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In Silico Repositioning-Chemogenomics Strategy Identifies New Drugs with Potential Activity against Multiple Life Stages of Schistosoma mansoni

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      Abstract

      Morbidity and mortality caused by schistosomiasis are serious public health problems in developing countries. Because praziquantel is the only drug in therapeutic use, the risk of drug resistance is a concern. In the search for new schistosomicidal drugs, we performed a target-based chemogenomics screen of a dataset of 2,114 proteins to identify drugs that are approved for clinical use in humans that may be active against multiple life stages of Schistosoma mansoni. Each of these proteins was treated as a potential drug target, and its amino acid sequence was used to interrogate three databases: Therapeutic Target Database (TTD), DrugBank and STITCH. Predicted drug-target interactions were refined using a combination of approaches, including pairwise alignment, conservation state of functional regions and chemical space analysis. To validate our strategy, several drugs previously shown to be active against Schistosoma species were correctly predicted, such as clonazepam, auranofin, nifedipine, and artesunate. We were also able to identify 115 drugs that have not yet been experimentally tested against schistosomes and that require further assessment. Some examples are aprindine, gentamicin, clotrimazole, tetrabenazine, griseofulvin, and cinnarizine. In conclusion, we have developed a systematic and focused computer-aided approach to propose approved drugs that may warrant testing and/or serve as lead compounds for the design of new drugs against schistosomes.

      Author Summary

      Schistosomiasis is a neglected tropical disease caused by schistosome parasites that affects millions of people worldwide. The current reliance on a single drug (Praziquantel) for treatment and control of the disease calls for the urgent discovery of novel schistosomicidal agents. One approach that can expedite drug discovery is to find new uses for existing approved drugs, a practice known as drug repositioning. Currently, modern drug repositioning strategies entail the search for compounds that act on a specific target, often a protein known or suspected to be required for survival of the parasite. Drug repositioning approaches for schistosomiasis are now greatly facilitated by the availability of comprehensive schistosome genome data in user-friendly databases. Here, we report a drug repositioning computational strategy that involves identification of novel schistosomicidal drug candidates using similarity between schistosome proteins and known drug targets. Researchers can now use the list of predicted drugs as a basis for deciding which potential schistosomicidal candidates can be tested experimentally.

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      Most cited references 96

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      Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.

      In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.
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        UniProt: the Universal Protein knowledgebase.

        To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.
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          DrugBank: a comprehensive resource for in silico drug discovery and exploration

          DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14 000 protein or drug target sequences are linked to these drug entries. Each DrugCard entry contains >80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Many data fields are hyperlinked to other databases (KEGG, PubChem, ChEBI, PDB, Swiss-Prot and GenBank) and a variety of structure viewing applets. The database is fully searchable supporting extensive text, sequence, chemical structure and relational query searches. Potential applications of DrugBank include in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. DrugBank is available at .
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            Author and article information

            Affiliations
            [1 ]LabMol – Laboratory for Drug Design and Modeling, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
            [2 ]Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
            [3 ]Instituto de Química, Universidade Federal de Goiás, Goiaânia, Brazil
            [4 ]Centro de Malária e Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
            Khon Kaen University, Thailand
            Author notes

            The authors have declared that no competing interests exist.

            Conceived and designed the experiments: BJN JCBB PVLC CHA. Performed the experiments: BJN RCB. Analyzed the data: BJN RCB PVLC CHA. Contributed reagents/materials/analysis tools: RCB JCBB PVLC CHA. Wrote the paper: BJN RCB PVLC CHA.

            Contributors
            Role: Editor
            Journal
            PLoS Negl Trop Dis
            PLoS Negl Trop Dis
            plos
            plosntds
            PLoS Neglected Tropical Diseases
            Public Library of Science (San Francisco, USA )
            1935-2727
            1935-2735
            January 2015
            8 January 2015
            : 9
            : 1
            25569258
            4287566
            PNTD-D-14-01001
            10.1371/journal.pntd.0003435
            (Editor)

            This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

            Counts
            Pages: 12
            Funding
            During this study RCN was supported by a fellowship from the Center for a Livable Future and a Fogarty National Institutes of Health training grant 1D43TW008273. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors received no specific funding for this work.
            Categories
            Research Article
            Biology and Life Sciences
            Organisms
            Animals
            Invertebrates
            Helminths
            Schistosoma
            Schistosoma Mansoni
            Medicine and Health Sciences
            Pharmacology
            Drug Research and Development
            Drug Design
            Computer-Aided Drug Design
            Custom metadata
            The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files.

            Infectious disease & Microbiology

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