Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition

Detalhes bibliográficos
Autor(a) principal: Teixeira, Olívia
Data de Publicação: 2023
Outros Autores: Martins, Ingrid Bernardes Santana [UNESP], Froes, Thamires Quadros, de Araujo, Alexandre Suman [UNESP], Nonato, Maria Cristina
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1016/j.bbagen.2023.130378
http://hdl.handle.net/11449/248818
Resumo: Tuberculosis (TB) is a leading cause of death worldwide. TB represents a serious public health threat, and it is characterized by high transmission rates, prevalence in impoverished regions, and high co-infection rates with HIV. Moreover, the serious side effects of long-term treatment that decrease patient adherence, and the emergence of multi-resistant strains of Mycobacterium tuberculosis, the causing agent of TBs, pose several challenges for its eradication. The search for a new TB treatment is necessary and urgent. Dihydroorotate dehydrogenase (DHODH) is responsible for the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. DHODH has been considered an attractive target against infectious diseases. As a first step towards exploiting DHODH as a drug target against TB, we performed a full kinetic characterization of both bacterial MtDHODH and its human ortholog (HsDHDOH) using both substrates coenzyme Q0 (Q0) and vitamin K3 (K3). MtDHODH follows a ping-pong mechanism of catalysis and shares similar catalytic parameters with the human enzyme. Serendipitously, Q0 was found to inhibit MtDHODH (KI (Q0) = 138 ± 31 μM). To the best of our knowledge, Q0 is the first non-orotate like dihydroorotate-competitive inhibitor for class 2 DHODHs ever described. Molecular dynamics simulations along with in silico solvent mapping allowed us to successfully probe protein flexibility and correlate it with the druggability of binding sites. Together, our results provide the starting point for the design of a new generation of potent and selective inhibitors against MtDHODH.
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spelling Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibitionEnzyme kineticsHomology modelingIn silico solvent mappingInhibitionMolecular dynamics simulationTuberculosis (TB) is a leading cause of death worldwide. TB represents a serious public health threat, and it is characterized by high transmission rates, prevalence in impoverished regions, and high co-infection rates with HIV. Moreover, the serious side effects of long-term treatment that decrease patient adherence, and the emergence of multi-resistant strains of Mycobacterium tuberculosis, the causing agent of TBs, pose several challenges for its eradication. The search for a new TB treatment is necessary and urgent. Dihydroorotate dehydrogenase (DHODH) is responsible for the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. DHODH has been considered an attractive target against infectious diseases. As a first step towards exploiting DHODH as a drug target against TB, we performed a full kinetic characterization of both bacterial MtDHODH and its human ortholog (HsDHDOH) using both substrates coenzyme Q0 (Q0) and vitamin K3 (K3). MtDHODH follows a ping-pong mechanism of catalysis and shares similar catalytic parameters with the human enzyme. Serendipitously, Q0 was found to inhibit MtDHODH (KI (Q0) = 138 ± 31 μM). To the best of our knowledge, Q0 is the first non-orotate like dihydroorotate-competitive inhibitor for class 2 DHODHs ever described. Molecular dynamics simulations along with in silico solvent mapping allowed us to successfully probe protein flexibility and correlate it with the druggability of binding sites. Together, our results provide the starting point for the design of a new generation of potent and selective inhibitors against MtDHODH.Centro Nacional de Processamento de Alto Desempenho em São PauloUniversidade Estadual PaulistaFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)Laboratório de Cristalografia de Proteínas Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, SPCenter for the Research and Advancement in Fragments and molecular Targets (CRAFT) Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo, SPInstituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de Janeiro, RJInstituto de Biociências Letras e Ciências Exatas Departamento de Física UNESP, SPInstituto de Biociências Letras e Ciências Exatas Departamento de Física UNESP, SPFAPESP: 2019/25532-1FAPESP: 2020/16316-0CNPq: 409272/2021-3CAPES: 88887.643249/2021-00Universidade de São Paulo (USP)Universidade Federal do Rio de Janeiro (UFRJ)Universidade Estadual Paulista (UNESP)Teixeira, OlíviaMartins, Ingrid Bernardes Santana [UNESP]Froes, Thamires Quadrosde Araujo, Alexandre Suman [UNESP]Nonato, Maria Cristina2023-07-29T13:54:31Z2023-07-29T13:54:31Z2023-07-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.bbagen.2023.130378Biochimica et Biophysica Acta - General Subjects, v. 1867, n. 7, 2023.1872-80060304-4165http://hdl.handle.net/11449/24881810.1016/j.bbagen.2023.1303782-s2.0-85159115113Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBiochimica et Biophysica Acta - General Subjectsinfo:eu-repo/semantics/openAccess2023-07-29T13:54:31Zoai:repositorio.unesp.br:11449/248818Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:47:12.342188Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
title Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
spellingShingle Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
Teixeira, Olívia
Enzyme kinetics
Homology modeling
In silico solvent mapping
Inhibition
Molecular dynamics simulation
title_short Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
title_full Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
title_fullStr Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
title_full_unstemmed Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
title_sort Kinetic and structural studies of Mycobacterium tuberculosis dihydroorotate dehydrogenase reveal new insights into class 2 DHODH inhibition
author Teixeira, Olívia
author_facet Teixeira, Olívia
Martins, Ingrid Bernardes Santana [UNESP]
Froes, Thamires Quadros
de Araujo, Alexandre Suman [UNESP]
Nonato, Maria Cristina
author_role author
author2 Martins, Ingrid Bernardes Santana [UNESP]
Froes, Thamires Quadros
de Araujo, Alexandre Suman [UNESP]
Nonato, Maria Cristina
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidade de São Paulo (USP)
Universidade Federal do Rio de Janeiro (UFRJ)
Universidade Estadual Paulista (UNESP)
dc.contributor.author.fl_str_mv Teixeira, Olívia
Martins, Ingrid Bernardes Santana [UNESP]
Froes, Thamires Quadros
de Araujo, Alexandre Suman [UNESP]
Nonato, Maria Cristina
dc.subject.por.fl_str_mv Enzyme kinetics
Homology modeling
In silico solvent mapping
Inhibition
Molecular dynamics simulation
topic Enzyme kinetics
Homology modeling
In silico solvent mapping
Inhibition
Molecular dynamics simulation
description Tuberculosis (TB) is a leading cause of death worldwide. TB represents a serious public health threat, and it is characterized by high transmission rates, prevalence in impoverished regions, and high co-infection rates with HIV. Moreover, the serious side effects of long-term treatment that decrease patient adherence, and the emergence of multi-resistant strains of Mycobacterium tuberculosis, the causing agent of TBs, pose several challenges for its eradication. The search for a new TB treatment is necessary and urgent. Dihydroorotate dehydrogenase (DHODH) is responsible for the stereospecific oxidation of (S)-dihydroorotate (DHO) to orotate during the fourth and only redox step of the de novo pyrimidine nucleotide biosynthetic pathway. DHODH has been considered an attractive target against infectious diseases. As a first step towards exploiting DHODH as a drug target against TB, we performed a full kinetic characterization of both bacterial MtDHODH and its human ortholog (HsDHDOH) using both substrates coenzyme Q0 (Q0) and vitamin K3 (K3). MtDHODH follows a ping-pong mechanism of catalysis and shares similar catalytic parameters with the human enzyme. Serendipitously, Q0 was found to inhibit MtDHODH (KI (Q0) = 138 ± 31 μM). To the best of our knowledge, Q0 is the first non-orotate like dihydroorotate-competitive inhibitor for class 2 DHODHs ever described. Molecular dynamics simulations along with in silico solvent mapping allowed us to successfully probe protein flexibility and correlate it with the druggability of binding sites. Together, our results provide the starting point for the design of a new generation of potent and selective inhibitors against MtDHODH.
publishDate 2023
dc.date.none.fl_str_mv 2023-07-29T13:54:31Z
2023-07-29T13:54:31Z
2023-07-01
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1016/j.bbagen.2023.130378
Biochimica et Biophysica Acta - General Subjects, v. 1867, n. 7, 2023.
1872-8006
0304-4165
http://hdl.handle.net/11449/248818
10.1016/j.bbagen.2023.130378
2-s2.0-85159115113
url http://dx.doi.org/10.1016/j.bbagen.2023.130378
http://hdl.handle.net/11449/248818
identifier_str_mv Biochimica et Biophysica Acta - General Subjects, v. 1867, n. 7, 2023.
1872-8006
0304-4165
10.1016/j.bbagen.2023.130378
2-s2.0-85159115113
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Biochimica et Biophysica Acta - General Subjects
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
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