The Molecular Structure of Epoxide Hydrolase B from Mycobacterium tuberculosis and Its Complex with a Urea-Based Inhibitor

Bichitra K. Biswal, Christophe Morisseau, Grace Garen, Maia M. Cherney, Craig Garen, Chunying Niu, Bruce D. Hammock, Michael N G James

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Mycobacterium tuberculosis (Mtb), the intracellular pathogen that infects macrophages primarily, is the causative agent of the infectious disease tuberculosis in humans. The Mtb genome encodes at least six epoxide hydrolases (EHs A to F). EHs convert epoxides to trans-dihydrodiols and have roles in drug metabolism as well as in the processing of signaling molecules. Herein, we report the crystal structures of unbound Mtb EHB and Mtb EHB bound to a potent, low-nanomolar (IC50 ≈ 19 nM) urea-based inhibitor at 2.1 and 2.4 Å resolution, respectively. The enzyme is a homodimer; each monomer adopts the classical α/β hydrolase fold that composes the catalytic domain; there is a cap domain that regulates access to the active site. The catalytic triad, comprising Asp104, His333 and Asp302, protrudes from the catalytic domain into the substrate binding cavity between the two domains. The urea portion of the inhibitor is bound in the catalytic cavity, mimicking, in part, the substrate binding; the two urea nitrogen atoms donate hydrogen bonds to the nucleophilic carboxylate of Asp104, and the carbonyl oxygen of the urea moiety receives hydrogen bonds from the phenolic oxygen atoms of Tyr164 and Tyr272. The phenolic oxygen groups of these two residues provide electrophilic assistance during the epoxide hydrolytic cleavage. Upon inhibitor binding, the binding-site residues undergo subtle structural rearrangement. In particular, the side chain of Ile137 exhibits a rotation of around 120° about its Cα-Cβ bond in order to accommodate the inhibitor. These findings have not only shed light on the enzyme mechanism but also have opened a path for the development of potent inhibitors with good pharmacokinetic profiles against all Mtb EHs of the α/β type.

Original languageEnglish (US)
Pages (from-to)897-912
Number of pages16
JournalJournal of Molecular Biology
Volume381
Issue number4
DOIs
StatePublished - Sep 12 2008

Fingerprint

Epoxide Hydrolases
Molecular Structure
Mycobacterium tuberculosis
Urea
Catalytic Domain
Epoxy Compounds
Oxygen
Hydrogen
Hydrolases
Enzymes
Inhibitory Concentration 50
Communicable Diseases
Tuberculosis
Nitrogen
Pharmacokinetics
Macrophages
Binding Sites
Genome
Pharmaceutical Preparations

Keywords

  • enzyme mechanism
  • epoxide hydrolase
  • hydrolase fold
  • inhibitor design
  • Mycobacterium tuberculosis

ASJC Scopus subject areas

  • Virology

Cite this

The Molecular Structure of Epoxide Hydrolase B from Mycobacterium tuberculosis and Its Complex with a Urea-Based Inhibitor. / Biswal, Bichitra K.; Morisseau, Christophe; Garen, Grace; Cherney, Maia M.; Garen, Craig; Niu, Chunying; Hammock, Bruce D.; James, Michael N G.

In: Journal of Molecular Biology, Vol. 381, No. 4, 12.09.2008, p. 897-912.

Research output: Contribution to journalArticle

Biswal, BK, Morisseau, C, Garen, G, Cherney, MM, Garen, C, Niu, C, Hammock, BD & James, MNG 2008, 'The Molecular Structure of Epoxide Hydrolase B from Mycobacterium tuberculosis and Its Complex with a Urea-Based Inhibitor', Journal of Molecular Biology, vol. 381, no. 4, pp. 897-912. https://doi.org/10.1016/j.jmb.2008.06.030
Biswal, Bichitra K. ; Morisseau, Christophe ; Garen, Grace ; Cherney, Maia M. ; Garen, Craig ; Niu, Chunying ; Hammock, Bruce D. ; James, Michael N G. / The Molecular Structure of Epoxide Hydrolase B from Mycobacterium tuberculosis and Its Complex with a Urea-Based Inhibitor. In: Journal of Molecular Biology. 2008 ; Vol. 381, No. 4. pp. 897-912.
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AU - Cherney, Maia M.

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AU - Niu, Chunying

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