DDIEM: Drug Database for Inborn Errors of Metabolism

Overview

Journal Orphanet J Rare Dis

Publisher Biomed Central

Specialty General Medicine

Date 2020 Jun 13

PMID 32527280

Citations 7

Authors

Marwa Abdelhakim

Eunice McMurray

Ali Raza Syed

Senay Kafkas

Allan Anthony Kamau

Paul N Schofield

Robert Hoehndorf

Affiliations

Soon will be listed here.

Abstract

Background: Inborn errors of metabolism (IEM) represent a subclass of rare inherited diseases caused by a wide range of defects in metabolic enzymes or their regulation. Of over a thousand characterized IEMs, only about half are understood at the molecular level, and overall the development of treatment and management strategies has proved challenging. An overview of the changing landscape of therapeutic approaches is helpful in assessing strategic patterns in the approach to therapy, but the information is scattered throughout the literature and public data resources.

Results: We gathered data on therapeutic strategies for 300 diseases into the Drug Database for Inborn Errors of Metabolism (DDIEM). Therapeutic approaches, including both successful and ineffective treatments, were manually classified by their mechanisms of action using a new ontology.

Conclusions: We present a manually curated, ontologically formalized knowledgebase of drugs, therapeutic procedures, and mitigated phenotypes. DDIEM is freely available through a web interface and for download at http://ddiem.phenomebrowser.net.

Citing Articles

Applications of quantitative metabolomics to revolutionize early diagnosis of inborn errors of metabolism in India.

Chandran J, Bellad A, Ramarajan M, Rangiah K Anal Sci Adv. 2024; 2(11-12):546-563.

PMID: 38715861 PMC: 10989570. DOI: 10.1002/ansa.202100010.

Drug Repurposing and Lysosomal Storage Disorders: A Trick to Treat.

Mele B, Rossetti F, Cubellis M, Monticelli M, Andreotti G Genes (Basel). 2024; 15(3).

PMID: 38540351 PMC: 10970111. DOI: 10.3390/genes15030290.

Dietary Inflammatory Potential in Pediatric Diseases: A Narrative Review.

Tosi M, Montanari C, Bona F, Tricella C, Agostinelli M, Dolor J Nutrients. 2023; 15(24).

PMID: 38140353 PMC: 10745369. DOI: 10.3390/nu15245095.

Child and adolescent psychiatrists' use, attitudes, and understanding of genetic testing and pharmacogenetics in clinical practice.

Soda T, Merner A, Small B, Torgerson L, Munoz K, Austin J Psychiatry Res. 2023; 325:115246.

PMID: 37172398 PMC: 10365566. DOI: 10.1016/j.psychres.2023.115246.

A novel computational drug repurposing approach for Systemic Lupus Erythematosus (SLE) treatment using Semantic Web technologies.

Noor A, Assiri A Saudi J Biol Sci. 2021; 28(7):3886-3892.

PMID: 34220244 PMC: 8241633. DOI: 10.1016/j.sjbs.2021.03.068.

References

Westermark K, Holm B, Soderholm M, Llinares-Garcia J, Riviere F, Aarum S . European regulation on orphan medicinal products: 10 years of experience and future perspectives. Nat Rev Drug Discov. 2011; 10(5):341-9. DOI: 10.1038/nrd3445. View

Lee J, Wasserman W, Hoffmann G, van Karnebeek C, Blau N . Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism. Genet Med. 2017; 20(1):151-158. PMC: 5763153. DOI: 10.1038/gim.2017.108. View

Ferreira C, van Karnebeek C, Vockley J, Blau N . A proposed nosology of inborn errors of metabolism. Genet Med. 2018; 21(1):102-106. PMC: 6286709. DOI: 10.1038/s41436-018-0022-8. View

Braun M, Farag-El-Massah S, Xu K, Cote T . Emergence of orphan drugs in the United States: a quantitative assessment of the first 25 years. Nat Rev Drug Discov. 2010; 9(7):519-22. DOI: 10.1038/nrd3160. View

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K . KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2016; 45(D1):D353-D361. PMC: 5210567. DOI: 10.1093/nar/gkw1092. View

Sansone S, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister A . FAIRsharing as a community approach to standards, repositories and policies. Nat Biotechnol. 2019; 37(4):358-367. PMC: 6785156. DOI: 10.1038/s41587-019-0080-8. View

Hoehndorf R, Slater L, Schofield P, Gkoutos G . Aber-OWL: a framework for ontology-based data access in biology. BMC Bioinformatics. 2015; 16:26. PMC: 4384359. DOI: 10.1186/s12859-015-0456-9. View

Correa-Giannella M, Freire D, Cavaleiro A, Fortes M, Giorgi R, Pereira M . Hyperinsulinism/hyperammonemia (HI/HA) syndrome due to a mutation in the glutamate dehydrogenase gene. Arq Bras Endocrinol Metabol. 2013; 56(8):485-9. DOI: 10.1590/s0004-27302012000800004. View

Ginocchio V, Brunetti-Pierri N . Progress toward improved therapies for inborn errors of metabolism. Hum Mol Genet. 2015; 25(R1):R27-35. DOI: 10.1093/hmg/ddv418. View

10.

Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A . ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 2007; 36(Database issue):D344-50. PMC: 2238832. DOI: 10.1093/nar/gkm791. View

11.

Sun W, Zheng W, Simeonov A . Drug discovery and development for rare genetic disorders. Am J Med Genet A. 2017; 173(9):2307-2322. PMC: 5662129. DOI: 10.1002/ajmg.a.38326. View

12.

Kim S, Thiessen P, Bolton E, Chen J, Fu G, Gindulyte A . PubChem Substance and Compound databases. Nucleic Acids Res. 2015; 44(D1):D1202-13. PMC: 4702940. DOI: 10.1093/nar/gkv951. View

13.

Nomura N, Kamiya K, Ikeda K, Yui N, Chiga M, Sohara E . Treatment with 17-allylamino-17-demethoxygeldanamycin ameliorated symptoms of Bartter syndrome type IV caused by mutated Bsnd in mice. Biochem Biophys Res Commun. 2013; 441(3):544-9. DOI: 10.1016/j.bbrc.2013.10.129. View

14.

Serrano J . LiverTox: An online information resource and a site for case report submission on drug-induced liver injury. Clin Liver Dis (Hoboken). 2019; 4(1):22-25. PMC: 6448728. DOI: 10.1002/cld.388. View

15.

Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S . ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. 2018; 47(D1):D1186-D1194. PMC: 6323956. DOI: 10.1093/nar/gky1036. View

16.

Rutten M, Rots M, Oosterveer M . Exploiting epigenetics for the treatment of inborn errors of metabolism. J Inherit Metab Dis. 2019; 43(1):63-70. PMC: 7041640. DOI: 10.1002/jimd.12093. View

17.

Carvalho T, Schuh R, Pasqualim G, Pellenz F, Filippi-Chiela E, Giugliani R . CRISPR-Cas9-mediated gene editing in human MPS I fibroblasts. Gene. 2018; 678:33-37. DOI: 10.1016/j.gene.2018.08.004. View

18.

Yasuda M, Bishop D, Fowkes M, Cheng S, Gan L, Desnick R . AAV8-mediated gene therapy prevents induced biochemical attacks of acute intermittent porphyria and improves neuromotor function. Mol Ther. 2009; 18(1):17-22. PMC: 2839207. DOI: 10.1038/mt.2009.250. View

19.

Smith C, Eppig J . Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens. J Biomed Semantics. 2015; 6:11. PMC: 4378007. DOI: 10.1186/s13326-015-0009-1. View

20.

Lachmann R, Platt F . Substrate reduction therapy for glycosphingolipid storage disorders. Expert Opin Investig Drugs. 2001; 10(3):455-66. DOI: 10.1517/13543784.10.3.455. View