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

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...

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Bibliographic Details
Published in:Biochimica et biophysica acta. General subjects 2023-07, Vol.1867 (7), p.130378-130378, Article 130378
Main Authors: Teixeira, Olívia, Martins, Ingrid Bernardes Santana, Froes, Thamires Quadros, de Araujo, Alexandre Suman, Nonato, Maria Cristina
Format: Article
Language:English
Subjects:
Binding Sites
Dihydroorotate Dehydrogenase
Enzyme kinetics
Homology modeling
Humans
In silico solvent mapping
Inhibition
Molecular dynamics simulation
Mycobacterium tuberculosis - metabolism
Oxidation-Reduction
Oxidoreductases Acting on CH-CH Group Donors - chemistry
Oxidoreductases Acting on CH-CH Group Donors - metabolism
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Summary: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. [Display omitted] •MtDHODH catalyzes dihydroorotate (DHO) oxidation by a ping-pong mechanism.•MtDHODH was evaluated by in silico solvent mapping and molecular dynamics studies.•Coenzyme Q0 (Q0) was identified as a DHO-competitive inhibitor for class 2 DHODHs.•Inhibitor selectivity for MtDHODH over HsDHODH can be achieved.
ISSN:0304-4165
1872-8006
DOI:10.1016/j.bbagen.2023.130378