TDR Targets

Last updated
TDR Targets
TDR Targets Logo.png
Content
DescriptionChemogenomics resource for neglected diseases
Data types
captured
Genomics, Medicinal Chemistry
Organisms Human Pathogens that cause Neglected Tropical Diseases (NTDs): Plasmodium, Trypanosoma, Leishmania, Mycobacterium, Chlamydia, Treponema, Wolbachia endosymbionts, Giardia, Entamoeba, Trichomonas, Schistosoma, Echinococcus, Onchocerca, Brugia, Loa_loa,
Contact
Research center UNSAM, CONICET
Laboratory Flag of Argentina.svg Trypanosomatics Laboratory, UNSAM
Authors Fernán Agüero, Lionel Urán Landaburu, Santiago Carmona, María Paula Magariños, Ariel J Berenstein, Santiago Videla, Ariel Chernomoretz, Parag Maru, Dhanasekaran Shanmugam (current). Gregory Crowther, Matt Berriman, Stuart Ralph, David Roos, Wes Van Voorhis (past).
Primary citationUrán Landaburu L et al. (2019) [1]
Release date2007
Access
Website https://tdrtargets.org
Tools
Web Perl MVC (Catalyst_(software), DBIx::Class)
Miscellaneous
Versioning TDR Targets 6
Data release
frequency
18 months
Version6
Curation policyyes

The TDR Targets database is a bioinformatics project that seeks to exploit the availability of diverse genomic and chemical datasets to facilitate the identification and prioritization of drugs and drug targets in neglected disease pathogens. [2] TDR in the name of the database stands from the popular abbreviation for a special programme within the World Health Organization, whose focus is Tropical Disease Research. The project was jumpstarted by funds from this programme (see Special Programme for Research and Training in Tropical Diseases), and the initial focus of the resource was on organisms/diseases of high priority for this Programme.

The database functions both as a website, where researchers can look for information on targets or compounds of interest, or as a tool for prioritization of targets in whole genomes. [3] When prioritizing genes, individual database queries are used to specify one or more desirable or undesirable criteria. The output of each query will be a set of genes (e.g. all genes that produce a lethal phenotype upon a genetic knockout); and different combinations of gene sets can be obtained using standard set operators (Union, Intersection, Subtraction), including the possibility of weighting genes present in more than one set (this is particularly useful when calculating Unions). A number of prioritizations obtained with this tool have been published, [4] demonstrating a number of use cases.

The database currently hosts information for 21 bacterial and eukaryotic pathogens, and for > 2 million bioactive compounds. Information integrated into the TDR Targets database comes from disparate data sources, and therefore cannot be considered a primary data repository.

The database has seen 6 major releases since its launch in 2007, which coincided with expansion of phylogenetic coverage (e.g. inclusion of helminth genomes in release 2), incorporation of new functionalities (e.g. chemical similarity and substructure searches in release 4), major data updates to keep the database in sync with upstream data providers (in release 5), and the incorporation of a multilayer network model [5] to guide Drug_repositioning through nice user-friendly visualizations (in release 6).

See also

ChEMBL

Related Research Articles

Tropical diseases are diseases that are prevalent in or unique to tropical and subtropical regions. The diseases are less prevalent in temperate climates, due in part to the occurrence of a cold season, which controls the insect population by forcing hibernation. However, many were present in northern Europe and northern America in the 17th and 18th centuries before modern understanding of disease causation. The initial impetus for tropical medicine was to protect the health of colonial settlers, notably in India under the British Raj. Insects such as mosquitoes and flies are by far the most common disease carrier, or vector. These insects may carry a parasite, bacterium or virus that is infectious to humans and animals. Most often disease is transmitted by an insect "bite", which causes transmission of the infectious agent through subcutaneous blood exchange. Vaccines are not available for most of the diseases listed here, and many do not have cures.

Helminthiasis Any macroparasitic disease caused by helminths

Helminthiasis, also known as worm infection, is any macroparasitic disease of humans and other animals in which a part of the body is infected with parasitic worms, known as helminths. There are numerous species of these parasites, which are broadly classified into tapeworms, flukes, and roundworms. They often live in the gastrointestinal tract of their hosts, but they may also burrow into other organs, where they induce physiological damage.

Neglected tropical diseases Diverse group of tropical infection diseases which are common in developing countries

Neglected tropical diseases (NTDs) are a diverse group of tropical infections which are common in low-income populations in developing regions of Africa, Asia, and the Americas. They are caused by a variety of pathogens such as viruses, bacteria, protozoa and parasitic worms (helminths). These diseases are contrasted with the big three infectious diseases, which generally receive greater treatment and research funding. In sub-Saharan Africa, the effect of these diseases as a group is comparable to malaria and tuberculosis. NTD co-infection can also make HIV/AIDS and tuberculosis more deadly.

Mycobacterium africanum is a species of Mycobacterium that is most commonly found in West African countries, where it is estimated to cause up to 40% of pulmonary tuberculosis. The symptoms of infection resemble those of M. tuberculosis.

Alan Fairlamb

Alan Hutchinson Fairlamb, CBE, FRSE, FLS, FMedSci, FRSB is a Wellcome Trust Principal Research Fellow and Professor of Biochemistry in the Division of Biological Chemistry and Drug Discovery at the School of Life Sciences, University of Dundee, Scotland. From 2006-2011 he was a member of the Scientific and Technical Advisory Committee of the Special Programme for Research and Training in Tropical Diseases (TDR) -- an independent global programme of scientific collaboration co-sponsored by UNICEF, UNDP, the World Bank and WHO. Currently he is a member of the governing board of the Tres Cantos Open Lab Foundation, whose aim is to accelerate the discovery and development of medicines to tackle diseases of the developing world in an open collaborative manner.

Cruzipain is a cysteine protease expressed by Trypanosoma cruzi.

Anthelmintic Antiparasitic drugs that expel parasitic worms (helminths) from the body

Anthelmintics or antihelminthics are a group of antiparasitic drugs that expel parasitic worms (helminths) and other internal parasites from the body by either stunning or killing them and without causing significant damage to the host. They may also be called vermifuges or vermicides. Anthelmintics are used to treat people who are infected by helminths, a condition called helminthiasis. These drugs are also used to treat infected animals.

Mycetoma is a chronic infection in the skin caused by either bacteria (actinomycetoma) or fungi (eumycetoma), typically resulting in a triad of painless firm skin lumps, the formation of weeping sinuses, and a discharge that contains grains. 80% occur in feet.

ChEMBL Chemical database of bioactive molecules with drug-like properties

ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug-like properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK.

Wendy Gibson is Professor of Protozoology at University of Bristol, specialising in trypanosomes and molecular parasitology.

Druggability is a term used in drug discovery to describe a biological target that is known to or is predicted to bind with high affinity to a drug. Furthermore, by definition, the binding of the drug to a druggable target must alter the function of the target with a therapeutic benefit to the patient. The concept of druggability is most often restricted to small molecules but also has been extended to include biologic medical products such as therapeutic monoclonal antibodies.

Fenarimol Chemical compound

Fenarimol, sold under the tradenames Bloc, Rimidin and Rubigan, is a fungicide which acts against rusts, blackspot and mildew fungi. It is used on ornamental plants, trees, lawns, tomatoes, peppers, eggplants, cucumbers and melons. It is mainly used to control powdery mildew. It works by inhibiting the fungus's biosynthesis of important steroid molecules.

Edward Thomas Ryan

Edward Thomas Ryan is an American microbiologist, immunologist, and physician at Harvard University and Massachusetts General Hospital. Ryan served as President of the American Society of Tropical Medicine and Hygiene from 2009 to 2010. Ryan is Professor of Immunology and Infectious Diseases at the Harvard T.H. Chan School of Public Health, Professor of Medicine at Harvard Medical School, and Director of Global Infectious Diseases at the Massachusetts General Hospital. Ryan's research and clinical focus has been on infectious diseases associated with residing in, immigrating from, or traveling through resource-limited areas. Ryan is a Fellow of the American Society of Microbiology, the American Society of Tropical Medicine and Hygiene, the American College of Physicians, and the Infectious Diseases Society of America.

Uche Veronica Amazigo is a professor of Medical Parasitology and public health specialist. She is a fellow of the Nigerian Academy of Science who was elected into the Academy's Fellowship at its Annual General Meeting held in January 2015. In 2012, she won the Prince Mahidol Award for outstanding contributions to public health. She is best known for her research on onchocerciasis and her consequent contributions to the World Health Organization (WHO).

Mass deworming Treating large numbers of people, particularly children, for helminthiasis and schistosomiasis

Mass deworming, also called preventive chemotherapy, is the process of treating large numbers of people, particularly children, for helminthiasis and schistosomiasis in areas with a high prevalence of these conditions. It involves treating everyone – often all children who attend schools, using existing infrastructure to save money – rather than testing first and then only treating selectively. Serious side effects have not been reported when administering the medication to those without worms, and testing for the infection is many times more expensive than treating it. So for the same amount of money, mass deworming can treat more people more cost-effectively than selective deworming. Mass deworming is one example of mass drug administration.

Candidatus Ornithobacterium hominis is a gram-negative bacterial species that colonises the human respiratory tract. Despite being related to the bird pathogen O. rhinotracheale, it is not a zoonosis. It has been detected in microbiome data from people around the world, including The Gambia, Madagascar and Central African Republic, Kenya, Mae La refugee camp in Thailand, rural Venezuela, Australia, and Fiji.

Neglected tropical diseases in India are a group of bacterial, parasitic, viral, and fungal infections that are common in low income countries but receive little funding to address them. Neglected tropical diseases are common in India.

Kala azar in India refers to the special circumstances of the disease kala azar as it exists in India. Kala azar is a major health problem in India with an estimated 146,700 new cases per year as of 2012. In the disease a parasite causes sickness after migrating to internal organs such as the liver, spleen and bone marrow. If left untreated the disease almost always results in the death. Signs and symptoms include fever, weight loss, fatigue, anemia, and substantial swelling of the liver and spleen.

The Global Programme to Eliminate Lymphatic Filariasis (GPELF) is a World Health Organization project to eradicate the Filarioidea worms which cause the disease lymphatic filariasis and also treat the people who already have the infection.

The eradication of lymphatic filariasis is the ongoing attempt to eradicate the Filarioidea worms which cause the disease lymphatic filariasis and also treat the people who already have the infection.

References

  1. Urán Landaburu, Lionel; Berenstein, Ariel J.; Videla, Santiago; Maru, Parag; Shanmugam, Dhanasekaran; Chernomoretz, Ariel; Agüero, Fernán (2019). "TDR Targets 6: Driving drug discovery for human pathogens through intensive chemogenomic data integration". Nucleic Acids Research. 48 (D1): D992–D1005. doi: 10.1093/nar/gkz999 . PMC   7145610 . PMID   31680154.
  2. "TDR Targets website (https://tdrtargets.org)".
  3. Agüero, Fernán; Al-Lazikani, Bissan; Aslett, Martin; Berriman, Matthew; Buckner, Frederick S.; Campbell, Robert K.; Carmona, Santiago; Carruthers, Ian M.; Chan, A. W. Edith; Chen, Feng; Crowther, Gregory J.; Doyle, Maria A.; Hertz-Fowler, Christiane; Hopkins, Andrew L.; McAllister, Gregg; Nwaka, Solomon; Overington, John P.; Pain, Arnab; Paolini, Gaia V.; Pieper, Ursula; Ralph, Stuart A.; Riechers, Aaron; Roos, David S.; Sali, Andrej; Shanmugam, Dhanasekaran; Suzuki, Takashi; Van Voorhis, Wesley C.; Verlinde, Christophe L. M. J. (2008). "Genomic-scale prioritization of drug targets: The TDR Targets database". Nature Reviews Drug Discovery. 7 (11): 900–907. doi:10.1038/nrd2684. PMC   3184002 . PMID   18927591.
  4. Crowther, Gregory J.; Shanmugam, Dhanasekaran; Carmona, Santiago J.; Doyle, Maria A.; Hertz-Fowler, Christiane; Berriman, Matthew; Nwaka, Solomon; Ralph, Stuart A.; Roos, David S.; Van Voorhis, Wesley C.; Agüero, Fernán (2010). "Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an in Silico Approach". PLOS Neglected Tropical Diseases. 4 (8): e804. doi:10.1371/journal.pntd.0000804. PMC   2927427 . PMID   20808766.
  5. Berenstein, Ariel José; Magariños, María Paula; Chernomoretz, Ariel; Agüero, Fernán (2016). "A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases". PLOS Neglected Tropical Diseases. 10 (1): e0004300. doi:10.1371/journal.pntd.0004300. PMC   4703370 . PMID   26735851.