ECOdrug: a database connecting drugs and conservation of their targets across species

Abstract Pharmaceuticals are designed to interact with specific molecular targets in humans and these targets generally have orthologs in other species. This provides opportunities for the drug discovery community to use alternative model species for drug development. It also means, however, there is potential for mode of action related effects in non-target wildlife species as many pharmaceuticals reach the environment through patient use and manufacturing wastes. Acquiring insight in drug target ortholog predictions across species and taxonomic groups has proven difficult because of the lack of an optimal strategy and because necessary information is spread across multiple and diverse sources and platforms. We introduce a new research platform tool, ECOdrug, that reliably connects drugs to their protein targets across divergent species. It harmonizes ortholog predictions from multiple sources via a simple user interface underpinning critical applications for a wide range of studies in pharmacology, ecotoxicology and comparative evolutionary biology. ECOdrug can be used to identify species with drug targets and identify drugs that interact with those targets. As such, it can be applied to support intelligent targeted drug safety testing by ensuring appropriate and relevant species are selected in ecological risk assessments. ECOdrug is freely accessible and available at: http://www.ecodrug.org.

[1]  Erik L. L. Sonnhammer,et al.  InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic , 2014, Nucleic Acids Res..

[2]  Jim J. Ryan,et al.  Use of acute and chronic ecotoxicity data in environmental risk assessment of pharmaceuticals , 2016, Environmental toxicology and chemistry.

[3]  Richard A Brain,et al.  Herbicidal effects of statin pharmaceuticals in Lemna gibba. , 2006, Environmental science & technology.

[4]  Wei Liu,et al.  Species-Specific Expansion and Molecular Evolution of the 3-hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Plants , 2014, PloS one.

[5]  E. Koonin,et al.  Functional and evolutionary implications of gene orthology , 2013, Nature Reviews Genetics.

[6]  Leszek P. Pryszcz,et al.  MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score , 2010, Nucleic acids research.

[7]  Erik Kristiansson,et al.  Evolutionary conservation of human drug targets in organisms used for environmental risk assessments. , 2008, Environmental science & technology.

[8]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[9]  Karen Augustine-Rauch,et al.  In Vitro Developmental Toxicology Screens: A Report on the Progress of the Methodology and Future Applications. , 2016, Chemical research in toxicology.

[10]  Edwin J. Routledge,et al.  Identification of Estrogenic Chemicals in STW Effluent. 1. Chemical Fractionation and in Vitro Biological Screening , 1998 .

[11]  L Filipe C Castro,et al.  Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history , 2014, Proceedings of the Royal Society B: Biological Sciences.

[12]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[13]  Matthew J Winter,et al.  A multi-endpoint in vivo larval zebrafish (Danio rerio) model for the assessment of integrated cardiovascular function. , 2014, Journal of pharmacological and toxicological methods.

[14]  Jean-Pierre Valentin,et al.  Validation of a larval zebrafish locomotor assay for assessing the seizure liability of early-stage development drugs. , 2008, Journal of pharmacological and toxicological methods.

[15]  Edwin J. Routledge,et al.  Identification of Estrogenic Chemicals in STW Effluent. 2. In Vivo Responses in Trout and Roach , 1998 .

[16]  Evgeny M. Zdobnov,et al.  OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software , 2014, Nucleic Acids Res..

[17]  Davide Heller,et al.  eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences , 2015, Nucleic Acids Res..

[18]  Ina Ebert,et al.  Pharmaceuticals in the environment—Global occurrences and perspectives , 2016, Environmental toxicology and chemistry.

[19]  Ryan D. Hernandez,et al.  Rock, Paper, Scissors: Harnessing Complementarity in Ortholog Detection Methods Improves Comparative Genomic Inference , 2015, G3: Genes, Genomes, Genetics.

[20]  Adrian M. Altenhoff,et al.  Standardized benchmarking in the quest for orthologs , 2016, Nature Methods.

[21]  Kyungho Choi,et al.  Pharmaceuticals and Personal Care Products in the Environment: What Are the Big Questions? , 2012, Environmental health perspectives.

[22]  Organización Mundial de la Salud Guidelines for ATC classification and DDD assignment , 1996 .

[23]  David S. Wishart,et al.  DrugBank 4.0: shedding new light on drug metabolism , 2013, Nucleic Acids Res..

[24]  Arcady R. Mushegian,et al.  Computational methods for Gene Orthology inference , 2011, Briefings Bioinform..

[25]  Caroline Moermond,et al.  Commentary on the draft revised guideline on the environmental risk assessment of medicinal products for human use , 2019, Environmental Sciences Europe.

[26]  George Papadatos,et al.  The ChEMBL bioactivity database: an update , 2013, Nucleic Acids Res..

[27]  V. Rodwell,et al.  The 3-hydroxy-3-methylglutaryl coenzyme-A (HMG-CoA) reductases , 2004, Genome Biology.

[28]  Rodrigo Lopez,et al.  Analysis Tool Web Services from the EMBL-EBI , 2013, Nucleic Acids Res..

[29]  G. Pentheroudakis,et al.  Thyroid cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. , 2010, Annals of oncology : official journal of the European Society for Medical Oncology.

[30]  Vincent Laudet,et al.  Evolution of ligands, receptors and metabolizing enzymes of thyroid signaling , 2017, Molecular and Cellular Endocrinology.

[31]  Tudor I. Oprea,et al.  A comprehensive map of molecular drug targets , 2016, Nature Reviews Drug Discovery.

[32]  Daniel L Villeneuve,et al.  Editor's Highlight: Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS): A Web-Based Tool for Addressing the Challenges of Cross-Species Extrapolation of Chemical Toxicity. , 2016, Toxicological sciences : an official journal of the Society of Toxicology.

[33]  Gautier Koscielny,et al.  Ensembl Genomes: Extending Ensembl across the taxonomic space , 2009, Nucleic Acids Res..