From structural biology to designing therapy for inborn errors of metabolism

Journal of Inherited Metabolic Disease

Volumn 39, Issue 4, 2016, Pages 489-498

  Yue, Wyatt W ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; COBALAMIN; ENZYME; GLYCOGEN; PROTEIN;

ALLOSTERISM; ARTICLE; BIOCHEMICAL ANALYSIS; BIOLOGY; CATALYSIS; COWORKER; ENZYME DEFECT; ENZYME STRUCTURE; GLYCOGEN METABOLISM; HUMAN; INBORN ERROR OF METABOLISM; MOLECULE; MUTATION; PROTEIN PROTEIN INTERACTION; CHEMISTRY; DRUG DEVELOPMENT; METABOLIC ENGINEERING; METABOLISM; MOLECULAR LIBRARY; PROCEDURES;

COMPUTATIONAL BIOLOGY; DRUG DISCOVERY; HUMANS; METABOLIC ENGINEERING; METABOLISM, INBORN ERRORS; MOLECULAR CHAPERONES; PROTEINS; SMALL MOLECULE LIBRARIES;

EID: 84973121809     PISSN: 01418955     EISSN: 15732665     Source Type: Journal    
DOI: 10.1007/s10545-016-9923-3     Document Type: Article

References (55)

1. Arakawa T, Ejima D, Kita Y, Tsumoto K (2006) Small molecule pharmacological chaperones: from thermodynamic stabilization to pharmaceutical drugs. Biochim Biophys Acta 1764:1677–1687
2. Balmer C, Pandey AV, Rufenacht V et al (2014) Mutations and polymorphisms in the human argininosuccinate lyase (ASL) gene. Hum Mutat 35:27–35
3. Bartesaghi A, Merk A, Banerjee S et al (2015) 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor. Science 348:1147–1151
4. Bateman KS, Cherney MM, Mahuran DJ, Tropak M, James MN (2011) Crystal structure of beta-hexosaminidase B in complex with pyrimethamine, a potential pharmacological chaperone. J Med Chem 54:1421–1429
5. Beaulieu CL, Samuels ME, Ekins S et al (2012) A generalizable pre-clinical research approach for orphan disease therapy. Orphanet J Rare Dis 7:39
6. Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE (2013) Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 14:681–691
7. Boyd RE, Lee G, Rybczynski P et al (2013) Pharmacological chaperones as therapeutics for lysosomal storage diseases. J Med Chem 56:2705–2725
8. Burda P, Schafer A, Suormala T et al (2015) Insights into severe 5,10-methylenetetrahydrofolate reductase deficiency: molecular genetic and enzymatic characterization of 76 patients. Hum Mutat 36:611–621
9. Chaikuad A, Froese DS, Berridge G, von Delft F, Oppermann U, Yue WW (2011) Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis. Proc Natl Acad Sci U S A 108:21028–21033
10. Ebrahimi-Fakhari D, Saffari A, Wahlster L, et al (2016) Congenital disorders of autophagy: an emerging novel class of inborn errors of neuro-metabolism. Brain 139:317–337
11. Forny P, Froese DS, Suormala T, Yue WW, Baumgartner MR (2014) Functional characterization and categorization of missense mutations that cause methylmalonyl-CoA mutase (MUT) deficiency. Hum Mutat 35:1449–1458
12. Froese DS, Gravel RA (2010) Genetic disorders of vitamin B12 metabolism: eight complementation groups — eight genes. Expert Rev Mol Med 12:e37
13. Froese DS, Kochan G, Muniz JR et al (2010) Structures of the human GTPase MMAA and vitamin B12-dependent methylmalonyl-CoA mutase and insight into their complex formation. J Biol Chem 285:38204–38213
14. Froese DS, Krojer T, Wu X et al (2012) Structure of MMACHC reveals an arginine-rich pocket and a domain-swapped dimer for its B12 processing function. Biochemistry 51:5083–5090
15. Froese DS, Forouhar F, Tran TH et al (2013) Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations. Structure 21:1182–1192
16. Froese DS, Kopec J, Fitzpatrick F et al (2015a) Structural insights into the MMACHC-MMADHC protein complex involved in vitamin B12 trafficking. J Biol Chem 290:29167–29177
17. Froese DS, Michaeli A, McCorvie TJ et al (2015b) Structural basis of glycogen branching enzyme deficiency and pharmacologic rescue by rational peptide design. Hum Mol Genet 24:5667–5676
18. Guce AI, Clark NE, Rogich JJ, Garman SC (2011) The molecular basis of pharmacological chaperoning in human alpha-galactosidase. Chem Biol 18:1521–1526
19. Jaffe EK, Lawrence SH (2012) Allostery and the dynamic oligomerization of porphobilinogen synthase. Arch Biochem Biophys 519:144–153
20. Jaffe EK, Stith L, Lawrence SH, Andrake M, Dunbrack RL Jr (2013) A new model for allosteric regulation of phenylalanine hydroxylase: implications for disease and therapeutics. Arch Biochem Biophys 530:73–82
21. Jorge-Finnigan A, Brasil S, Underhaug J et al (2013) Pharmacological chaperones as a potential therapeutic option in methylmalonic aciduria cblB type. Hum Mol Genet 22:3680–3689
22. Kakhlon O, Glickstein H, Feinstein N et al (2013) Polyglucosan neurotoxicity caused by glycogen branching enzyme deficiency can be reversed by inhibition of glycogen synthase. J Neurochem 127:101–113
23. Kang TS, Stevens RC (2009) Structural aspects of therapeutic enzymes to treat metabolic disorders. Hum Mutat 30:1591–1610
24. Landon MR, Lieberman RL, Hoang QQ et al (2009) Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comput Aided Mol Des 23:491–500
25. Makley LN, McMenimen KA, DeVree BT et al (2015) Pharmacological chaperone for alpha-crystallin partially restores transparency in cataract models. Science 350:674–677
26. Marugan JJ, Zheng W, Ferrer M et al (2010) Discovery, SAR, and biological evaluation of a non-inhibitory chaperone for acid alpha glucosidase. In Probe Reports from the NIH Molecular Libraries Program Bethesda (MD)
27. McCorvie TJ, Timson DJ (2013) In silico prediction of the effects of mutations in the human UDP-galactose 4′-epimerase gene: towards a predictive framework for type III galactosemia. Gene 524:95–104
28. McCorvie TJ, Kopec J, Hyung SJ et al (2014) Inter-domain communication of human cystathionine beta-synthase: structural basis of S-adenosyl-L-methionine activation. J Biol Chem 289:36018–36030
29. Muntau AC, Leandro J, Staudigl M, Mayer F, Gersting SW (2014) Innovative strategies to treat protein misfolding in inborn errors of metabolism: pharmacological chaperones and proteostasis regulators. J Inherit Metab Dis 37:505–523
30. Osman KT, Edwards A (2014) Structural genomics of human proteins. Methods Mol Biol 1140:27–34
31. Parenti G, Andria G, Valenzano KJ (2015) Pharmacological chaperone therapy: preclinical development, clinical translation, and prospects for the treatment of lysosomal storage disorders. Mol Ther 23:1138–1148
32. Patel D, Kopec J, Fitzpatrick F, McCorvie TJ, Yue WW (2016) Structural basis for ligand-dependent dimerization of phenylalanine hydroxylase regulatory domain. Sci Rep 6:23748. doi:10.1038/srep23748
33. Patnaik S, Zheng W, Choi JH et al (2012) Discovery, structure-activity relationship, and biological evaluation of noninhibitory small molecule chaperones of glucocerebrosidase. J Med Chem 55:5734–5748
34. Pederson BA, Turnbull J, Epp JR et al (2013) Inhibiting glycogen synthesis prevents Lafora disease in a mouse model. Ann Neurol 74:297–300
35. Pey AL, Majtan T, Sanchez-Ruiz JM, Kraus JP (2013) Human cystathionine beta-synthase (CBS) contains two classes of binding sites for S-adenosylmethionine (SAM): complex regulation of CBS activity and stability by SAM. Biochem J 449:109–121
36. Platt FM, Jeyakumar M (2008) Substrate reduction therapy. Acta Paediatr 97:88–93
37. Porto C, Ferrara MC, Meli M et al (2012) Pharmacological enhancement of alpha-glucosidase by the allosteric chaperone N-acetylcysteine. Mol Ther 20:2201–2211
38. Riemersma M, Froese DS, van Tol W et al (2015) Human ISPD Is a cytidyltransferase required for dystroglycan o-mannosylation. Chem Biol 22:1643–1652
39. Santos-Sierra S, Kirchmair J, Perna AM et al (2012) Novel pharmacological chaperones that correct phenylketonuria in mice. Hum Mol Genet 21:1877–1887
40. Schiffmann R (2015) The consequences of genetic and pharmacologic reduction in sphingolipid synthesis. J Inherit Metab Dis 38:77–84
41. Segalat L (2007) Loss-of-function genetic diseases and the concept of pharmaceutical targets. Orphanet J Rare Dis 2:30
42. Shafqat N, Kavanagh KL, Sass JO et al (2013) A structural mapping of mutations causing succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency. J Inherit Metab Dis 36:983–987
43. Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E (2013) Molecular mechanisms of disease-causing missense mutations. J Mol Biol 425:3919–3936
44. Studer RA, Dessailly BH, Orengo CA (2013) Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. Biochem J 449:581–594
45. Su XD, Zhang H, Terwilliger TC, Liljas A, Xiao J, Dong Y (2015) Protein crystallography from the perspective of technology developments. Crystallogr Rev 21:122–153
46. Suzuki Y, Ogawa S, Sakakibara Y (2009) Chaperone therapy for neuronopathic lysosomal diseases: competitive inhibitors as chemical chaperones for enhancement of mutant enzyme activities. Perspect Med Chem 3:7–19
47. Suzuki H, Ohto U, Higaki K et al (2014) Structural basis of pharmacological chaperoning for human beta-galactosidase. J Biol Chem 289:14560–14568
48. Torreblanca R, Lira-Navarrete E, Sancho J, Hurtado-Guerrero R (2012) Structural and mechanistic basis of the interaction between a pharmacological chaperone and human phenylalanine hydroxylase. Chembiochem 13:1266–1269
49. Wettstein S, Underhaug J, Perez B et al (2015) Linking genotypes database with locus-specific database and genotype-phenotype correlation in phenylketonuria. Eur J Hum Genet 23:302–309
50. Yoon H, Knight SA, Pandey A et al (2014) Frataxin-bypassing Isu1: characterization of the bypass activity in cells and mitochondria. Biochem J 459:71–81
51. Yue WW, Oppermann U (2011) High-throughput structural biology of metabolic enzymes and its impact on human diseases. J Inherit Metab Dis 34:575–581
52. Yue WW, Froese DS, Brennan PE (2014) The role of protein structural analysis in the next generation sequencing era. Top Curr Chem 336:67–98
53. Zeqiraj E, Tang X, Hunter RW et al (2014) Structural basis for the recruitment of glycogen synthase by glycogenin. Proc Natl Acad Sci U S A 111:E2831–2840
54. Zhang S, Roberts KM, Fitzpatrick PF (2014) Phenylalanine binding is linked to dimerization of the regulatory domain of phenylalanine hydroxylase. Biochemistry 53:6625–6627
55. Zickermann V, Wirth C, Nasiri H et al (2015) Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I. Science 347:44–49