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Structural basis of kynurenine 3-monooxygenase inhibition


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 ( under accession numbers 4J2W, 4J31, 4J33, 4J36 and 4J34.


  1. 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)

    Article  CAS  Google Scholar 

  2. 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)

    Article  CAS  Google Scholar 

  3. Zwilling, D. et al. Kynurenine 3-monooxygenase inhibition in blood ameliorates neurodegeneration. Cell 145, 863–874 (2011)

    Article  CAS  Google Scholar 

  4. Campesan, S. et al. The kynurenine pathway modulates neurodegeneration in a Drosophila model of Huntington’s disease. Curr. Biol. 21, 961–966 (2011)

    Article  CAS  Google Scholar 

  5. Green, E. W. et al. Drosophila eye color mutants as therapeutic tools for Huntington disease. Fly 6, 117–120 (2012)

    Article  CAS  Google Scholar 

  6. 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)

    Article  CAS  Google Scholar 

  7. Platten, M., Litzenburger, U. & Wick, W. The aryl hydrocarbon receptor in tumor immunity. Oncoimmunology 1, 396–397 (2012)

    Article  Google Scholar 

  8. 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)

    Article  CAS  Google Scholar 

  9. Filippini, P. et al. Emerging concepts on inhibitors of indoleamine 2,3-dioxygenase in rheumatic diseases. Curr. Med. Chem. 19, 5381–5393 (2012)

    Article  CAS  Google Scholar 

  10. 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)

    Article  CAS  Google Scholar 

  11. 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)

    Article  ADS  CAS  Google Scholar 

  12. 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)

    Article  ADS  CAS  Google Scholar 

  13. 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)

    Article  CAS  Google Scholar 

  14. 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)

    Article  CAS  Google Scholar 

  15. Guillemin, G. J. et al. Characterization of the kynurenine pathway in human neurons. J. Neurosci. 27, 12884–12892 (2007)

    Article  CAS  Google Scholar 

  16. 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)

    Article  CAS  Google Scholar 

  17. 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)

    Article  CAS  Google Scholar 

  18. 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)

    Article  CAS  Google Scholar 

  19. 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)

    Article  CAS  Google Scholar 

  20. 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)

    Article  Google Scholar 

  21. Clark, C. J. et al. Prolonged survival of a murine model of cerebral malaria by kynurenine pathway inhibition. Infect. Immun. 73, 5249–5251 (2005)

    Article  CAS  Google Scholar 

  22. Reinhart, P. H. & Kelly, J. W. Treating the periphery to ameliorate neurodegenerative diseases. Cell 145, 813–814 (2011)

    Article  CAS  Google Scholar 

  23. 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)

    Article  CAS  Google Scholar 

  24. 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)

    Article  CAS  Google Scholar 

  25. 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)

    Article  CAS  Google Scholar 

  26. Palfey, B. A. & McDonald, C. A. Control of catalysis in flavin-dependent monooxygenases. Arch. Biochem. Biophys. 493, 26–36 (2010)

    Article  CAS  Google Scholar 

  27. 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)

    Article  CAS  Google Scholar 

  28. 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)

    Article  CAS  Google Scholar 

  29. 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)

    Article  CAS  Google Scholar 

  30. 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)

    Article  CAS  Google Scholar 

  31. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

    Article  CAS  Google Scholar 

  32. McCoy, A. J., Storoni, L. C. & Read, R. J. Simple algorithm for a maximum-likelihood SAD function. Acta Crystallogr. D 60, 1220–1228 (2004)

    Article  Google Scholar 

  33. 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)

    Article  CAS  Google Scholar 

  34. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  35. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    Article  CAS  Google Scholar 

  36. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  37. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)

    Article  CAS  Google Scholar 

  38. Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005)

    Article  CAS  Google Scholar 

  39. 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)

    Article  CAS  Google Scholar 

  40. 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)

    Article  CAS  Google Scholar 

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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 and Affiliations



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).

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