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Madeira F, Madhusoodanan N, Lee J, Eusebi A, Niewielska A, Tivey ARN, Meacham S, Lopez R, Butcher S. Using EMBL-EBI Services via Web Interface and Programmatically via Web Services. Curr Protoc 2024; 4:e1065. [PMID: 38857087 DOI: 10.1002/cpz1.1065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The European Bioinformatics Institute (EMBL-EBI)'s Job Dispatcher framework provides access to a wide range of core databases and analysis tools that are of key importance in bioinformatics. As well as providing web interfaces to these resources, web services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web services clients provided in Perl, Python, and Java or who would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Retrieving data from EMBL-EBI using Dbfetch via the web interface Alternate Protocol 1: Retrieving data from EMBL-EBI using WSDbfetch via the REST interface Alternate Protocol 2: Retrieving data from EMBL-EBI using Dbfetch via RESTful web services with Python client Support Protocol 1: Installing Python REST web services clients Basic Protocol 2: Sequence similarity search using FASTA search via the web interface Alternate Protocol 3: Sequence similarity search using FASTA via RESTful web services with Perl client Support Protocol 2: Installing Perl REST web services clients Basic Protocol 3: Sequence similarity search using NCBI BLAST+ RESTful web services with Python client Basic Protocol 4: Sequence similarity search using HMMER3 phmmer REST web services with Perl client and Docker Support Protocol 3: Installing Docker and running the EMBL-EBI client container Basic Protocol 5: Protein functional analysis using InterProScan 5 RESTful web services with the Python client and Docker Alternate Protocol 4: Protein functional analysis using InterProScan 5 RESTful web services with the Java client Support Protocol 4: Installing Java web services clients Basic Protocol 6: Multiple sequence alignment using Clustal Omega via web interface Alternate Protocol 5: Multiple sequence alignment using Clustal Omega with Perl client and Docker Support Protocol 5: Exploring the RESTful API with OpenAPI User Inferface.
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Affiliation(s)
- Fábio Madeira
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nandana Madhusoodanan
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Joonheung Lee
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alberto Eusebi
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ania Niewielska
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Adrian R N Tivey
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stuart Meacham
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Rodrigo Lopez
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah Butcher
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Gupta Y, Sharma N, Singh S, Romero JG, Rajendran V, Mogire RM, Kashif M, Beach J, Jeske W, Poonam, Ogutu BR, Kanzok SM, Akala HM, Legac J, Rosenthal PJ, Rademacher DJ, Durvasula R, Singh AP, Rathi B, Kempaiah P. The Multistage Antimalarial Compound Calxinin Perturbates P. falciparum Ca 2+ Homeostasis by Targeting a Unique Ion Channel. Pharmaceutics 2022; 14:1371. [PMID: 35890267 PMCID: PMC9319510 DOI: 10.3390/pharmaceutics14071371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/30/2022] [Accepted: 06/07/2022] [Indexed: 12/22/2022] Open
Abstract
Malaria elimination urgently needs novel antimalarial therapies that transcend resistance, toxicity, and high costs. Our multicentric international collaborative team focuses on developing multistage antimalarials that exhibit novel mechanisms of action. Here, we describe the design, synthesis, and evaluation of a novel multistage antimalarial compound, 'Calxinin'. A compound that consists of hydroxyethylamine (HEA) and trifluoromethyl-benzyl-piperazine. Calxinin exhibits potent inhibitory activity in the nanomolar range against the asexual blood stages of drug-sensitive (3D7), multidrug-resistant (Dd2), artemisinin-resistant (IPC4912), and fresh Kenyan field isolated Plasmodium falciparum strains. Calxinin treatment resulted in diminished maturation of parasite sexual precursor cells (gametocytes) accompanied by distorted parasite morphology. Further, in vitro liver-stage testing with a mouse model showed reduced parasite load at an IC50 of 79 nM. A single dose (10 mg/kg) of Calxinin resulted in a 30% reduction in parasitemia in mice infected with a chloroquine-resistant strain of the rodent parasite P. berghei. The ex vivo ookinete inhibitory concentration within mosquito gut IC50 was 150 nM. Cellular in vitro toxicity assays in the primary and immortalized human cell lines did not show cytotoxicity. A computational protein target identification pipeline identified a putative P. falciparum membrane protein (Pf3D7_1313500) involved in parasite calcium (Ca2+) homeostasis as a potential Calxinin target. This highly conserved protein is related to the family of transient receptor potential cation channels (TRP-ML). Target validation experiments showed that exposure of parasitized RBCs (pRBCs) to Calxinin induces a rapid release of intracellular Ca2+ from pRBCs; leaving de-calcinated parasites trapped in RBCs. Overall, we demonstrated that Calxinin is a promising antimalarial lead compound with a novel mechanism of action and with potential therapeutic, prophylactic, and transmission-blocking properties against parasites resistant to current antimalarials.
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Affiliation(s)
- Yash Gupta
- Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.G.); (R.D.)
| | - Neha Sharma
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, New Delhi 110021, India; (N.S.); (S.S.)
| | - Snigdha Singh
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, New Delhi 110021, India; (N.S.); (S.S.)
| | - Jesus G. Romero
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
- School of Biology, Institute of Experimental Biology, Central University of Venezuela, Caracas 1040, Venezuela
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India;
| | - Reagan M. Mogire
- Centre Clinical Research, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya; (R.M.M.); (B.R.O.); (H.M.A.)
| | - Mohammad Kashif
- Infectious Diseases Laboratory, National Institute of Immunology, New Delhi 110067, India; (M.K.); (A.P.S.)
| | - Jordan Beach
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
| | - Walter Jeske
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi, New Delhi 110021, India;
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi 110007, India
| | - Bernhards R. Ogutu
- Centre Clinical Research, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya; (R.M.M.); (B.R.O.); (H.M.A.)
| | - Stefan M. Kanzok
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Hoseah M. Akala
- Centre Clinical Research, Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya; (R.M.M.); (B.R.O.); (H.M.A.)
| | - Jennifer Legac
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA; (J.L.); (P.J.R.)
| | - Philip J. Rosenthal
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA; (J.L.); (P.J.R.)
| | - David J. Rademacher
- Stritch School of Medicine, Loyola University Chicago, Chicago, IL 60660, USA; (J.G.R.); (J.B.); (W.J.); (D.J.R.)
- Core Imaging Facility and Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Ravi Durvasula
- Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.G.); (R.D.)
| | - Agam P. Singh
- Infectious Diseases Laboratory, National Institute of Immunology, New Delhi 110067, India; (M.K.); (A.P.S.)
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College, University of Delhi, New Delhi 110021, India; (N.S.); (S.S.)
- Delhi School of Public Health, Institute of Eminence, University of Delhi, New Delhi 110007, India
| | - Prakasha Kempaiah
- Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (Y.G.); (R.D.)
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Jukič M, Janežič D, Bren U. Potential Novel Thioether-Amide or Guanidine-Linker Class of SARS-CoV-2 Virus RNA-Dependent RNA Polymerase Inhibitors Identified by High-Throughput Virtual Screening Coupled to Free-Energy Calculations. Int J Mol Sci 2021; 22:11143. [PMID: 34681802 PMCID: PMC8540652 DOI: 10.3390/ijms222011143] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new pathogen from the family of Coronaviridae that caused a global pandemic of COVID-19 disease. In the absence of effective antiviral drugs, research of novel therapeutic targets such as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) becomes essential. This viral protein is without a human counterpart and thus represents a unique prospective drug target. However, in vitro biological evaluation testing on RdRp remains difficult and is not widely available. Therefore, we prepared a database of commercial small-molecule compounds and performed an in silico high-throughput virtual screening on the active site of the SARS-CoV-2 RdRp using ensemble docking. We identified a novel thioether-amide or guanidine-linker class of potential RdRp inhibitors and calculated favorable binding free energies of representative hits by molecular dynamics simulations coupled with Linear Interaction Energy calculations. This innovative procedure maximized the respective phase-space sampling and yielded non-covalent inhibitors representing small optimizable molecules that are synthetically readily accessible, commercially available as well as suitable for further biological evaluation and mode of action studies.
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Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Dušanka Janežič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia;
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, SI-6000 Koper, Slovenia
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Madeira F, Madhusoodanan N, Lee J, Tivey ARN, Lopez R. Using EMBL-EBI Services via Web Interface and Programmatically via Web Services. ACTA ACUST UNITED AC 2019; 66:e74. [PMID: 31039604 DOI: 10.1002/cpbi.74] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The European Bioinformatics Institute (EMBL-EBI) provides access to a wide range of core databases and analysis tools that are of key importance in bioinformatics. As well as providing web interfaces to these resources, web services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web service clients provided in Perl, Python, and Java, or would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Fábio Madeira
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nandana Madhusoodanan
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Joon Lee
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Adrian R N Tivey
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Rodrigo Lopez
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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