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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Giorgini, F. et al. Histone deacetylase inhibition modulates kynurenine pathway activation in yeast, microglia, and mice expressing a mutant huntingtin fragment. J. Biol. Chem. 283, 7390–7400 (2008)
Giorgini, F., Guidetti, P., Nguyen, Q., Bennett, S. C. & Muchowski, P. J. A genomic screen in yeast implicates kynurenine 3-monooxygenase as a therapeutic target for Huntington disease. Nature Genet. 37, 526–531 (2005)
Zwilling, D. et al. Kynurenine 3-monooxygenase inhibition in blood ameliorates neurodegeneration. Cell 145, 863–874 (2011)
Campesan, S. et al. The kynurenine pathway modulates neurodegeneration in a Drosophila model of Huntington’s disease. Curr. Biol. 21, 961–966 (2011)
Green, E. W. et al. Drosophila eye color mutants as therapeutic tools for Huntington disease. Fly 6, 117–120 (2012)
Schwarcz, R., Bruno, J. P., Muchowski, P. J. & Wu, H.-Q. Kynurenines in the mammalian brain: when physiology meets pathology. Nature Rev. Neurosci. 13, 465–477 (2012)
Platten, M., Litzenburger, U. & Wick, W. The aryl hydrocarbon receptor in tumor immunity. Oncoimmunology 1, 396–397 (2012)
Liu, X., Newton, R. C., Friedman, S. M. & Scherle, P. A. Indoleamine 2,3-dioxygenase, an emerging target for anti-cancer therapy. Curr. Cancer Drug Targets 9, 938–952 (2009)
Filippini, P. et al. Emerging concepts on inhibitors of indoleamine 2,3-dioxygenase in rheumatic diseases. Curr. Med. Chem. 19, 5381–5393 (2012)
Stone, T. W. & Perkins, M. N. Quinolinic acid: a potent endogenous excitant at amino acid receptors in CNS. Eur. J. Pharmacol. 72, 411–412 (1981)
Schwarcz, R., Whetsell, W. O., Jr & Mangano, R. M. Quinolinic acid: an endogenous metabolite that produces axon-sparing lesions in rat brain. Science 219, 316–318 (1983)
Okuda, S., Nishiyama, N., Saito, H. & Katsuki, H. Hydrogen peroxide-mediated neuronal cell death induced by an endogenous neurotoxin, 3-hydroxykynurenine. Proc. Natl Acad. Sci. USA 93, 12553–12558 (1996)
Copeland, C. S., Neale, S. A. & Salt, T. E. Actions of xanthurenic acid, a putative endogenous group II metabotropic glutamate receptor agonist, on sensory transmission in the thalamus. Neuropharmacology 66, 133–142 (2013)
Fazio, F. et al. Cinnabarinic acid, an endogenous metabolite of the kynurenine pathway, activates type 4 metabotropic glutamate receptors. Mol. Pharmacol. 81, 643–656 (2012)
Guillemin, G. J. et al. Characterization of the kynurenine pathway in human neurons. J. Neurosci. 27, 12884–12892 (2007)
Guillemin, G. J., Smith, D. G., Smythe, G. A., Armati, P. J. & Brew, B. J. Expression of the kynurenine pathway enzymes in human microglia and macrophages. Adv. Exp. Med. Biol. 527, 105–112 (2003)
Cozzi, A., Carpenedo, R. & Moroni, F. Kynurenine hydroxylase inhibitors reduce ischemic brain damage: studies with (m-nitrobenzoyl)-alanine (mNBA) and 3,4-dimethoxy-[-N-4-(nitrophenyl)thiazol-2yl]-benzenesulfonamide (Ro 61–8048) in models of focal or global brain ischemia. J. Cereb. Blood Flow Metab. 19, 771–777 (1999)
Moroni, F. et al. Studies on the neuroprotective action of kynurenine mono-oxygenase inhibitors in post-ischemic brain damage. Adv. Exp. Med. Biol. 527, 127–136 (2003)
Richter, A. & Hamann, M. The kynurenine 3-hydroxylase inhibitor Ro 61–8048 improves dystonia in a genetic model of paroxysmal dyskinesia. Eur. J. Pharmacol. 478, 47–52 (2003)
Samadi, P. et al. Effect of kynurenine 3-hydroxylase inhibition on the dyskinetic and antiparkinsonian responses to levodopa in Parkinsonian monkeys. Mov. Disord. 20, 792–802 (2005)
Clark, C. J. et al. Prolonged survival of a murine model of cerebral malaria by kynurenine pathway inhibition. Infect. Immun. 73, 5249–5251 (2005)
Reinhart, P. H. & Kelly, J. W. Treating the periphery to ameliorate neurodegenerative diseases. Cell 145, 813–814 (2011)
Sapko, M. T. et al. Endogenous kynurenate controls the vulnerability of striatal neurons to quinolinate: implications for Huntingtons’s disease. Exp. Neurol. 197, 31–40 (2006)
Ceresoli-Borroni, G., Guidetti, P., Amori, L., Pellicciari, R. & Schwarcz, R. Perinatal kynurenine 3-hydroxylase inhibition in rodents: pathophysiological implications. J. Neurosci. Res. 85, 845–854 (2007)
Uemura, T. & Hirai, K. l-kynurenine 3-monooxygenase from mitochondrial outer membrane of pig liver: purification, some properties, and monoclonal antibodies directed to the enzyme. J. Biochem. 123, 253–262 (1998)
Palfey, B. A. & McDonald, C. A. Control of catalysis in flavin-dependent monooxygenases. Arch. Biochem. Biophys. 493, 26–36 (2010)
van Berkel, W. J. H., Kamerbeek, N. M. & Fraaije, M. W. Flavoprotein monooxygenases, a diverse class of oxidative biocatalysts. J. Biotechnol. 124, 670–689 (2006)
McCulloch, K. M., Mukherjee, T., Begley, T. P. & Ealick, S. E. Structure of the PLP degradative enzyme 2-methyl-3- hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti MAFF303099 and its mechanistic implications. Biochemistry 48, 4139–4149 (2009)
Ortiz-Maldonado, M., Ballou, D. P. & Massey, V. A rate-limiting conformational change of the flavin in p-hydroxybenzoate hydroxylase is necessary for ligand exchange and catalysis: studies with 8-mercapto- and 8-hydroxy-flavins. Biochemistry 40, 1091–1101 (2001)
Fukui, S., Schwarcz, R., Rapoport, S. I., Takada, Y. & Smith, Q. R. Blood–brain barrier transport of kynurenines: implications for brain synthesis and metabolism. J. Neurochem. 56, 2007–2017 (1991)
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)
McCoy, A. J., Storoni, L. C. & Read, R. J. Simple algorithm for a maximum-likelihood SAD function. Acta Crystallogr. D 60, 1220–1228 (2004)
Terwilliger, T. C. et al. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr. D 64, 61–69 (2008)
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)
Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005)
Cornell, W. D. et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179–5197 (1995)
Jakalian, A., Jack, D. B. & Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 23, 1623–1641 (2002)
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.
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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