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Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase

The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We pre...

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Autores principales: Kim, Heung-Bok, Bacik, John-Paul, Wu, Ruilian, Jha, Ramesh K., Hebron, Michaeline, Triandafillou, Catherine, McCown, Joseph E., Baek, Nam-In, Kim, Jeong Han, Kim, Young Jae, Goulding, Celia W., Strauss, Charlie E. M., Schmidt, Jurgen G., Shetye, Gauri S., Ryoo, Sungweon, Jo, Eun-Kyeong, Jeon, Young Ho, Hung, Li-Wei, Terwilliger, Thomas C., Kim, Chang-Yub
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9671377/
https://www.ncbi.nlm.nih.gov/pubmed/36395154
http://dx.doi.org/10.1371/journal.pone.0277670
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author Kim, Heung-Bok
Bacik, John-Paul
Wu, Ruilian
Jha, Ramesh K.
Hebron, Michaeline
Triandafillou, Catherine
McCown, Joseph E.
Baek, Nam-In
Kim, Jeong Han
Kim, Young Jae
Goulding, Celia W.
Strauss, Charlie E. M.
Schmidt, Jurgen G.
Shetye, Gauri S.
Ryoo, Sungweon
Jo, Eun-Kyeong
Jeon, Young Ho
Hung, Li-Wei
Terwilliger, Thomas C.
Kim, Chang-Yub
author_facet Kim, Heung-Bok
Bacik, John-Paul
Wu, Ruilian
Jha, Ramesh K.
Hebron, Michaeline
Triandafillou, Catherine
McCown, Joseph E.
Baek, Nam-In
Kim, Jeong Han
Kim, Young Jae
Goulding, Celia W.
Strauss, Charlie E. M.
Schmidt, Jurgen G.
Shetye, Gauri S.
Ryoo, Sungweon
Jo, Eun-Kyeong
Jeon, Young Ho
Hung, Li-Wei
Terwilliger, Thomas C.
Kim, Chang-Yub
author_sort Kim, Heung-Bok
collection PubMed
description The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies.
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spelling pubmed-96713772022-11-18 Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase Kim, Heung-Bok Bacik, John-Paul Wu, Ruilian Jha, Ramesh K. Hebron, Michaeline Triandafillou, Catherine McCown, Joseph E. Baek, Nam-In Kim, Jeong Han Kim, Young Jae Goulding, Celia W. Strauss, Charlie E. M. Schmidt, Jurgen G. Shetye, Gauri S. Ryoo, Sungweon Jo, Eun-Kyeong Jeon, Young Ho Hung, Li-Wei Terwilliger, Thomas C. Kim, Chang-Yub PLoS One Research Article The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies. Public Library of Science 2022-11-17 /pmc/articles/PMC9671377/ /pubmed/36395154 http://dx.doi.org/10.1371/journal.pone.0277670 Text en https://creativecommons.org/publicdomain/zero/1.0/This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Kim, Heung-Bok
Bacik, John-Paul
Wu, Ruilian
Jha, Ramesh K.
Hebron, Michaeline
Triandafillou, Catherine
McCown, Joseph E.
Baek, Nam-In
Kim, Jeong Han
Kim, Young Jae
Goulding, Celia W.
Strauss, Charlie E. M.
Schmidt, Jurgen G.
Shetye, Gauri S.
Ryoo, Sungweon
Jo, Eun-Kyeong
Jeon, Young Ho
Hung, Li-Wei
Terwilliger, Thomas C.
Kim, Chang-Yub
Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase
title Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase
title_full Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase
title_fullStr Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase
title_full_unstemmed Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase
title_short Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase
title_sort label-free affinity screening, design and synthesis of inhibitors targeting the mycobacterium tuberculosis l-alanine dehydrogenase
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9671377/
https://www.ncbi.nlm.nih.gov/pubmed/36395154
http://dx.doi.org/10.1371/journal.pone.0277670
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