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Structural basis of kynurenine 3-monooxygenase inhibition

Abstract

Inhibition of kynurenine 3-monooxygenase (KMO), an enzyme in the eukaryotic tryptophan catabolic pathway (that is, kynurenine pathway), leads to amelioration of Huntington’s-disease-relevant phenotypes in yeast, fruitfly and mouse models1,2,3,4,5, as well as in a mouse model of Alzheimer’s disease3. KMO is a flavin adenine dinucleotide (FAD)-dependent monooxygenase and is located in the outer mitochondrial membrane where it converts l-kynurenine to 3-hydroxykynurenine. Perturbations in the levels of kynurenine pathway metabolites have been linked to the pathogenesis of a spectrum of brain disorders6, as well as cancer7,8 and several peripheral inflammatory conditions9. Despite the importance of KMO as a target for neurodegenerative disease, the molecular basis of KMO inhibition by available lead compounds has remained unknown. Here we report the first crystal structure of Saccharomyces cerevisiae KMO, in the free form and in complex with the tight-binding inhibitor UPF 648. UPF 648 binds close to the FAD cofactor and perturbs the local active-site structure, preventing productive binding of the substrate l-kynurenine. Functional assays and targeted mutagenesis reveal that the active-site architecture and UPF 648 binding are essentially identical in human KMO, validating the yeast KMO–UPF 648 structure as a template for structure-based drug design. This will inform the search for new KMO inhibitors that are able to cross the blood–brain barrier in targeted therapies against neurodegenerative diseases such as Huntington’s, Alzheimer’s and Parkinson’s diseases.

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Figure 1: Inhibition of KMO by UPF 648.
Figure 2: Yeast KMO crystal structure.
Figure 3: The Saccharomyces cerevisiae KMO active site.
Figure 4: Mechanism and importance of Arg 83.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in the Protein Data Bank (http://www.pdb.org) under accession numbers 4J2W, 4J31, 4J33, 4J36 and 4J34.

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Acknowledgements

We thank R. Schwarcz for supplying UPF 648. We also thank E. McKenzie for expressing human KMO. We also thank Diamond Light Source for access to MX beamlines.

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Authors

Contributions

N.S.S., F.G., D.L. and T.F.O. initiated the project, designed experiments, analysed data and wrote the manuscript; M.A. cloned purified and crystallized proteins and performed biochemical assays; C.L. crystallized proteins, collected and processed diffraction data; D.J.H. developed and analysed some of the biochemical assays; P.L. performed molecular modelling of l-KYN binding.

Corresponding author

Correspondence to Nigel S. Scrutton.

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The authors declare no competing financial interests.

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Amaral, M., Levy, C., Heyes, D. et al. Structural basis of kynurenine 3-monooxygenase inhibition. Nature 496, 382–385 (2013). https://doi.org/10.1038/nature12039

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