information can guide Eis inhibitor design.

Original language	English
Pages (from-to)	1581-1594
Number of pages	14
Journal	ACS Chemical Biology
Volume	15
Issue number	6
DOIs	https://doi.org/10.1021/acschembio.0c00184
State	Published - Jun 19 2020

Bibliographical note

Funding Information:
This study was funded by a National Institutes of Health (NIH) Grant AI090048 (to S.G.-T.), a grant from the Firland Foundation (to S.G.-T.), a grant from the Center for Chemical Genomics (CCG) at the University of Michigan (to S.G.-T.), as well as by startup funds from the College of Pharmacy at the University of Kentucky (to S.G.-T. and O.V.T). We thank the UK PharmNMR Center (in the College of Pharmacy) for NMR support and S. Van Lanen for managing the LCMS system used in this study. We thank S. Vander Roest, M. Larsen, and P. Kirchhoff from the CCG at the University of Michigan for their help with HTS. We thank J. J. Johnson and R. M. Holmes for synthesizing and characterizing a few of the molecules presented in this manuscript. We thank C. Hou for assistance with the protein purification and crystallization. We also thank S. Chowdhury and B. Berube for discussion and technical assistance with metabolic stability assays. Use of trade names is for identification only and does not constitute endorsement by the U.S. Department of Health and Human Services, the U.S. Public Health Service, or the CDC. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the funding agency.

Publisher Copyright:
Copyright © 2020 American Chemical Society.

ASJC Scopus subject areas

Biochemistry
Molecular Medicine

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1021/acschembio.0c00184

Cite this

Punetha, A., Ngo, H. X., Holbrook, S. Y. L., Green, K. D., Willby, M. J., Bonnett, S. A., Krieger, K., Krieger, K., Dennis, E. K., Posey, J. E., Parish, T., Parish, T., Tsodikov, O. V., Tsodikov, O. V., Garneau-Tsodikova, S., & Garneau-Tsodikova, S. (2020). Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis. ACS Chemical Biology, 15(6), 1581-1594. https://doi.org/10.1021/acschembio.0c00184

@article{3e71ce5c2811450eab9d69e541a1fea2,

title = "Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis",

abstract = "The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis (Mtb) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb, we designed and optimized structurally unique thieno[2,3-d]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-d]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro. This study showcases how structural information can guide Eis inhibitor design.",

author = "Ankita Punetha and Ngo, {Huy X.} and Holbrook, {Selina Y.L.} and Green, {Keith D.} and Willby, {Melisa J.} and Bonnett, {Shilah A.} and Kyle Krieger and Kyle Krieger and Dennis, {Emily K.} and Posey, {James E.} and Tanya Parish and Tanya Parish and Tsodikov, {Oleg V.} and Tsodikov, {Oleg V.} and Sylvie Garneau-Tsodikova and Sylvie Garneau-Tsodikova",

note = "Funding Information: This study was funded by a National Institutes of Health (NIH) Grant AI090048 (to S.G.-T.), a grant from the Firland Foundation (to S.G.-T.), a grant from the Center for Chemical Genomics (CCG) at the University of Michigan (to S.G.-T.), as well as by startup funds from the College of Pharmacy at the University of Kentucky (to S.G.-T. and O.V.T). We thank the UK PharmNMR Center (in the College of Pharmacy) for NMR support and S. Van Lanen for managing the LCMS system used in this study. We thank S. Vander Roest, M. Larsen, and P. Kirchhoff from the CCG at the University of Michigan for their help with HTS. We thank J. J. Johnson and R. M. Holmes for synthesizing and characterizing a few of the molecules presented in this manuscript. We thank C. Hou for assistance with the protein purification and crystallization. We also thank S. Chowdhury and B. Berube for discussion and technical assistance with metabolic stability assays. Use of trade names is for identification only and does not constitute endorsement by the U.S. Department of Health and Human Services, the U.S. Public Health Service, or the CDC. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the funding agency. Publisher Copyright: Copyright {\textcopyright} 2020 American Chemical Society.",

year = "2020",

month = jun,

day = "19",

doi = "10.1021/acschembio.0c00184",

language = "English",

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Punetha, A, Ngo, HX, Holbrook, SYL, Green, KD, Willby, MJ, Bonnett, SA, Krieger, K, Krieger, K, Dennis, EK, Posey, JE, Parish, T, Parish, T, Tsodikov, OV, Tsodikov, OV , Garneau-Tsodikova, S & Garneau-Tsodikova, S 2020, 'Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis', ACS Chemical Biology, vol. 15, no. 6, pp. 1581-1594. https://doi.org/10.1021/acschembio.0c00184

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T1 - Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis

AU - Punetha, Ankita

AU - Ngo, Huy X.

AU - Holbrook, Selina Y.L.

AU - Green, Keith D.

AU - Willby, Melisa J.

AU - Bonnett, Shilah A.

AU - Krieger, Kyle

AU - Dennis, Emily K.

AU - Posey, James E.

AU - Parish, Tanya

AU - Tsodikov, Oleg V.

AU - Garneau-Tsodikova, Sylvie

N1 - Funding Information: This study was funded by a National Institutes of Health (NIH) Grant AI090048 (to S.G.-T.), a grant from the Firland Foundation (to S.G.-T.), a grant from the Center for Chemical Genomics (CCG) at the University of Michigan (to S.G.-T.), as well as by startup funds from the College of Pharmacy at the University of Kentucky (to S.G.-T. and O.V.T). We thank the UK PharmNMR Center (in the College of Pharmacy) for NMR support and S. Van Lanen for managing the LCMS system used in this study. We thank S. Vander Roest, M. Larsen, and P. Kirchhoff from the CCG at the University of Michigan for their help with HTS. We thank J. J. Johnson and R. M. Holmes for synthesizing and characterizing a few of the molecules presented in this manuscript. We thank C. Hou for assistance with the protein purification and crystallization. We also thank S. Chowdhury and B. Berube for discussion and technical assistance with metabolic stability assays. Use of trade names is for identification only and does not constitute endorsement by the U.S. Department of Health and Human Services, the U.S. Public Health Service, or the CDC. The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the funding agency. Publisher Copyright: Copyright © 2020 American Chemical Society.

PY - 2020/6/19

Y1 - 2020/6/19

N2 - The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis (Mtb) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb, we designed and optimized structurally unique thieno[2,3-d]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-d]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro. This study showcases how structural information can guide Eis inhibitor design.

AB - The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis (Mtb) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb, we designed and optimized structurally unique thieno[2,3-d]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-d]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro. This study showcases how structural information can guide Eis inhibitor design.

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Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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