TDR Targets is currently led and run by the Trypanosomatics group at IIBIO-UNSAM (Argentina) with help with external collaborators worldwide.
The team at IIBIO-UNSAM
Lionel Urán Landaburu, PhD Student (UNSAM), Fellow of the National Research Council (CONICET, Argentina)
Fernán Agüero, Group Leader (UNSAM), Principal Investigator, National Research Council (CONICET, Argentina)
Ariel Chernomoretz, Santiago Videla, Ariel Berenstein, Fundación Instituto Leloir, Buenos Aires, Argentina
Dhanasekaran Shanmugam, Council of Scientific and Industrial Research – National Chemical Laboratory, Mumbai, India
Matt Berriman, Magdalena Zarowiecki Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
The TDR Target Project was jumpstarted in 2005 after a call for applications was launched by TDR (the Special Programme for Research and Training in Tropical Diseases (UNICEF / UNDP / World Bank / WHO). As a result of that call five groups were funded to develop a portfolio of candidate drug targets for neglected tropical diseases, which shortly turned into the development of a database/web-based resource for prioritizing targets for human pathogens.
Former Team and Collaborators:
María Paula Magariños, Santiago Carmona, Universidad de San Martín, San Martín, Buenos Aires, Argentina
David S Roos, Dhany Shanmugam, University of Pennsylvania, Philadelphia, PA, USA
Wes Van Voorhis, Greg Crowther, Aaron Riechers, University of Washington, Seattle, WA, USA
Matt Berriman, Arnab Pain, Takashi Suzuki, Christiane Hertz-Fowler, Wellcome Trust Sanger Institute, Hinxton, UK
Stuart Ralph, Maria Doyle, University of Melbourne, Melbourne, Victoria, Australia
Algorithms and development of our network model for navigating the chemogenomics data space:
(2016) A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. Berenstein AJ, Magariños MP, Chernomoretz A, Agüero F. PLOS Neglected Tropical Diseases 10(1): e0004300.
First appeareance of bioactive compounds and chemical searches in TDR Targets:
(2012) TDR Targets: a chemogenomics resource for neglected diseases. Magariños MP, Carmona SJ, Crowther GJ, Ralph SA, Roos DS, Shanmugam D, Van Voorhis WC, Agüero F. Nucleic Acids Research 40(Database issue): D1118-27.
Application of TDR Targets to prioritize targets in important pathogens:
(2010) Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. Crowther GJ, Shanmugam D, Carmona SJ, Doyle MA, Hertz-Fowler C, Berriman M, Nwaka S, Ralph SA, Roos DS, Van Voorhis WC, Agüero F. PLOS Neglected Tropical Diseases 4(8): e804.
First release of TDR Targets
(2008) Genomic-scale prioritization of drug targets: the TDR Targets database. Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL. Nature Reviews Drug Discovery 7(11): 900-7.
Data in TDR Targets is obtained from upstream databases or provided by independent researchers through curation of the literature. For a list of the data integrated into TDR Targets and the related publications see Data Sets.
Please cite the authors and data providers when you use their data.
Genomic Data was obtained from the public domain (GenBank) or downstream providers of these data, such as Ensembl (Human, Mouse, Rat), EuPathDB (Unicellular Eukaryotic Pathogens), Wormbase (C. elegans), Wormbase Parasite (Helminths), Mycobrowser (Mycobacteria), SGD (Yeast), FlyBase (Drosophila).
Chemogenomic Networks in TDR Targets were built as described in Berenstein AJ et al.(2016)
EC Numbers, Pfam Domains, Ontology Terms were computationally assigned using interproscan, or the KEGG Automatic Annotation Server (KAAS). Ontology Terms are derived from the BTO (BRENDA tissue / enzyme source), CARO (Common Anatomy Reference), ECO (Evidence Codes), FAO (Fungal Anatomy), GO (Gene Ontology), MI (Molecular Interactions), MP (Mammalian Phenotypes), NEWT (Taxonomy,) PATO (Phenotypes and Traits), PLO (Plasmodium Life Cycle), REX (Physicochemical processes) and SO ontologies, and were obtained from the OBO Foundry.
Essentiality data (genome-wide lethal, inviable, loss of fitness or similar phenotyes) were curated from the literature.
PICTO-Glaxo-2013-0067 (2014-2018) Joint funding from GlaxoSmithKline Argentina and the National Agency for the Promotion of Science and Technology, Argentina (ANPCyT).
IN-1405 (2015-2018) Indo-Argentina Bilateral Cooperation Project, Joint Funding from the Indian Department of Science and Technology (DST) and the Argentinian Ministry of Science and Technology (MINCyT).
PICT-2010-1479 (2011-2014) National Agency for the Promotion of Science and Technology, Argentina (ANPCyT).
Fogarty International Center D43TW007888 (2010-2013) Fellowship Support (MP Magariños), Training Programme in Infectious Diseases (IIBIO-UNSAM, Argentina -- University of Georgia, USA)
WHO/TDR-A9606 (2005-2012) Special Programme for Research and Training in Tropical Diseases, World Health Organization.
The TDR Targets project would like to thank those who over time have contributed with data, their own time or resources to help create this diverse resource.
Hagai Ginsburg (MPMP), for help with P. falciparum pathways, EC numbers, and curation of bioactive compounds against Malaria.
Anna Gaulton and John Overington, for help with integrating ChEMBL data, and for early access to a pre-release version of ChEMBL.
Feng Chen and Omar Harb, University of Pennsylvania, for help with integrating OrthoMCL data.
Gaia Paolini and Andrew Hopkins (Pfizer Sandwich), for the druggability and compound desirability data.
Bissan Al-Lazikani, Edith Chan and John Overington (Inpharmatica) for the mapping of pathogen proteins against Starlite and the druggability index.
Ursula Pieper, Ben Webb, and Andrej Sali (University of California at San Francisco) for the genome-wide modelling of the pathogen proteins.
Tilde Carlow and Kshitiz Chaudhary (New England Biolabs) for the C. elegans RNAi data.
Bob Campbell (Marine Biological Laboratory, Woods Hole, MA) for the mapping of parasite genes against proteins in DrugBank.
Peter Ertl, Novartis Institutes for Biomedical Research, for the JME Java Molecule Editor.
The data at this site is provided freely for public use, through the contributions of many researchers including those involved in curating data from the literature. The data is not guaranteed to be accurate as it often reflects the results of ongoing research.
When using data from the TDR Targets project, please cite the original publications and contributors of that data. Please see "Citing TDR Targets" and "Data Sources and Providers" sections in this page.
TDR Targets (also referred to as ‘we’ throughout this document) is committed to protecting its users’ data and privacy. The purpose of this page is to provide you with information about how the data we collect from users of this website is used or shared. We may update this Privacy Notice from time to time. We encourage you to visit this page frequently and take note of the date updated field above.
We do not use or share any of your personal information for any purpose unrelated to the functionality of the websites.
In TDR Targets, we carry chemogenomic information for both pathogens and non-pathogenic model organisms. The selection of organisms was based on historic (funding) or phylogenetic reasons (e.g. to support orthology-based inferences).
We try to provide information to facilitate drug discovery in a wide selection of organisms. To simplify the process of prioritizing drug targets and to focus our use of limited resources, we have two tiers of organisms:
Tier 1 organisms are those for which we aim to provide a complete-data expierence. In case of human pathogens, you can run prioritizations on these organisms. In case of model organisms, we aim to provide as much information as possible on available bioactive compounds, known drug targets, etc.
Tier 2 organisms are those for which we integrate only partial data. Model (non-pathogenic) organisms are included for comparative purposes, as many of these are hosts of parasitic organisms. Also, model organisms (humans, mice) provide a wealth of chemical information for repurposing / repositioning exercises. These organisms may be used to run 'inference by orthology' queries in some cases.
Tier 1 – Pathogen Organisms in TDR Targets:
Apicomplexa: Plasmodium falciparum, P. vivax, P. berghei, T. gondii
Kinetoplastids / Trypanosomatids: Trypanosoma cruzi, Trypanosoma brucei, Leishmania major Other Protozoans / Lower Eukaryotes: Giardia lamblia, Trichomonas vaginalis, Entamoeba histolytica
Helminths / Nematoda: Brugia malayi, Loa loa
Helminths / Flatworms: Schistosoma mansoni, Echinococcus granulosus, E. multilocularis
Bacteria: Chlamydia trachomatis, Mycobacterium leprae, M. tuberculosis, M. ulcerans, Wolbachia (endosymbiont of B. malayi)
Tier 2 – Other organisms (for phylogenetic queries):
Apicomplexa: P. knowlesi, P. yoelii, Cryptosporidium parvum, C. hominis, Teileria parva, Neospora caninum
Kinetoplastids / Trypanosomatids: T. brucei gambiense, T. congolense, L. infantum, L. braziliensis, L. mexicana
Fungi / Eukaryotes: Candida albicans
Helminths / Flatworms: S. japonicum
Bacteria: Treponema pallidum
Tier 2 – Model Organisms (non-pathogenic):
Mammals: Human, Mouse, Rat
Metazoan / Plants: Arabidopsis thaliana, Oriza sativa
Metazoan / Invertebrates: Drosophila melanogaster (fruit fly)
Helminths / Nematoda: Caenorhabditis elegans
Helminths / Flatworms: Schmidtea mediterranea (planaria)
Amoebozoa / Eukaryotes: Dictyostelium discoideum (slime mold)
Fungi / Eukaryotes: Saccharomyces cerevisiae (yeast)
Bacteria: Escherichia coli