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Jalencas X, Berg H, Espeland LO, Sreeramulu S, Kinnen F, Richter C, Georgiou C, Yadrykhinsky V, Specker E, Jaudzems K, Miletić T, Harmel R, Gribbon P, Schwalbe H, Brenk R, Jirgensons A, Zaliani A, Mestres J. Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection. RSC Med Chem 2024; 15:1176-1188. [PMID: 38665834 PMCID: PMC11042166 DOI: 10.1039/d3md00724c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 04/28/2024] Open
Abstract
The EU-OPENSCREEN (EU-OS) European Research Infrastructure Consortium (ERIC) is a multinational, not-for-profit initiative that integrates high-capacity screening platforms and chemistry groups across Europe to facilitate research in chemical biology and early drug discovery. Over the years, the EU-OS has assembled a high-throughput screening compound collection, the European Chemical Biology Library (ECBL), that contains approximately 100 000 commercially available small molecules and a growing number of thousands of academic compounds crowdsourced through our network of European and non-European chemists. As an extension of the ECBL, here we describe the computational design, quality control and use case screenings of the European Fragment Screening Library (EFSL) composed of 1056 mini and small chemical fragments selected from a substructure analysis of the ECBL. Access to the EFSL is open to researchers from both academia and industry. Using EFSL, eight fragment screening campaigns using different structural and biophysical methods have successfully identified fragment hits in the last two years. As one of the highlighted projects for antibiotics, we describe the screening by Bio-Layer Interferometry (BLI) of the EFSL, the identification of a 35 μM fragment hit targeting the beta-ketoacyl-ACP synthase 2 (FabF), its binding confirmation to the protein by X-ray crystallography (PDB 8PJ0), its subsequent rapid exploration of its surrounding chemical space through hit-picking of ECBL compounds that contain the fragment hit as a core substructure, and the final binding confirmation of two follow-up hits by X-ray crystallography (PDB 8R0I and 8R1V).
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Affiliation(s)
- Xavier Jalencas
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88 08003 Barcelona Spain
| | - Hannes Berg
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Ludvik Olai Espeland
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
- Department of Chemistry, University of Bergen Allégaten 41 5007 Bergen Norway
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Franziska Kinnen
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Christian Richter
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Charis Georgiou
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
| | | | - Edgar Specker
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis Aizkraules 21 Riga LV-1006 Latvia
| | - Tanja Miletić
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Robert Harmel
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Phil Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) Schnackenburgallee 114 22525 Hamburg Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) Theodor Stern Kai 7 60590 Frankfurt Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Instruct-ERIC Oxford House, Parkway Court, John Smith Drive Oxford OX4 2JY UK
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
- Computational Biology Unit, University of Bergen Thormøhlensgate 55 5008 Bergen Norway
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis Aizkraules 21 Riga LV-1006 Latvia
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) Schnackenburgallee 114 22525 Hamburg Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) Theodor Stern Kai 7 60590 Frankfurt Germany
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88 08003 Barcelona Spain
- Institut de Quimica Computacional i Catalisi, Facultat de Ciencies, Universitat de Girona Maria Aurelia Capmany 69 17003 Girona Catalonia Spain
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Martinez-Sevillano M, Falaguera MJ, Mestres J. CIPSI: An open chemical intellectual property service for medicinal chemists. Mol Inform 2024; 43:e202300221. [PMID: 38010631 DOI: 10.1002/minf.202300221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023]
Abstract
The availability of patent chemical data offers public access to a chemical space that is not well covered by other sources collecting small molecules from scholarly literature. However, open applications to facilitate the search and analysis of biologically-relevant molecular structures present in patents are still largely missing. We have developed CIPSI, an open Chemical Intellectual Property Service @ IMIM to assist medicinal chemists in searching and analysing molecules in SureChEMBL patents. The current version contains 6,240,500 molecules from 236,689 pharmacological patents, of which 5,949,214 are confidently assigned to core chemical structures reminiscent of the Markush structure in the patent claim. The platform includes some graphical tools to facilitate comparative patent analyses between drugs, chemical substructures, and company assignees. CIPSI is available at https://cipsi.org.
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Affiliation(s)
- Maria Martinez-Sevillano
- Systems Pharmacology, Research Group on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Doctor Aiguader 88, 08028, Barcelona, Spain
| | - Maria J Falaguera
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Jordi Mestres
- Systems Pharmacology, Research Group on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Doctor Aiguader 88, 08028, Barcelona, Spain
- Institut de Quimica Computacional i Catalisi, Facultat de Ciencies, Universitat de Girona, Maria Aurelia Capmany 69, 17003, Girona, Spain
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3
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Keller DA, Bassan A, Amberg A, Burns Naas LA, Chambers J, Cross K, Hall F, Jahnke GD, Luniwal A, Manganelli S, Mestres J, Mihalchik-Burhans AL, Woolley D, Tice RR. In silico approaches in carcinogenicity hazard assessment: case study of pregabalin, a nongenotoxic mouse carcinogen. Front Toxicol 2023; 5:1234498. [PMID: 38026843 PMCID: PMC10679394 DOI: 10.3389/ftox.2023.1234498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
In silico toxicology protocols are meant to support computationally-based assessments using principles that ensure that results can be generated, recorded, communicated, archived, and then evaluated in a uniform, consistent, and reproducible manner. We investigated the availability of in silico models to predict the carcinogenic potential of pregabalin using the ten key characteristics of carcinogens as a framework for organizing mechanistic studies. Pregabalin is a single-species carcinogen producing only one type of tumor, hemangiosarcomas in mice via a nongenotoxic mechanism. The overall goal of this exercise is to test the ability of in silico models to predict nongenotoxic carcinogenicity with pregabalin as a case study. The established mode of action (MOA) of pregabalin is triggered by tissue hypoxia, leading to oxidative stress (KC5), chronic inflammation (KC6), and increased cell proliferation (KC10) of endothelial cells. Of these KCs, in silico models are available only for selected endpoints in KC5, limiting the usefulness of computational tools in prediction of pregabalin carcinogenicity. KC1 (electrophilicity), KC2 (genotoxicity), and KC8 (receptor-mediated effects), for which predictive in silico models exist, do not play a role in this mode of action. Confidence in the overall assessments is considered to be medium to high for KCs 1, 2, 5, 6, 7 (immune system effects), 8, and 10 (cell proliferation), largely due to the high-quality experimental data. In order to move away from dependence on animal data, development of reliable in silico models for prediction of oxidative stress, chronic inflammation, immunosuppression, and cell proliferation will be critical for the ability to predict nongenotoxic compound carcinogenicity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jordi Mestres
- Chemotargets SL, Parc Científic de Barcelona, Barcelona, Spain
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Montes-Grajales D, Garcia-Serna R, Mestres J. Impact of the COVID-19 pandemic on the spontaneous reporting and signal detection of adverse drug events. Sci Rep 2023; 13:18817. [PMID: 37914862 PMCID: PMC10620227 DOI: 10.1038/s41598-023-46275-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023] Open
Abstract
External factors severely affecting in a short period of time the spontaneous reporting of adverse events (AEs) can significantly impact drug safety signal detection. Coronavirus disease 2019 (COVID-19) represented an enormous challenge for health systems, with over 767 million cases and massive vaccination campaigns involving over 70% of the worldwide population. This study investigates the potential masking effect on certain AEs caused by the substantial increase in reports solely related to COVID-19 vaccines within various spontaneous reporting systems (SRSs). Three SRSs were used to monitor AEs reporting before and during the pandemic, namely, the World Health Organisation (WHO) global individual case safety reports database (VigiBase®), the United States Food and Drug Administration Adverse Event Reporting System (FAERS) and the Japanese Adverse Drug Event Report database (JADER). Findings revealed a sudden over-reporting of 35 AEs (≥ 200%) during the pandemic, with an increment of the RRF value in 2021 of at least double the RRF reported in 2020. This translates into a substantial reduction in signals of disproportionate reporting (SDR) due to the massive inclusion of COVID-19 vaccine reports. To mitigate the masking effect of COVID-19 vaccines in post-marketing SRS analyses, we recommend utilizing COVID-19-corrected versions for a more accurate assessment.
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Affiliation(s)
- Diana Montes-Grajales
- Chemotargets SL, Parc Científic de Barcelona, Baldiri Reixac 4 (TR-03), 08028, Barcelona, Catalonia, Spain
| | - Ricard Garcia-Serna
- Chemotargets SL, Parc Científic de Barcelona, Baldiri Reixac 4 (TR-03), 08028, Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Chemotargets SL, Parc Científic de Barcelona, Baldiri Reixac 4 (TR-03), 08028, Barcelona, Catalonia, Spain.
- Institut de Quimica Computacional i Catalisi, Facultat de Ciencies, Universitat de Girona, Maria Aurelia Capmany 69, 17003, Girona, Catalonia, Spain.
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Borau C, Wertheim KY, Hervas-Raluy S, Sainz-DeMena D, Walker D, Chisholm R, Richmond P, Varella V, Viceconti M, Montero A, Gregori-Puigjané E, Mestres J, Kasztelnik M, García-Aznar JM. A multiscale orchestrated computational framework to reveal emergent phenomena in neuroblastoma. Comput Methods Programs Biomed 2023; 241:107742. [PMID: 37572512 DOI: 10.1016/j.cmpb.2023.107742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023]
Abstract
Neuroblastoma is a complex and aggressive type of cancer that affects children. Current treatments involve a combination of surgery, chemotherapy, radiotherapy, and stem cell transplantation. However, treatment outcomes vary due to the heterogeneous nature of the disease. Computational models have been used to analyse data, simulate biological processes, and predict disease progression and treatment outcomes. While continuum cancer models capture the overall behaviour of tumours, and agent-based models represent the complex behaviour of individual cells, multiscale models represent interactions at different organisational levels, providing a more comprehensive understanding of the system. In 2018, the PRIMAGE consortium was formed to build a cloud-based decision support system for neuroblastoma, including a multi-scale model for patient-specific simulations of disease progression. In this work we have developed this multi-scale model that includes data such as patient's tumour geometry, cellularity, vascularization, genetics and type of chemotherapy treatment, and integrated it into an online platform that runs the simulations on a high-performance computation cluster using Onedata and Kubernetes technologies. This infrastructure will allow clinicians to optimise treatment regimens and reduce the number of costly and time-consuming clinical trials. This manuscript outlines the challenging framework's model architecture, data workflow, hypothesis, and resources employed in its development.
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Affiliation(s)
- C Borau
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Mechanical Engineering Department, University of Zaragoza, Zaragoza, Spain.
| | - K Y Wertheim
- Department of Computer Science and InsigneoInstitute for In Silico Medicine, University of Sheffield, Sheffield, United Kingdom; Centre of Excellence for Data Science, Artificial Intelligence and Modelling and School of Computer Science, University of Hull, Kingston upon Hull, United Kingdom
| | - S Hervas-Raluy
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Mechanical Engineering Department, University of Zaragoza, Zaragoza, Spain
| | - D Sainz-DeMena
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Mechanical Engineering Department, University of Zaragoza, Zaragoza, Spain
| | - D Walker
- Department of Computer Science and InsigneoInstitute for In Silico Medicine, University of Sheffield, Sheffield, United Kingdom
| | - R Chisholm
- Department of Computer Science and InsigneoInstitute for In Silico Medicine, University of Sheffield, Sheffield, United Kingdom
| | - P Richmond
- Department of Computer Science and InsigneoInstitute for In Silico Medicine, University of Sheffield, Sheffield, United Kingdom
| | - V Varella
- Department of Industrial Engineering, Alma Mater Studiorum - University of Bologna, Bologna, Italy; Medical Technology Lab, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - M Viceconti
- Department of Industrial Engineering, Alma Mater Studiorum - University of Bologna, Bologna, Italy; Medical Technology Lab, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - A Montero
- Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | - E Gregori-Puigjané
- Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | - J Mestres
- Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), Barcelona, Spain
| | - M Kasztelnik
- ACC Cyfronet, AGH University of Science and Technology, Kraków, Poland
| | - J M García-Aznar
- Multiscale in Mechanical and Biological Engineering (M2BE), Aragon Institute of Engineering Research (I3A), Mechanical Engineering Department, University of Zaragoza, Zaragoza, Spain
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6
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Furuhama A, Kitazawa A, Yao J, Matos Dos Santos CE, Rathman J, Yang C, Ribeiro JV, Cross K, Myatt G, Raitano G, Benfenati E, Jeliazkova N, Saiakhov R, Chakravarti S, Foster RS, Bossa C, Battistelli CL, Benigni R, Sawada T, Wasada H, Hashimoto T, Wu M, Barzilay R, Daga PR, Clark RD, Mestres J, Montero A, Gregori-Puigjané E, Petkov P, Ivanova H, Mekenyan O, Matthews S, Guan D, Spicer J, Lui R, Uesawa Y, Kurosaki K, Matsuzaka Y, Sasaki S, Cronin MTD, Belfield SJ, Firman JW, Spînu N, Qiu M, Keca JM, Gini G, Li T, Tong W, Hong H, Liu Z, Igarashi Y, Yamada H, Sugiyama KI, Honma M. Evaluation of QSAR models for predicting mutagenicity: outcome of the Second Ames/QSAR international challenge project. SAR QSAR Environ Res 2023; 34:983-1001. [PMID: 38047445 DOI: 10.1080/1062936x.2023.2284902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/13/2023] [Indexed: 12/05/2023]
Abstract
Quantitative structure-activity relationship (QSAR) models are powerful in silico tools for predicting the mutagenicity of unstable compounds, impurities and metabolites that are difficult to examine using the Ames test. Ideally, Ames/QSAR models for regulatory use should demonstrate high sensitivity, low false-negative rate and wide coverage of chemical space. To promote superior model development, the Division of Genetics and Mutagenesis, National Institute of Health Sciences, Japan (DGM/NIHS), conducted the Second Ames/QSAR International Challenge Project (2020-2022) as a successor to the First Project (2014-2017), with 21 teams from 11 countries participating. The DGM/NIHS provided a curated training dataset of approximately 12,000 chemicals and a trial dataset of approximately 1,600 chemicals, and each participating team predicted the Ames mutagenicity of each trial chemical using various Ames/QSAR models. The DGM/NIHS then provided the Ames test results for trial chemicals to assist in model improvement. Although overall model performance on the Second Project was not superior to that on the First, models from the eight teams participating in both projects achieved higher sensitivity than models from teams participating in only the Second Project. Thus, these evaluations have facilitated the development of QSAR models.
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Affiliation(s)
- A Furuhama
- Division of Genetics and Mutagenesis (DGM), National Institute of Health Sciences (NIHS), Kawasaki, Japan
| | - A Kitazawa
- Division of Genetics and Mutagenesis (DGM), National Institute of Health Sciences (NIHS), Kawasaki, Japan
| | - J Yao
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials (Chinese Academy of Sciences), Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences (SIOC, CAS), Shanghai, China
| | - C E Matos Dos Santos
- Department of Computational Toxicology and In Silico Innovations, Altox Ltd, São Paulo-SP, Brazil
| | - J Rathman
- MN-AM, Nuremberg, Germany/Columbus, OH, USA
| | - C Yang
- MN-AM, Nuremberg, Germany/Columbus, OH, USA
| | | | - K Cross
- In Silico Department, Instem, Conshohocken, PA, USA
| | - G Myatt
- In Silico Department, Instem, Conshohocken, PA, USA
| | - G Raitano
- Laboratory of Environmental Toxicology and Chemistry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS (IRFMN), Milano, Italy
| | - E Benfenati
- Laboratory of Environmental Toxicology and Chemistry, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS (IRFMN), Milano, Italy
| | | | | | | | | | - C Bossa
- Environment and Health Department, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - C Laura Battistelli
- Environment and Health Department, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - R Benigni
- Environment and Health Department, Istituto Superiore di Sanità (ISS), Rome, Italy
- Alpha-PreTox, Rome, Italy
| | - T Sawada
- Faculty of Regional Studies, Gifu University, Gifu, Japan
- xenoBiotic Inc, Gifu, Japan
| | - H Wasada
- Faculty of Regional Studies, Gifu University, Gifu, Japan
| | - T Hashimoto
- Faculty of Regional Studies, Gifu University, Gifu, Japan
| | - M Wu
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - R Barzilay
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - P R Daga
- Simulations Plus, Lancaster, CA, USA
| | - R D Clark
- Simulations Plus, Lancaster, CA, USA
| | | | | | | | - P Petkov
- LMC - Bourgas University, Bourgas, Bulgaria
| | - H Ivanova
- LMC - Bourgas University, Bourgas, Bulgaria
| | - O Mekenyan
- LMC - Bourgas University, Bourgas, Bulgaria
| | - S Matthews
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - D Guan
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - J Spicer
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - R Lui
- Computational Pharmacology & Toxicology Laboratory, Discipline of Pharmacology, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Y Uesawa
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Tokyo, Japan
| | - K Kurosaki
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Tokyo, Japan
| | - Y Matsuzaka
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Tokyo, Japan
| | - S Sasaki
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Tokyo, Japan
| | - M T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - S J Belfield
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - J W Firman
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - N Spînu
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - M Qiu
- Evergreen AI, Inc, Toronto, Canada
| | - J M Keca
- Evergreen AI, Inc, Toronto, Canada
| | - G Gini
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Milano, Italy
| | - T Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration (NCTR/FDA), Jefferson, AR, USA
| | - W Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration (NCTR/FDA), Jefferson, AR, USA
| | - H Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration (NCTR/FDA), Jefferson, AR, USA
| | - Z Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration (NCTR/FDA), Jefferson, AR, USA
- Integrative Toxicology, Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals, Inc, Ridgefield, CT, USA
| | - Y Igarashi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - H Yamada
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - K-I Sugiyama
- Division of Genetics and Mutagenesis (DGM), National Institute of Health Sciences (NIHS), Kawasaki, Japan
| | - M Honma
- Division of Genetics and Mutagenesis (DGM), National Institute of Health Sciences (NIHS), Kawasaki, Japan
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Falaguera MJ, Mestres J. Illuminating the Chemical Space of Untargeted Proteins. J Chem Inf Model 2023; 63:2689-2698. [PMID: 37074232 DOI: 10.1021/acs.jcim.2c01364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
According to the Illuminating the Druggable Genome (IDG) initiative, 90% of the proteins encoded by the human genome still lack an identified active ligand, that is, a small molecule with biologically relevant binding potency or functional activity in an in vitro assay. Under this scenario, there is an urgent need for new approaches to chemically address these yet untargeted proteins. It is widely recognized that the best starting point for generating novel small molecules for proteins is to exploit the expected polypharmacology of known active ligands across phylogenetically related proteins following the paradigm that similar proteins are likely to interact with similar ligands. Here, we introduce a computational strategy to identify privileged structures that, when chemically expanded, are highly probable to contain active small molecules for untargeted proteins. The protocol was first tested on a set of 576 currently targeted proteins having at least one protein family sibling the year before their first active ligand was reported. A privileged structure contained in active ligands that were identified in the following years was correctly anticipated for 214 (37%) of those targeted proteins, a lower-bound recall estimate when considering data completeness issues. When applied to a set of 1184 untargeted potential druggable genes in cancer, the identification of privileged structures from known bioactive ligands of protein family siblings allowed for extracting a priority list of diverse commercially available small molecules for 960 of them. Assuming a minimum success rate of 37%, the chemical library selections should be able to deliver active ligands for at least 355 currently untargeted proteins associated with cancer.
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Affiliation(s)
- Maria J Falaguera
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Parc de Recerca Biomedica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
- Chemotargets SL, Parc Cientific de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Parc de Recerca Biomedica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
- Chemotargets SL, Parc Cientific de Barcelona, Baldiri Reixac 4, 08028 Barcelona, Catalonia, Spain
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8
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Solanes-Cabús M, Paredes E, Limón E, Basora J, Alarcón I, Veganzones I, Conangla L, Casado N, Ortega Y, Mestres J, Acezat J, Deniel J, Cabré JJ, Ruiz DS, Sánchez M, Illa A, Viñas I, Montero JJ, Cantero FX, Rodriguez A, Martín F, Baré M, Ripollés R, Castellet M, Lozano J, Sisó-Almirall A. Primary and Community Care Transformation in Post-COVID Era: Nationwide General Practitioner Survey. Int J Environ Res Public Health 2023; 20:1600. [PMID: 36674354 PMCID: PMC9866570 DOI: 10.3390/ijerph20021600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Introduction: The health emergency caused by COVID-19 has led to substantial changes in the usual working system of primary healthcare centers and in relations with users. The Catalan Society of Family and Community Medicine designed a survey that aimed to collect the opinions and facilitate the participation of its partners on what the future work model of general practitioners (GPs) should look like post-COVID-19. Methodology: Online survey of Family and Community Medicine members consisting of filiation data, 22 Likert-type multiple-choice questions grouped in five thematic axes, and a free text question. Results: The number of respondents to the questionnaire was 1051 (22.6% of all members): 83.2% said they spent excessive time on bureaucratic tasks; 91.8% were against call center systems; 66% believed that home care is the responsibility of every family doctor; 77.5% supported continuity of care as a fundamental value of patient-centered care; and >90% defended the contracting of complementary tests and first hospital visits from primary healthcare (PHC). Conclusions: The survey responses describe a strong consensus on the identity and competencies of the GP and on the needs of and the threats to the PHC system. The demand for an increase in health resources, greater professional leadership, elimination of bureaucracy, an increase in the number of health professionals, and greater management autonomy, are the axes towards which a new era in PHC should be directed.
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Affiliation(s)
- Mònica Solanes-Cabús
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Onze de Setembre, Institut Català de la Salut, 25005 Lleida, Spain
| | - Eugeni Paredes
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Onze de Setembre, Institut Català de la Salut, 25005 Lleida, Spain
| | - Esther Limón
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Ronda Prim, Mataró, Institut Català de la Salut, 08302 Barcelona, Spain
| | - Josep Basora
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- IDIAP Jordi Gol, Institut Català de la Salut, 08007 Barcelona, Spain
| | - Iris Alarcón
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Service Dreta i Muntanya Barcelona, Institut Català de la Salut, 08007 Barcelona, Spain
| | - Irene Veganzones
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- School of Medicine, Vic University, 08500 Barcelona, Spain
| | - Laura Conangla
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Badalona Centre, Institut Català de la Salut, 08911 Barcelona, Spain
| | - Núria Casado
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Nova Lloreda, Badalona Serveis Assistencials, 08917 Barcelona, Spain
| | - Yolanda Ortega
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Salou, Institut Català de la Salut, 43005 Tarragona, Spain
| | - Jordi Mestres
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Sanllehy, Institut Català de la Salut, 08024 Barcelona, Spain
| | - Jordi Acezat
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Casernes, Institut Català de la Salut, 08030 Barcelona, Spain
| | - Joan Deniel
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Multiprofessional Teaching Unit of Primary Care in Catalunya Central, Institut Català de la Salut, 08272 Barcelona, Spain
| | - Joan Josep Cabré
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Reus-1, Institut Català de la Salut, 43202 Tarragona, Spain
| | - Daniel Sánchez Ruiz
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Sardenya, ACEBA, 08025 Barcelona, Spain
| | - Marcos Sánchez
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Les Corts, CAPSBE, 08028 Barcelona, Spain
| | - Aroa Illa
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Celrà, Institut Català de la Salut, 17460 Girona, Spain
| | - Ignasi Viñas
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Montilivi-Vilaroja, Institut Català de la Salut, 17003 Girona, Spain
| | - Juan José Montero
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Rocafonda, Institut Català de la Salut, 08304 Barcelona, Spain
| | - Francesc Xavier Cantero
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Igualada Urbà, Institut Català de la Salut, 08700 Barcelona, Spain
| | - Anna Rodriguez
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Santa Eugènia de Berga, Institut Català de la Salut, 08507 Barcelona, Spain
| | - Francisco Martín
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Healthcare Research Support Unit, Departament of Primary Care Camp de Tarragona, Institut Català de la Salut, 43202 Tarragona, Spain
| | - Montserrat Baré
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Creu Alta, Institut Català de la Salut, 08208 Barcelona, Spain
| | - Rosa Ripollés
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Temple, Institut Català de la Salut, Terres de l’Ebre, 43500 Tarragona, Spain
| | - Montse Castellet
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Dr. Joan Mirabell, Institut Català de la Salut, 08006 Barcelona, Spain
| | - Joan Lozano
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
| | - Antoni Sisó-Almirall
- Family Phisician, Exective Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain
- Primary Care Center Les Corts, CAPSBE, 08028 Barcelona, Spain
- Department of Medicine, University of Barcelona, 08036 Barcelona, Spain
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9
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Bajorath J, Chávez-Hernández AL, Duran-Frigola M, Fernández-de Gortari E, Gasteiger J, López-López E, Maggiora GM, Medina-Franco JL, Méndez-Lucio O, Mestres J, Miranda-Quintana RA, Oprea TI, Plisson F, Prieto-Martínez FD, Rodríguez-Pérez R, Rondón-Villarreal P, Saldívar-Gonzalez FI, Sánchez-Cruz N, Valli M. Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds. J Cheminform 2022; 14:82. [PMID: 36461094 PMCID: PMC9716667 DOI: 10.1186/s13321-022-00661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15-17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. During the meeting, applications, challenges, and opportunities in drug discovery, de novo drug design, ADME-Tox (absorption, distribution, metabolism, excretion and toxicity) property predictions, organic chemistry, peptides, and antibiotic resistance were discussed. The program along with the recordings of all sessions are freely available at https://www.difacquim.com/english/events/2022-colloquium/ .
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Affiliation(s)
- Jürgen Bajorath
- grid.10388.320000 0001 2240 3300Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53113 Bonn, Germany
| | - Ana L. Chávez-Hernández
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Miquel Duran-Frigola
- Ersilia Open Source Initiative, Cambridge, UK ,grid.7722.00000 0001 1811 6966Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia Spain
| | - Eli Fernández-de Gortari
- grid.420330.60000 0004 0521 6935Nanosafety Laboratory, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Johann Gasteiger
- grid.5330.50000 0001 2107 3311Computer-Chemie-Centrum, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Edgar López-López
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico ,grid.512574.0Department of Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), 07360 Mexico City, Mexico
| | - Gerald M. Maggiora
- grid.134563.60000 0001 2168 186XBIO5 Institute, University of Arizona, Tucson, AZ 85721 USA
| | - José L. Medina-Franco
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | | | - Jordi Mestres
- grid.5841.80000 0004 1937 0247Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), 08028 Barcelona, Catalonia Spain ,grid.20522.370000 0004 1767 9005Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomedica (PRBB), 08003 Barcelona, Catalonia Spain
| | | | - Tudor I. Oprea
- grid.266832.b0000 0001 2188 8502Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131 USA ,grid.8761.80000 0000 9919 9582Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at Gothenburg University, 40530 Gothenburg, Sweden ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark ,Present Address: Roivant Discovery Sciences, Inc., 451 D Street, Boston, MA 02210 USA
| | - Fabien Plisson
- grid.512574.0Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Irapuato Unit, 36824 Irapuato, Gto Mexico
| | - Fernando D. Prieto-Martínez
- grid.9486.30000 0001 2159 0001Chemistry Institute, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Raquel Rodríguez-Pérez
- grid.419481.10000 0001 1515 9979Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Paola Rondón-Villarreal
- grid.442204.40000 0004 0486 1035Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Calle 70 No. 55-210, 680003 Santander, Bucaramanga Colombia
| | - Fernanda I. Saldívar-Gonzalez
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Norberto Sánchez-Cruz
- grid.5841.80000 0004 1937 0247Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), 08028 Barcelona, Catalonia Spain ,grid.9486.30000 0001 2159 0001Instituto de Química, Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Yucatán, 97357 Ucú, Mexico
| | - Marilia Valli
- grid.410543.70000 0001 2188 478XNuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University-UNESP, Araraquara, Brazil
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10
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Galyan SM, Ewald CY, Jalencas X, Masrani S, Meral S, Mestres J. Fragment-based virtual screening identifies a first-in-class preclinical drug candidate for Huntington's disease. Sci Rep 2022; 12:19642. [PMID: 36385140 PMCID: PMC9668931 DOI: 10.1038/s41598-022-21900-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022] Open
Abstract
Currently, there are no therapies available to modify the disease progression of Huntington's disease (HD). Recent clinical trial failures of antisense oligonucleotide candidates in HD have demonstrated the need for new therapeutic approaches. Here, we developed a novel in-silico fragment scanning approach across the surface of mutant huntingtin (mHTT) polyQ and predicted four hit compounds. Two rounds of compound analoging using a strategy of testing structurally similar compounds in an affinity assay rapidly identified GLYN122. In vitro, GLYN122 directly binds and reduces mHTT and induces autophagy in neurons. In vivo, our results confirm that GLYN122 can reduce mHTT in the cortex and striatum of the R/2 mouse model of Huntington's disease and subsequently improve motor symptoms. Thus, the in-vivo pharmacology profile of GLYN122 is a potential new preclinical candidate for the treatment of HD.
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Affiliation(s)
| | - Collin Y. Ewald
- grid.5801.c0000 0001 2156 2780Laboratory of Extracellular Matrix Regeneration, Department of Health Sciences and Technology, Institute of Translational Medicine, ETH Zürich, 8603 Schwerzenbach, Switzerland
| | - Xavier Jalencas
- grid.5841.80000 0004 1937 0247Chemotargets SL, Parc Científic de Barcelona, 08028 Barcelona, Catalonia Spain ,IMIM Hospital del Mar Medical Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia Spain
| | - Shyam Masrani
- Medicxi Ventures, 25 Great Pulteney St, London, W1F 9NH UK
| | - Selin Meral
- Biomedical Center Munich of the University of Munich, Großhaderner Str. 9, 82152 Planegg, Germany
| | - Jordi Mestres
- grid.5841.80000 0004 1937 0247Chemotargets SL, Parc Científic de Barcelona, 08028 Barcelona, Catalonia Spain ,IMIM Hospital del Mar Medical Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia Spain
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11
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Faria M, Bellot M, Bedrossiantz J, Ramírez JRR, Prats E, Garcia-Reyero N, Gomez-Canela C, Mestres J, Rovira X, Barata C, Oliván LMG, Llebaria A, Raldua D. Environmental levels of carbaryl impair zebrafish larvae behaviour: The potential role of ADRA2B and HTR2B. J Hazard Mater 2022; 431:128563. [PMID: 35248961 DOI: 10.1016/j.jhazmat.2022.128563] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
The insecticide carbaryl is commonly found in indirectly exposed freshwater ecosystems at low concentrations considered safe for fish communities. In this study, we showed that after only 24 h of exposure to environmental concentrations of carbaryl (0.066-660 ng/L), zebrafish larvae exhibit impairments in essential behaviours. Interestingly, the observed behavioural effects induced by carbaryl were acetylcholinesterase-independent. To elucidate the molecular initiating event that resulted in the observed behavioural effects, in silico predictions were followed by in vitro validation. We identified two target proteins that potentially interacted with carbaryl, the α2B adrenoceptor (ADRA2B) and the serotonin 2B receptor (HTR2B). Using a pharmacological approach, we then tested the hypothesis that carbaryl had antagonistic interactions with both receptors. Similar to yohimbine and SB204741, which are prototypic antagonists of ADRA2B and HTR2B, respectively, carbaryl increased the heart rate of zebrafish larvae. When we compared the behavioural effects of a 24-h exposure to these pharmacological antagonists with those of carbaryl, a high degree of similarity was found. These results strongly suggest that antagonism of both ADRA2B and HTR2B is the molecular initiating event that leads to adverse outcomes in zebrafish larvae that have undergone 24 h of exposure to environmentally relevant levels of carbaryl.
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Affiliation(s)
- Melissa Faria
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18, 08034 Barcelona, Spain
| | - Marina Bellot
- Department of Analytical Chemistry and Applied (Chromatography section), School of Engineering, Institut Químic de Sarrià-Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Juliette Bedrossiantz
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18, 08034 Barcelona, Spain
| | - Jonathan Ricardo Rosas Ramírez
- Laboratorio de Toxicología Ambiental, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón intersección Paseo Tollocan s/n. Col. Residencial Colón, 50120 Toluca, Estado de México, Mexico
| | - Eva Prats
- Research and Development Center (CID-CSIC), Jordi Girona 18, 08034 Barcelona, Spain
| | - Natalia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Cristian Gomez-Canela
- Department of Analytical Chemistry and Applied (Chromatography section), School of Engineering, Institut Químic de Sarrià-Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Jordi Mestres
- Chemotargets, IMIM-Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Xavier Rovira
- MCS, Laboratory of Medicinal Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
| | - Carlos Barata
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18, 08034 Barcelona, Spain
| | - Leobardo Manuel Gómez Oliván
- Laboratorio de Toxicología Ambiental, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón intersección Paseo Tollocan s/n. Col. Residencial Colón, 50120 Toluca, Estado de México, Mexico
| | - Amadeu Llebaria
- MCS, Laboratory of Medicinal Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), 08034 Barcelona, Spain
| | - Demetrio Raldua
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18, 08034 Barcelona, Spain.
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12
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Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ, Oprea TI. A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. J Chem Inf Model 2022; 62:718-729. [PMID: 35057621 PMCID: PMC10790216 DOI: 10.1021/acs.jcim.1c00431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the event of an outbreak due to an emerging pathogen, time is of the essence to contain or to mitigate the spread of the disease. Drug repositioning is one of the strategies that has the potential to deliver therapeutics relatively quickly. The SARS-CoV-2 pandemic has shown that integrating critical data resources to drive drug-repositioning studies, involving host-host, host-pathogen, and drug-target interactions, remains a time-consuming effort that translates to a delay in the development and delivery of a life-saving therapy. Here, we describe a workflow we designed for a semiautomated integration of rapidly emerging data sets that can be generally adopted in a broad network pharmacology research setting. The workflow was used to construct a COVID-19 focused multimodal network that integrates 487 host-pathogen, 63 278 host-host protein, and 1221 drug-target interactions. The resultant Neo4j graph database named "Neo4COVID19" is made publicly accessible via a web interface and via API calls based on the Bolt protocol. Details for accessing the database are provided on a landing page (https://neo4covid19.ncats.io/). We believe that our Neo4COVID19 database will be a valuable asset to the research community and will catalyze the discovery of therapeutics to fight COVID-19.
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Affiliation(s)
| | - Vishal B. Siramshetty
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Praveen Kumar
- Department of Internal Medicine, University of New Mexico School of Medicine, 1 University of New Mexico, Albuquerque, NM 87131, USA
- Department of Computer Science, University of New Mexico, 1 University of New Mexico Albuquerque, NM 87131, USA
| | - Manideep Gurumurthy
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Busola Grillo
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Biju Mathew
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Dimitrios Metaxatos
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Mark Backus
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Tim Mierzwa
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Reid Simon
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Ivan Grishagin
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
- Rancho BioSciences LLC., 16955 Via Del Campo Suite 200, San Diego, CA 92127, USA
| | - Laura Brovold
- Rancho BioSciences LLC., 16955 Via Del Campo Suite 200, San Diego, CA 92127, USA
| | - Ewy A. Mathé
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Alexander G. Godfrey
- National Center for Advancing Translational Sciences, Rockville, 9800 Medical Center Dr., MD 20850, USA
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Lars J. Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences,University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Tudor I. Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, 1 University of New Mexico, Albuquerque, NM 87131, USA
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences,University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
- UNM Comprehensive Cancer Center, 1201 Camino de Salud NE, Albuquerque, NM 87102, USA
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
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13
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Gray B, Baruteau AE, Antolin AA, Pittman A, Sarganas G, Molokhia M, Blom MT, Bastiaenen R, Bardai A, Priori SG, Napolitano C, Weeke PE, Shakir SA, Haverkamp W, Mestres J, Winkel BG, Witney AA, Chis-Ster I, Sangaralingam A, Camm AJ, Tfelt-Hansen J, Roden DM, Tan HL, Garbe E, Sturkenboom M, Behr ER. Rare Variation in Drug Metabolism and Long QT Genes and the Genetic Susceptibility to Acquired Long QT Syndrome. Circ Genom Precis Med 2022; 15:e003391. [PMID: 35113648 DOI: 10.1161/circgen.121.003391] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Acquired long QT syndrome (aLQTS) is a serious unpredictable adverse drug reaction. Pharmacogenomic markers may predict risk. METHODS Among 153 aLQTS patients (mean age 58 years [range, 14-88], 98.7% White, 85.6% symptomatic), computational methods identified proteins interacting most significantly with 216 QT-prolonging drugs. All cases underwent sequencing of 31 candidate genes arising from this analysis or associating with congenital LQTS. Variants were filtered using a minor allele frequency <1% and classified for susceptibility for aLQTS. Gene-burden analyses were then performed comparing the primary cohort to control exomes (n=452) and an independent replication aLQTS exome sequencing cohort. RESULTS In 25.5% of cases, at least one rare variant was identified: 22.2% of cases carried a rare variant in a gene associated with congenital LQTS, and in 4% of cases that variant was known to be pathogenic or likely pathogenic for congenital LQTS; 7.8% cases carried a cytochrome-P450 (CYP) gene variant. Of 12 identified CYP variants, 11 (92%) were in an enzyme known to metabolize at least one culprit drug to which the subject had been exposed. Drug-drug interactions that affected culprit drug metabolism were found in 19% of cases. More than one congenital LQTS variant, CYP gene variant, or drug interaction was present in 7.8% of cases. Gene-burden analyses of the primary cohort compared to control exomes (n=452), and an independent replication aLQTS exome sequencing cohort (n=67) and drug-tolerant controls (n=148) demonstrated an increased burden of rare (minor allele frequency<0.01) variants in CYP genes but not LQTS genes. CONCLUSIONS Rare susceptibility variants in CYP genes are emerging as potentially important pharmacogenomic risk markers for aLQTS and could form part of personalized medicine approaches in the future.
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Affiliation(s)
- Belinda Gray
- Cardiology Clinical Academic Group, Molecular & Clinical Sciences Research Institute, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, United Kingdom (B.G., A.-E.B., R.B., A.S., A.J.C., E.R.B.)
| | - Alban-Elouen Baruteau
- Cardiology Clinical Academic Group, Molecular & Clinical Sciences Research Institute, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, United Kingdom (B.G., A.-E.B., R.B., A.S., A.J.C., E.R.B.)
- L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU Nantes, Nantes, France (A.-E.B.)
| | - Albert A Antolin
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute & University Pompeu Fabra, Parc de Recerca Biomedica, Barcelona, Catalonia, Spain (A.A.A., M.J.M.)
| | - Alan Pittman
- Genetics Research Centre (A.P.), St George's University of London, United Kingdom
| | - Giselle Sarganas
- Clinical Pharmacology & Toxicology, Charite Universitaetsmedizin, Berlin, Germany (G.S.)
| | - Mariam Molokhia
- Department of Population Health Sciences, King's College London, United Kingdom (M.M.)
| | - Marieke T Blom
- Heart Centre AMC, Department of Experimental & Clinical Cardiology, Academic Medical Center, Amsterdam, the Netherlands (M.T.B., A.B., H.L.T.)
| | - Rachel Bastiaenen
- Cardiology Clinical Academic Group, Molecular & Clinical Sciences Research Institute, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, United Kingdom (B.G., A.-E.B., R.B., A.S., A.J.C., E.R.B.)
| | - Abdenasser Bardai
- Heart Centre AMC, Department of Experimental & Clinical Cardiology, Academic Medical Center, Amsterdam, the Netherlands (M.T.B., A.B., H.L.T.)
| | - Silvia G Priori
- Molecular Cardiology, IRCCS ICS Maugeri, Pavia, Italy (S.G.P., C.N.)
- Department of Molecular Medicine, University of Pavia, Italy (S.G.P., C.N.)
| | - Carlo Napolitano
- Molecular Cardiology, IRCCS ICS Maugeri, Pavia, Italy (S.G.P., C.N.)
- Department of Molecular Medicine, University of Pavia, Italy (S.G.P., C.N.)
| | - Peter E Weeke
- L'institut du thorax, INSERM, CNRS, UNIV Nantes, CHU Nantes, Nantes, France (A.-E.B.)
- Departments of Medicine, Pharmacology & Biomedical Informatics Vanderbilt University Medical Centre (P.E.W., D.M.R.)
| | - Saad A Shakir
- Drug Safety Research Unit, Bursledon Hall, Blundell Lane, Southampton, United Kingdom (S.A.S.)
- Associate Department of the School of Pharmacy & Biomedical Sciences, University of Portsmouth, United Kingdom (S.A.S.)
| | - Wilhelm Haverkamp
- Charité-Campus Virchow-Klinikum (CVK), Department of Cardiology, Berlin, Germany (W.H.)
| | - Jordi Mestres
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute & University Pompeu Fabra, Parc de Recerca Biomedica, Barcelona, Catalonia, Spain (A.A.A., M.J.M.)
| | - Bo Gregers Winkel
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Copenhagen, Denmark (B.W., J.T.-H.)
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Denmark (P.E.W., B.W., J.T.-H.)
| | - Adam A Witney
- Institute of Infection & Immunity (A.A.W., I.C.-S.), St George's University of London, United Kingdom
| | - Irina Chis-Ster
- Institute of Infection & Immunity (A.A.W., I.C.-S.), St George's University of London, United Kingdom
| | - Ajanthah Sangaralingam
- Cardiology Clinical Academic Group, Molecular & Clinical Sciences Research Institute, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, United Kingdom (B.G., A.-E.B., R.B., A.S., A.J.C., E.R.B.)
| | - A John Camm
- Cardiology Clinical Academic Group, Molecular & Clinical Sciences Research Institute, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, United Kingdom (B.G., A.-E.B., R.B., A.S., A.J.C., E.R.B.)
| | - Jacob Tfelt-Hansen
- Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Denmark (P.E.W., B.W., J.T.-H.)
- Department of Forensic Medicine, Faculty of Medical Sciences, University of Copenhagen, Denmark (B.W., J.T.-H.)
| | - Dan M Roden
- Departments of Medicine, Pharmacology & Biomedical Informatics Vanderbilt University Medical Centre (P.E.W., D.M.R.)
| | - Hanno L Tan
- Heart Centre AMC, Department of Experimental & Clinical Cardiology, Academic Medical Center, Amsterdam, the Netherlands (M.T.B., A.B., H.L.T.)
| | - Edeltraut Garbe
- Leibniz Institute for Prevention Research & Epidemiology - BIPS, Bremen, Germany (E.G.)
| | - Miriam Sturkenboom
- Julius Global Health, University Medical Center Utrecht, the Netherlands (M.S.)
| | - Elijah R Behr
- Cardiology Clinical Academic Group, Molecular & Clinical Sciences Research Institute, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, United Kingdom (B.G., A.-E.B., R.B., A.S., A.J.C., E.R.B.)
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14
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Tice RR, Bassan A, Amberg A, Anger LT, Beal MA, Bellion P, Benigni R, Birmingham J, Brigo A, Bringezu F, Ceriani L, Crooks I, Cross K, Elespuru R, Faulkner DM, Fortin MC, Fowler P, Frericks M, Gerets HHJ, Jahnke GD, Jones DR, Kruhlak NL, Lo Piparo E, Lopez-Belmonte J, Luniwal A, Luu A, Madia F, Manganelli S, Manickam B, Mestres J, Mihalchik-Burhans AL, Neilson L, Pandiri A, Pavan M, Rider CV, Rooney JP, Trejo-Martin A, Watanabe-Sailor KH, White AT, Woolley D, Myatt GJ. In Silico Approaches In Carcinogenicity Hazard Assessment: Current Status and Future Needs. Comput Toxicol 2021; 20. [PMID: 35368437 DOI: 10.1016/j.comtox.2021.100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Historically, identifying carcinogens has relied primarily on tumor studies in rodents, which require enormous resources in both money and time. In silico models have been developed for predicting rodent carcinogens but have not yet found general regulatory acceptance, in part due to the lack of a generally accepted protocol for performing such an assessment as well as limitations in predictive performance and scope. There remains a need for additional, improved in silico carcinogenicity models, especially ones that are more human-relevant, for use in research and regulatory decision-making. As part of an international effort to develop in silico toxicological protocols, a consortium of toxicologists, computational scientists, and regulatory scientists across several industries and governmental agencies evaluated the extent to which in silico models exist for each of the recently defined 10 key characteristics (KCs) of carcinogens. This position paper summarizes the current status of in silico tools for the assessment of each KC and identifies the data gaps that need to be addressed before a comprehensive in silico carcinogenicity protocol can be developed for regulatory use.
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Affiliation(s)
- Raymond R Tice
- RTice Consulting, Hillsborough, North Carolina, 27278, USA
| | | | - Alexander Amberg
- Sanofi Preclinical Safety, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Lennart T Anger
- Genentech, Inc., South San Francisco, California, 94080, USA
| | - Marc A Beal
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | | | | | - Jeffrey Birmingham
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
| | - Alessandro Brigo
- Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation, Center Basel, F. Hoffmann-La Roche Ltd, CH-4070, Basel, Switzerland
| | | | - Lidia Ceriani
- Humane Society International, 1000 Brussels, Belgium
| | - Ian Crooks
- British American Tobacco (Investments) Ltd, GR&D Centre, Southampton, SO15 8TL, United Kingdom
| | | | - Rosalie Elespuru
- Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, Maryland, 20993, USA
| | - David M Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marie C Fortin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey, 08855, USA
| | - Paul Fowler
- FSTox Consulting (Genetic Toxicology), Northamptonshire, United Kingdom
| | | | | | - Gloria D Jahnke
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Naomi L Kruhlak
- Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, Maryland, 20993, USA
| | - Elena Lo Piparo
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Juan Lopez-Belmonte
- Cuts Ice Ltd Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Amarjit Luniwal
- North American Science Associates (NAMSA) Inc., Minneapolis, Minnesota, 55426, USA
| | - Alice Luu
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Serena Manganelli
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | | | - Jordi Mestres
- IMIM Institut Hospital Del Mar d'Investigacions Mèdiques and Universitat Pompeu Fabra, Doctor Aiguader 88, Parc de Recerca Biomèdica, 08003 Barcelona, Spain; and Chemotargets SL, Baldiri Reixac 4, Parc Científic de Barcelona, 08028, Barcelona, Spain
| | | | - Louise Neilson
- Broughton Nicotine Services, Oak Tree House, Earby, Lancashire, BB18 6JZ United Kingdom
| | - Arun Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Cynthia V Rider
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | - John P Rooney
- Integrated Laboratory Systems, LLC., Morrisville, North Carolina, 27560, USA
| | | | - Karen H Watanabe-Sailor
- School of Mathematical and Natural Sciences, Arizona State University, West Campus, Glendale, Arizona, 85306, USA
| | - Angela T White
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
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15
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Sánchez-Cruz N, Medina-Franco JL, Mestres J, Barril X. Extended connectivity interaction features: improving binding affinity prediction through chemical description. Bioinformatics 2021; 37:1376-1382. [PMID: 33226061 DOI: 10.1093/bioinformatics/btaa982] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/27/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Machine-learning scoring functions (SFs) have been found to outperform standard SFs for binding affinity prediction of protein-ligand complexes. A plethora of reports focus on the implementation of increasingly complex algorithms, while the chemical description of the system has not been fully exploited. RESULTS Herein, we introduce Extended Connectivity Interaction Features (ECIF) to describe protein-ligand complexes and build machine-learning SFs with improved predictions of binding affinity. ECIF are a set of protein-ligand atom-type pair counts that take into account each atom's connectivity to describe it and thus define the pair types. ECIF were used to build different machine-learning models to predict protein-ligand affinities (pKd/pKi). The models were evaluated in terms of 'scoring power' on the Comparative Assessment of Scoring Functions 2016. The best models built on ECIF achieved Pearson correlation coefficients of 0.857 when used on its own, and 0.866 when used in combination with ligand descriptors, demonstrating ECIF descriptive power. AVAILABILITY AND IMPLEMENTATION Data and code to reproduce all the results are freely available at https://github.com/DIFACQUIM/ECIF. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Norberto Sánchez-Cruz
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomedica (PRBB), 08003 Barcelona, Catalonia, Spain
- Chemotargets SL, Parc Cientific de Barcelona (PCB), 08028 Barcelona, Catalonia, Spain
| | - Xavier Barril
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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16
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Faria M, Prats E, Rosas Ramírez JR, Bellot M, Bedrossiantz J, Pagano M, Valls A, Gomez-Canela C, Porta JM, Mestres J, Garcia-Reyero N, Faggio C, Gómez Oliván LM, Raldua D. Androgenic activation, impairment of the monoaminergic system and altered behavior in zebrafish larvae exposed to environmental concentrations of fenitrothion. Sci Total Environ 2021; 775:145671. [PMID: 33621872 DOI: 10.1016/j.scitotenv.2021.145671] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Fenitrothion is an organophosphorus insecticide usually found in aquatic ecosystems at concentrations in the range of low ng/L. In this manuscript we show that 24 h exposure to environmental concentrations of fenitrothion, from ng/L to low μg/L, altered basal locomotor activity, visual-motor response and acoustic/vibrational escape response of zebrafish larvae. Furthermore, fenitrothion and expression of gap43a, gfap, atp2b1a, and mbp exhibited a significant non-monotonic concentration-response relationship. Once determined that environmental concentrations of fenitrothion were neurotoxic for zebrafish larvae, a computational analysis identified potential protein targets of this compound. Some of the predictions, including interactions with acetylcholinesterase, monoamine-oxidases and androgen receptor (AR), were experimentally validated. Binding to AR was the most suitable candidate for molecular initiating event, as indicated by both the up-regulation of cyp19a1b and sult2st3 and the non-monotonic relationship found between fenitrothion and the observed responses. Finally, when the integrity of the monoaminergic system was evaluated, altered levels of L-DOPA, DOPAC, HVA and 5-HIAA were found, as well as a significant up-regulation of slc18a2 expression at the lowest concentrations of fenitrothion. These data strongly suggest that concentrations of fenitrothion commonly found in aquatic ecosystems present a significant environmental risk for fish communities.
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Affiliation(s)
- Melissa Faria
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18, 08034 Barcelona, Spain
| | - Eva Prats
- Research and Development Center (CID-CSIC), Jordi Girona 18, 08034 Barcelona, Spain
| | - Jonathan Ricardo Rosas Ramírez
- Laboratorio de Toxicología Ambiental, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón intersección Paseo Tollocan s/n. Col. Residencial Colón, 50120 Toluca, Estado de México, Mexico
| | - Marina Bellot
- Department of Analytical Chemistry and Applied (Chromatography section), School of Engineering, Institut Químic de Sarrià-Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Juliette Bedrossiantz
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18, 08034 Barcelona, Spain
| | - Maria Pagano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres, 31, 98166 Agata-Messina, Italy
| | - Arnau Valls
- Institut de Robòtica i Informàtica Industrial, CSIC-UPC, Barcelona, Spain
| | - Cristian Gomez-Canela
- Department of Analytical Chemistry and Applied (Chromatography section), School of Engineering, Institut Químic de Sarrià-Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Josep M Porta
- Institut de Robòtica i Informàtica Industrial, CSIC-UPC, Barcelona, Spain
| | - Jordi Mestres
- Systems Pharmacology, Research Group on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Chemotargets SL, Parc Científic de Barcelona, Barcelona, Spain
| | - Natalia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres, 31, 98166 Agata-Messina, Italy
| | - Leobardo Manuel Gómez Oliván
- Laboratorio de Toxicología Ambiental, Facultad de Química, Universidad Autónoma del Estado de México, Paseo Colón intersección Paseo Tollocan s/n. Col. Residencial Colón, 50120 Toluca, Estado de México, Mexico
| | - Demetrio Raldua
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona, 18, 08034 Barcelona, Spain.
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17
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Abstract
The SureChEMBL database provides open access to 17 million chemical entities mentioned in 14 million patents published since 1970. However, alongside with molecules covered by patent claims, the database is full of starting materials and intermediate products of little pharmacological relevance. Herein, we introduce a new filtering protocol to automatically select the core chemical structures best representing a congeneric series of pharmacologically relevant molecules in patents. The protocol is first validated against a selection of 890 SureChEMBL patents for which a total of 51,738 manually curated molecules are deposited in ChEMBL. Our protocol was able to select 92.5% of the molecules in ChEMBL from all 270,968 molecules in SureChEMBL for those patents. Subsequently, the protocol was applied to all 240,988 US pharmacological patents for which 9,111,706 molecules are available in SureChEMBL. The unsupervised filtering process selected 5,949,214 molecules (65.3% of the total number of molecules) that form highly congeneric chemical series in 188,795 of those patents (78.3% of the total number of patents). A SureChEMBL version enriched with molecules of pharmacological relevance is available for download at https://ftp.ebi.ac.uk/pub/databases/chembl/SureChEMBLccs.
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Affiliation(s)
- Maria J Falaguera
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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18
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Sisó-Almirall A, Brito-Zerón P, Conangla Ferrín L, Kostov B, Moragas Moreno A, Mestres J, Sellarès J, Galindo G, Morera R, Basora J, Trilla A, Ramos-Casals M. Long Covid-19: Proposed Primary Care Clinical Guidelines for Diagnosis and Disease Management. Int J Environ Res Public Health 2021; 18:4350. [PMID: 33923972 PMCID: PMC8073248 DOI: 10.3390/ijerph18084350] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/02/2021] [Accepted: 04/16/2021] [Indexed: 01/08/2023]
Abstract
Long COVID-19 may be defined as patients who, four weeks after the diagnosis of SARS-Cov-2 infection, continue to have signs and symptoms not explainable by other causes. The estimated frequency is around 10% and signs and symptoms may last for months. The main long-term manifestations observed in other coronaviruses (Severe Acute Respiratory Syndrome (SARS), Middle East respiratory syndrome (MERS)) are very similar to and have clear clinical parallels with SARS-CoV-2: mainly respiratory, musculoskeletal, and neuropsychiatric. The growing number of patients worldwide will have an impact on health systems. Therefore, the main objective of these clinical practice guidelines is to identify patients with signs and symptoms of long COVID-19 in primary care through a protocolized diagnostic process that studies possible etiologies and establishes an accurate differential diagnosis. The guidelines have been developed pragmatically by compiling the few studies published so far on long COVID-19, editorials and expert opinions, press releases, and the authors' clinical experience. Patients with long COVID-19 should be managed using structured primary care visits based on the time from diagnosis of SARS-CoV-2 infection. Based on the current limited evidence, disease management of long COVID-19 signs and symptoms will require a holistic, longitudinal follow up in primary care, multidisciplinary rehabilitation services, and the empowerment of affected patient groups.
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Affiliation(s)
- Antoni Sisó-Almirall
- Permanent Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain; (L.C.F.); (J.M.)
- Primary Care Centre Les Corts, Consorci d’Atenció Primària de Salut Barcelona Esquerra (CAPSBE), 08028 Barcelona, Spain;
- Primary Healthcare Transversal Research Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Pilar Brito-Zerón
- Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, 08036 Barcelona, Spain; (P.B.-Z.); (M.R.-C.)
- Autoimmune Diseases Unit, Department of Medicine, Hospital CIMA-Sanitas, 08034 Barcelona, Spain
- Department of Autoimmune Diseases, ICMiD, Hospital Clínic, 08036 Barcelona, Spain
| | - Laura Conangla Ferrín
- Permanent Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain; (L.C.F.); (J.M.)
| | - Belchin Kostov
- Primary Care Centre Les Corts, Consorci d’Atenció Primària de Salut Barcelona Esquerra (CAPSBE), 08028 Barcelona, Spain;
- Primary Healthcare Transversal Research Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya (UPC), 08034 Barcelona, Spain
| | - Anna Moragas Moreno
- Jaume I Health Centre, Institut Català de la Salut, Universitat Rovira i Virgili, 43005 Tarragona, Spain;
| | - Jordi Mestres
- Permanent Board of the Catalan Society of Family and Community Medicine (CAMFiC), 08009 Barcelona, Spain; (L.C.F.); (J.M.)
| | | | - Gisela Galindo
- Permanent Board of the Spanish Society of Family and Community Medicine (semFYC), 08009 Barcelona, Spain;
| | - Ramon Morera
- Board of Spanish Society of Managers of Primary Care (SEDAP), 28026 Madrid, Spain;
| | | | - Antoni Trilla
- Faculty of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain;
| | - Manuel Ramos-Casals
- Laboratory of Autoimmune Diseases Josep Font, IDIBAPS-CELLEX, 08036 Barcelona, Spain; (P.B.-Z.); (M.R.-C.)
- Department of Autoimmune Diseases, ICMiD, Hospital Clínic, 08036 Barcelona, Spain
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19
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Zahoránszky-Kőhalmi G, Siramshetty VB, Kumar P, Gurumurthy M, Grillo B, Mathew B, Metaxatos D, Backus M, Mierzwa T, Simon R, Grishagin I, Brovold L, Mathé EA, Hall MD, Michael SG, Godfrey AG, Mestres J, Jensen LJ, Oprea TI. A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. bioRxiv 2020:2020.11.04.369041. [PMID: 33173863 PMCID: PMC7654851 DOI: 10.1101/2020.11.04.369041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MOTIVATION In the event of an outbreak due to an emerging pathogen, time is of the essence to contain or to mitigate the spread of the disease. Drug repositioning is one of the strategies that has the potential to deliver therapeutics relatively quickly. The SARS-CoV-2 pandemic has shown that integrating critical data resources to drive drug-repositioning studies, involving host-host, hostpathogen and drug-target interactions, remains a time-consuming effort that translates to a delay in the development and delivery of a life-saving therapy. RESULTS Here, we describe a workflow we designed for a semi-automated integration of rapidly emerging datasets that can be generally adopted in a broad network pharmacology research setting. The workflow was used to construct a COVID-19 focused multimodal network that integrates 487 host-pathogen, 74,805 host-host protein and 1,265 drug-target interactions. The resultant Neo4j graph database named "Neo4COVID19" is accessible via a web interface and via API calls based on the Bolt protocol. We believe that our Neo4COVID19 database will be a valuable asset to the research community and will catalyze the discovery of therapeutics to fight COVID-19. AVAILABILITY https://neo4covid19.ncats.io.
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Affiliation(s)
| | | | - Praveen Kumar
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
- Department of Computer Science, University of New Mexico, Albuquerque, New Mexico, USA
| | | | - Busola Grillo
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Biju Mathew
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | | | - Mark Backus
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Tim Mierzwa
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Reid Simon
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Ivan Grishagin
- National Center for Advancing Translational Sciences, Rockville, MD, USA
- Rancho BioSciences LLC., San Diego, CA USA
| | | | - Ewy A. Mathé
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, Rockville, MD, USA
| | | | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Lars J. Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tudor I. Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- UNM Comprehensive Cancer Center, Albuquerque, NM, USA
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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20
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Martí-Bonmatí L, Alberich-Bayarri Á, Ladenstein R, Blanquer I, Segrelles JD, Cerdá-Alberich L, Gkontra P, Hero B, García-Aznar JM, Keim D, Jentner W, Seymour K, Jiménez-Pastor A, González-Valverde I, Martínez de Las Heras B, Essiaf S, Walker D, Rochette M, Bubak M, Mestres J, Viceconti M, Martí-Besa G, Cañete A, Richmond P, Wertheim KY, Gubala T, Kasztelnik M, Meizner J, Nowakowski P, Gilpérez S, Suárez A, Aznar M, Restante G, Neri E. PRIMAGE project: predictive in silico multiscale analytics to support childhood cancer personalised evaluation empowered by imaging biomarkers. Eur Radiol Exp 2020; 4:22. [PMID: 32246291 PMCID: PMC7125275 DOI: 10.1186/s41747-020-00150-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/24/2020] [Indexed: 03/12/2023] Open
Abstract
PRIMAGE is one of the largest and more ambitious research projects dealing with medical imaging, artificial intelligence and cancer treatment in children. It is a 4-year European Commission-financed project that has 16 European partners in the consortium, including the European Society for Paediatric Oncology, two imaging biobanks, and three prominent European paediatric oncology units. The project is constructed as an observational in silico study involving high-quality anonymised datasets (imaging, clinical, molecular, and genetics) for the training and validation of machine learning and multiscale algorithms. The open cloud-based platform will offer precise clinical assistance for phenotyping (diagnosis), treatment allocation (prediction), and patient endpoints (prognosis), based on the use of imaging biomarkers, tumour growth simulation, advanced visualisation of confidence scores, and machine-learning approaches. The decision support prototype will be constructed and validated on two paediatric cancers: neuroblastoma and diffuse intrinsic pontine glioma. External validation will be performed on data recruited from independent collaborative centres. Final results will be available for the scientific community at the end of the project, and ready for translation to other malignant solid tumours.
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Affiliation(s)
- Luis Martí-Bonmatí
- Medical Imaging Department, La Fe University and Polytechnic Hospital & Biomedical Imaging Research Group (GIBI230) at La Fe University and Polytechnic Hospital and Health Research Institute, Av. Fernando Abril Martorell 106, 46026, Valencia, Spain.
| | - Ángel Alberich-Bayarri
- Quantitative Imaging Biomarkers in Medicine, QUIBIM SL, Edificio Europa, Av. de Aragón, 30, Planta 12, 46021, Valencia, Spain
| | | | - Ignacio Blanquer
- Instituto de Instrumentación para Imagen Molecular (I3M), Universitat Politècnica de València (UPV), c\ Camino de Vera s/n, 46022, Valencia, Spain
| | - J Damian Segrelles
- Instituto de Instrumentación para Imagen Molecular (I3M), Universitat Politècnica de València (UPV), c\ Camino de Vera s/n, 46022, Valencia, Spain
| | - Leonor Cerdá-Alberich
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Av. Fernando Abril Martorell 106, Torre E, 46026, Valencia, Spain
| | - Polyxeni Gkontra
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Av. Fernando Abril Martorell 106, Torre E, 46026, Valencia, Spain
| | - Barbara Hero
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - J M García-Aznar
- Multiscale in Mechanical and Biological Engineering, Department of Mechanical Engineering, Universidad de Zaragoza, Zaragoza, Spain.,Aragón Institute of Engineering Research, Zaragoza, Spain
| | - Daniel Keim
- Department of Computer Science, University of Konstanz, Konstanz, Germany
| | - Wolfgang Jentner
- Department of Computer Science, University of Konstanz, Konstanz, Germany
| | | | - Ana Jiménez-Pastor
- Quantitative Imaging Biomarkers in Medicine, QUIBIM SL, Edificio Europa, Av. de Aragón, 30, Planta 12, 46021, Valencia, Spain
| | - Ismael González-Valverde
- Quantitative Imaging Biomarkers in Medicine, QUIBIM SL, Edificio Europa, Av. de Aragón, 30, Planta 12, 46021, Valencia, Spain
| | - Blanca Martínez de Las Heras
- Paediatric Oncology Unit, La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell 106, Torre G, 2 Floor, 46026, Valencia, Spain
| | - Samira Essiaf
- European Society for Paediatric Oncology, Brussels, Belgium
| | - Dawn Walker
- Department of Computer Science and Insigneo Institute of In Silico Medicine, University of Sheffield, Regent Court, 211 Portobello, Sheffield, UK
| | - Michel Rochette
- Simulation, Modelling and Engineering Software, Ansys Group, Montigny-le-Bretonneux, France
| | - Marian Bubak
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Jordi Mestres
- Chemotargets S.L., Carrer de Baldiri Reixac, 4-8 TI05A7 Torre I, planta 5, A7, 08028, Barcelona, Spain
| | - Marco Viceconti
- Department of Industrial Engineering, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Gracia Martí-Besa
- Biomedical Imaging Research Group (GIBI230), La Fe Health Research Institute, Av. Fernando Abril Martorell 106, Torre E, 46026, Valencia, Spain
| | - Adela Cañete
- Paediatric Oncology Unit, La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell 106, Torre G, 2 Floor, 46026, Valencia, Spain
| | - Paul Richmond
- Department of Computer Science and Insigneo Institute of In Silico Medicine, University of Sheffield, Regent Court, 211 Portobello, Sheffield, UK
| | - Kenneth Y Wertheim
- Department of Computer Science and Insigneo Institute of In Silico Medicine, University of Sheffield, Regent Court, 211 Portobello, Sheffield, UK
| | - Tomasz Gubala
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Marek Kasztelnik
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Jan Meizner
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | - Piotr Nowakowski
- ACC Cyfronet, AGH University of Science and Technology, Sano Centre for Computational Medicine, Nawojki 11, 30-950, Kraków, Poland
| | | | - Amelia Suárez
- Matical Innovation, Calle de Torija, 5, 28013, Madrid, Spain
| | - Mario Aznar
- Matical Innovation, Calle de Torija, 5, 28013, Madrid, Spain
| | - Giuliana Restante
- Department of Translational Research, University of Pisa, Chair Radiodiagnostica 3, Pisa University Hospital, Via Roma 67, 56126, Pisa, Italy
| | - Emanuele Neri
- Department of Translational Research, University of Pisa, Chair Radiodiagnostica 3, Pisa University Hospital, Via Roma 67, 56126, Pisa, Italy
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21
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Abstract
The ancient tradition of taking parts of a plant or preparing plant extracts for treating certain discomforts and maladies has long been lacking a scientific rationale to support its preparation and still widespread use in several parts of the world. In an attempt to address this challenge, we collected and integrated data connecting metabolites, plants, diseases, and proteins. A mechanistic hypothesis is generated when a metabolite is known to be present in a given plant, that plant is known to be used to treat a certain disease, that disease is known to be linked to the function of a given protein, and that protein is finally known or predicted to interact with the original metabolite. The construction of plant–protein networks from mutually connected metabolites and diseases facilitated the identification of plausible mechanisms of action for plants being used to treat analgesia, hypercholesterolemia, diarrhea, catarrh, and cough. Additional concrete examples using both experimentally known and computationally predicted, and subsequently experimentally confirmed, metabolite–protein interactions to close the connection circle between metabolites, plants, diseases, and proteins offered further proof of concept for the validity and scope of the approach to generate mode of action hypotheses for some of the therapeutic uses of remedial herbs.
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Affiliation(s)
- Joaquim Olivés
- Research Group on Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Barcelona, Spain.,Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
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22
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Dyballa S, Miñana R, Rubio-Brotons M, Cornet C, Pederzani T, Escaramis G, Garcia-Serna R, Mestres J, Terriente J. Comparison of Zebrafish Larvae and hiPSC Cardiomyocytes for Predicting Drug-Induced Cardiotoxicity in Humans. Toxicol Sci 2019; 171:283-295. [PMID: 31359052 PMCID: PMC6760275 DOI: 10.1093/toxsci/kfz165] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 12/15/2022] Open
Abstract
Cardiovascular drug toxicity is responsible for 17% of drug withdrawals in clinical phases, half of post-marketed drug withdrawals and remains an important adverse effect of several marketed drugs. Early assessment of drug-induced cardiovascular toxicity is mandatory and typically done in cellular systems and mammals. Current in vitro screening methods allow high-throughput but are biologically reductionist. The use of mammal models, which allow a better translatability for predicting clinical outputs, is low-throughput, highly expensive, and ethically controversial. Given the analogies between the human and the zebrafish cardiovascular systems, we propose the use of zebrafish larvae during early drug discovery phases as a balanced model between biological translatability and screening throughput for addressing potential liabilities. To this end, we have developed a high-throughput screening platform that enables fully automatized in vivo image acquisition and analysis to extract a plethora of relevant cardiovascular parameters: heart rate, arrhythmia, AV blockage, ejection fraction, and blood flow, among others. We have used this platform to address the predictive power of zebrafish larvae for detecting potential cardiovascular liabilities in humans. We tested a chemical library of 92 compounds with known clinical cardiotoxicity profiles. The cross-comparison with clinical data and data acquired from human induced pluripotent stem cell cardiomyocytes calcium imaging showed that zebrafish larvae allow a more reliable prediction of cardiotoxicity than cellular systems. Interestingly, our analysis with zebrafish yields similar predictive performance as previous validation meta-studies performed with dogs, the standard regulatory preclinical model for predicting cardiotoxic liabilities prior to clinical phases.
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Affiliation(s)
- Sylvia Dyballa
- ZeClinics SL, IGTP (German Trias and Pujol Institute), Badalona 08916, Spain
| | - Rafael Miñana
- ZeClinics SL, IGTP (German Trias and Pujol Institute), Badalona 08916, Spain
| | - Maria Rubio-Brotons
- ZeClinics SL, IGTP (German Trias and Pujol Institute), Badalona 08916, Spain
| | - Carles Cornet
- ZeClinics SL, IGTP (German Trias and Pujol Institute), Badalona 08916, Spain
| | - Tiziana Pederzani
- ZeClinics SL, IGTP (German Trias and Pujol Institute), Badalona 08916, Spain
| | - Georgia Escaramis
- CIBER Epidemiology and Public Health
- Department of Biomedicine, Faculty of Life Science and Health, University of Barcelona 08036, Barcelona, Spain
- Research Group on Statistics, Econometrics and Health (GRECS), UdG, Girona 17071, Spain
| | | | - Jordi Mestres
- Chemotargets SL, Parc Científic de Barcelona, Barcelona 08028, Spain
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, Barcelona 08002, Spain
- University Pompeu Fabra, PRBB (Barcelona Biomedical Research Park), Barcelona 08002, Spain
| | - Javier Terriente
- ZeClinics SL, IGTP (German Trias and Pujol Institute), Badalona 08916, Spain
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23
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Vogt I, Mestres J. Cover Picture: Information Loss in Network Pharmacology (Mol. Inf. 7/2019). Mol Inform 2019. [DOI: 10.1002/minf.201980701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ingo Vogt
- Research Group on Systems Pharmacology, Research Unit on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research InstituteUniversity Pompeu Fabra, Parc de Recerca Biomèdica (PRBB) Doctor Aiguader 88 08003 Barcelona, Catalonia Spain
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Unit on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research InstituteUniversity Pompeu Fabra, Parc de Recerca Biomèdica (PRBB) Doctor Aiguader 88 08003 Barcelona, Catalonia Spain
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24
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Bofill A, Jalencas X, Oprea TI, Mestres J. The human endogenous metabolome as a pharmacology baseline for drug discovery. Drug Discov Today 2019; 24:1806-1820. [PMID: 31226432 DOI: 10.1016/j.drudis.2019.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/17/2019] [Accepted: 06/12/2019] [Indexed: 01/01/2023]
Abstract
We have limited understanding of the variation in in vitro affinities of drugs for their targets. An analysis of a highly curated set of 815 interactions between 566 drugs and 129 primary targets reveals that 71% of drug-target affinities have values above that of the corresponding endogenous ligand, 96% of them fitting within a range of two orders of magnitude. Our findings suggest that the evolutionary optimised affinity of endogenous ligands for their native proteins can serve as a baseline for the primary pharmacology of drugs. We show that the degree of off-target selectivity and safety risks of drugs derived from their secondary pharmacology depend very much on that baseline. Thus, we propose a new approach for estimating safety margins.
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Affiliation(s)
- Andreu Bofill
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Xavier Jalencas
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Tudor I Oprea
- Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA; UNM Comprehensive Cancer Center, Albuquerque, NM, USA; Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.
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25
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Abstract
With the advent of increasing computational power and large-scale data acquisition, network analysis has become an attractive tool to study the organisation of complex systems and the interrelation of their constituent entities in various scientific domains. In many cases, relations only occur between entities of two different subsets, thereby forming a bipartite network. Often, the analysis of such bipartite networks involves the consideration of its two monopartite projections in order to focus on each entity subset individually as a means to deduce properties of the underlying original network. Although it is broadly acknowledged that this type of projection is not lossless, the inherent limitations of their interpretability are rarely discussed. In this work, we introduce two approaches for measuring the information loss associated with bipartite network projection. Application to two structurally distinct cases in network pharmacology, namely, drug-target and disease-gene bipartite networks, confirms that the major determinant of information loss is the degree of vertices omitted during the monopartite projection.
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Affiliation(s)
- Ingo Vogt
- Research Group on Systems Pharmacology, Research Unit on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, University Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Unit on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute, University Pompeu Fabra, Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
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26
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Brennecke P, Rasina D, Aubi O, Herzog K, Landskron J, Cautain B, Vicente F, Quintana J, Mestres J, Stechmann B, Ellinger B, Brea J, Kolanowski JL, Pilarski R, Orzaez M, Pineda-Lucena A, Laraia L, Nami F, Zielenkiewicz P, Paruch K, Hansen E, von Kries JP, Neuenschwander M, Specker E, Bartunek P, Simova S, Leśnikowski Z, Krauss S, Lehtiö L, Bilitewski U, Brönstrup M, Taskén K, Jirgensons A, Lickert H, Clausen MH, Andersen JH, Vicent MJ, Genilloud O, Martinez A, Nazaré M, Fecke W, Gribbon P. EU-OPENSCREEN: A Novel Collaborative Approach to Facilitate Chemical Biology. SLAS Discov 2019; 24:398-413. [PMID: 30616481 PMCID: PMC6764006 DOI: 10.1177/2472555218816276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/11/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022]
Abstract
Compound screening in biological assays and subsequent optimization of hits is indispensable for the development of new molecular research tools and drug candidates. To facilitate such discoveries, the European Research Infrastructure EU-OPENSCREEN was founded recently with the support of its member countries and the European Commission. Its distributed character harnesses complementary knowledge, expertise, and instrumentation in the discipline of chemical biology from 20 European partners, and its open working model ensures that academia and industry can readily access EU-OPENSCREEN's compound collection, equipment, and generated data. To demonstrate the power of this collaborative approach, this perspective article highlights recent projects from EU-OPENSCREEN partner institutions. These studies yielded (1) 2-aminoquinazolin-4(3 H)-ones as potential lead structures for new antimalarial drugs, (2) a novel lipodepsipeptide specifically inducing apoptosis in cells deficient for the pVHL tumor suppressor, (3) small-molecule-based ROCK inhibitors that induce definitive endoderm formation and can potentially be used for regenerative medicine, (4) potential pharmacological chaperones for inborn errors of metabolism and a familiar form of acute myeloid leukemia (AML), and (5) novel tankyrase inhibitors that entered a lead-to-candidate program. Collectively, these findings highlight the benefits of small-molecule screening, the plethora of assay designs, and the close connection between screening and medicinal chemistry within EU-OPENSCREEN.
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Affiliation(s)
- Philip Brennecke
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Dace Rasina
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Oscar Aubi
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Katja Herzog
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Johannes Landskron
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Bastien Cautain
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | | | - Jordi Quintana
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
| | - Jordi Mestres
- Department of Experimental and Health
Sciences, Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
- IMIM Hospital del Mar Medical Research
Institute, Research Program on Biomedical Informatics (GRIB), Barcelona, Spain
| | - Bahne Stechmann
- EU-OPENSCREEN, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Bernhard Ellinger
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
| | - Jose Brea
- Institute for Research in Molecular
Medicine and Chronic Diseases—BioFarma Research Group, University of Santiago de
Compostela, Santiago de Compostela, Spain
| | - Jacek L. Kolanowski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Radosław Pilarski
- Department of Molecular Probes and
Prodrugs, Institute of Bioorganic Chemistry—Polish Academy of Sciences, Poznan,
Poland
| | - Mar Orzaez
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | | | - Luca Laraia
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Faranak Nami
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | - Piotr Zielenkiewicz
- Department of Bioinformatics,
Institute of Biochemistry and Biophysics—Polish Academy of Sciences, Warsaw,
Poland
| | - Kamil Paruch
- Department of Chemistry—CZ-OPENSCREEN,
Masaryk University, Brno, Czech Republic
| | - Espen Hansen
- The Arctic University of Norway,
University of Tromsø, Marbio, Tromsø, Norway
| | - Jens P. von Kries
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Martin Neuenschwander
- Screening Unit, Leibniz Research
Institute for Molecular Pharmacology, Berlin, Germany
| | - Edgar Specker
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | - Petr Bartunek
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Sarka Simova
- Institute of Molecular Genetics of the
ASCR, CZ-OPENSCREEN, Prague, Czech Republic
| | - Zbigniew Leśnikowski
- Laboratory of Molecular Virology and
Biological Chemistry, Institute of Medical Biology—Polish Academy of Sciences, Łódź,
Poland
| | - Stefan Krauss
- Department of Immunology and
Transfusion Medicine, Oslo University Hospital, Oslo, Norway
- Hybrid Technology Hub—Centre of
Excellence—Institute of Basic Medical Sciences, University of Oslo, Oslo,
Norway
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular
Medicine—Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ursula Bilitewski
- Working Group Compound Profiling and
Screening, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Mark Brönstrup
- Department of Chemical Biology,
Helmholtz Centre for Infection Research, Brunswick, Germany
- German Center for Infection Research
(DZIF), partner site Hannover-Brunswick, Brunswick, Germany
| | - Kjetil Taskén
- Centre for Molecular Medicine
Norway–Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Department of Cancer
Immunology—Institute for Cancer Research, Oslo University Hospital, Oslo,
Norway
- K.G. Jebsen Centre for Cancer
Immunotherapy—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- K.G. Jebsen Centre for B Cell
Malignancies—Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Aigars Jirgensons
- Organic Synthesis Methodology Group,
Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Heiko Lickert
- Institute of Diabetes and Regeneration
Research, Helmholtz Centre Munich German Research Center for Environmental Health,
Neuherberg, Germany
| | - Mads H. Clausen
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Lyngby,
Denmark
- Technical University of Denmark,
DK-OPENSCREEN, Lyngby, Denmark
| | | | - Maria J. Vicent
- Screening Platform, Principe Felipe
Research Center, Valencia, Spain
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences
Technology Park, Granada, Spain
| | - Aurora Martinez
- Department of Biomedicine, University of
Bergen, Bergen, Norway
| | - Marc Nazaré
- Medicinal Chemistry Research Group,
Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany
| | | | - Philip Gribbon
- Fraunhofer Institute for Molecular
Biology and Applied Ecology IME, Screening Port, Hamburg, Germany
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27
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Abstract
Recent network and system biology analyses suggest that most complex diseases are regulated by robust and highly interconnected pathways that could be better modulated by small molecules binding to multiple biological targets. These pieces of evidence recently led to devote efforts on identifying single chemical entities that bind to two different disease-relevant targets. Here, we first predicted in silico and later confirmed in vitro that UPF 1069, a known bioactive poly(ADP-ribose) polymerase-1/2 (PARP1/2) molecule, and hydroxyfasudil, a known bioactive Rho-associated protein kinase-1/2 (ROCK1/2) molecule, have low-micromolar cross-affinity for ROCK1/2 and PARP1/2, respectively. These molecules can now be regarded as chemical seeds from which pharmacological tools could be generated to study the impact of dual inhibition of PARPs and ROCKs in preclinical models of a variety of complex diseases where both targets are involved.
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Martínez-Brotóns F, Oncins JR, Mestres J, Amargós V, Reynaldo C. Plasma Kallikrein-Kinin System in Patients with Uncomplicated Sepsis and Septic Shock-Comparison with Cardiogenic Shock. Thromb Haemost 2018. [DOI: 10.1055/s-0038-1645960] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
SummaryAlterations of the kallikrein-kinin system consistent with activation and increased consumption have been re2ported in septic patients and it has been suggested that this activation could contribute to the development of septic shock.The aim of this work was to confirm these alterations in septic patients and to investigate the possible existence of similar changes in subjects developing cardiogenic shock secondary to myocardial infarction as a model of non septic shock.Patients with septic shock, especially in fatal cases, showed a highly significant decrease in levels of factor XII, prekallikrein, high molecular weight kininogen (HMW-kininogen), α2-macro-globulin (α2-M) and antithrombin III (AT-III). C1-esterase inhibitor (C1-INH) activity was increased in uncomplicated sepsis but came back to normal or was slightly decreased in septic shock.Components and inhibitors of the kallikrein-kinin system were within normal limits in patients with cardiogenic shock.Our findings support the idea of a contribution of the kallikrein-kinin system to the development of septic shock though this system does not seem to play a significant role in the pathogenesis of cardiogenic shock or seem to be altered as a consequence of it.
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Affiliation(s)
| | - J R Oncins
- Intensive Care Unit, Hospital de Bellvitge, Barcelona, Spain
| | - J Mestres
- Intensive Care Unit, Hospital de Bellvitge, Barcelona, Spain
| | - V Amargós
- Intensive Care Unit, Hospital de Bellvitge, Barcelona, Spain
| | - C Reynaldo
- The Department of Hematology, Hospital de Bellvitge, Barcelona, Spain
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29
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Sanz F, Pognan F, Steger-Hartmann T, Díaz C, Cases M, Pastor M, Marc P, Wichard J, Briggs K, Watson DK, Kleinöder T, Yang C, Amberg A, Beaumont M, Brookes AJ, Brunak S, Cronin MTD, Ecker GF, Escher S, Greene N, Guzmán A, Hersey A, Jacques P, Lammens L, Mestres J, Muster W, Northeved H, Pinches M, Saiz J, Sajot N, Valencia A, van der Lei J, Vermeulen NPE, Vock E, Wolber G, Zamora I. Legacy data sharing to improve drug safety assessment: the eTOX project. Nat Rev Drug Discov 2017; 16:811-812. [PMID: 29026211 DOI: 10.1038/nrd.2017.177] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The sharing of legacy preclinical safety data among pharmaceutical companies and its integration with other information sources offers unprecedented opportunities to improve the early assessment of drug safety. Here, we discuss the experience of the eTOX project, which was established through the Innovative Medicines Initiative to explore this possibility.
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Affiliation(s)
- Ferran Sanz
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - François Pognan
- Novartis Institute for Biomedical Research, Basel, CH-4002, Switzerland
| | | | - Carlos Díaz
- Synapse Research Management Partners, 08007 Barcelona, Spain
| | | | | | - Manuel Pastor
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Philippe Marc
- Novartis Institute for Biomedical Research, Basel, CH-4002, Switzerland
| | | | | | | | | | - Chihae Yang
- Molecular Networks GmbH, 90411 Nürnberg, Germany
| | | | - Maria Beaumont
- GlaxoSmithKline Research and Development Ltd, Stevenage SG1 2NY, UK
| | | | - Søren Brunak
- Technical University of Denmark (DTU), 2800 Lyngby, Denmark
| | | | | | - Sylvia Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 30625 Hannover, Germany
| | - Nigel Greene
- Pfizer Ltd, Groton, Connecticut 06340, USA. Current affiliation: AstraZeneca, Waltham, Massachusettts 02451, USA
| | | | - Anne Hersey
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | | | | | | | - Marc Pinches
- AstraZeneca AB, SK10 2NA Cheshire, UK. Current affiliation: Lhasa Ltd, Leeds LS11 5PS, UK
| | - Javier Saiz
- Universitat Politècnica de València, 46022 València, Spain
| | | | - Alfonso Valencia
- ICREA, 08010 Barcelona, Spain & Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Johan van der Lei
- Erasmus Universitair Medisch Centrum, 3015 CE Rotterdam, The Netherlands
| | | | - Esther Vock
- Boehringer Ingelheim International GmbH, 88379 Biberach an der Riss, Germany
| | | | - Ismael Zamora
- Lead Molecular Design S.L., 08172 Sant Cugat del Vallès, Spain
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30
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Saadeh HA, Khasawneh MA, Samadi A, El-Haty IA, Satała G, Bojarski AJ, Ismaili L, Bautista-Aguilera ÓM, Yañez M, Mestres J, Marco-Contelles J. Design, Synthesis and Biological Evaluation of Potent Antioxidant 1-(2,5-Dimethoxybenzyl)-4-arylpiperazines and N
-Azolyl Substituted 2-(4-Arylpiperazin-1-yl). ChemistrySelect 2017. [DOI: 10.1002/slct.201700397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Haythem A. Saadeh
- Department of Chemistry; College of Science; United Arab Emirates University; Al Ain 15551 UAE
- Department of Chemistry; Faculty of Science; The University of Jordan; Amman 11942 Jordan
| | - Mohammad A. Khasawneh
- Department of Chemistry; College of Science; United Arab Emirates University; Al Ain 15551 UAE
| | - Abdelouahid Samadi
- Department of Chemistry; College of Science; United Arab Emirates University; Al Ain 15551 UAE
| | - Ismail A. El-Haty
- Department of Chemistry; College of Science; United Arab Emirates University; Al Ain 15551 UAE
| | - Grzegorz Satała
- Institute of Pharmacology; Polish Academy of Sciences; 12 Smętna Street 31-343 Kraków Poland
| | - Andrzej J. Bojarski
- Institute of Pharmacology; Polish Academy of Sciences; 12 Smętna Street 31-343 Kraków Poland
| | - Lhassane Ismaili
- Neurosciences Intégratives et Cliniques, EA 481; Univ. Bourgogne Franche-Comté; Laboratoire de Chimie Organique et Thérapeutique, UFR SMP; 19, rue Ambroise Paré F-25000 Besançon France
| | - Óscar M. Bautista-Aguilera
- Neurosciences Intégratives et Cliniques, EA 481; Univ. Bourgogne Franche-Comté; Laboratoire de Chimie Organique et Thérapeutique, UFR SMP; 19, rue Ambroise Paré F-25000 Besançon France
| | - Matilde Yañez
- Facultad de Farmacia; Departamento de Farmacología; Universidad de Santiago de Compostela; Campus Vida, Santiago de Compostela La Coruña Spain
| | - Jordi Mestres
- Research Group on Systems Pharmacology; Research Program on Biomedical Informatics (GRIB); IMIM Hospital del Mar Institute of Medical Research; Universitat Pompeu Fabra; Doctor Aiguader 88 08003 Barcelona Spain
| | - José Marco-Contelles
- Laboratory of Medicinal Chemistry (IQOG, CSIC); C/ Juan de la Cierva 3 28006- Madrid Spain
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31
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Bousquet J, Anto JM, Akdis M, Auffray C, Keil T, Momas I, Postma D, Valenta R, Wickman M, Cambon‐Thomsen A, Haahtela T, Lambrecht BN, Lodrup Carlsen KC, Koppelman GH, Sunyer J, Zuberbier T, Annesi‐Maesano I, Arno A, Bindslev‐Jensen C, De Carlo G, Forastiere F, Heinrich J, Kowalski ML, Maier D, Melén E, Palkonen S, Smit HA, Standl M, Wright J, Asarnoj A, Benet M, Ballardini N, Garcia‐Aymerich J, Gehring U, Guerra S, Hohman C, Kull I, Lupinek C, Pinart M, Skrindo I, Westman M, Smagghe D, Akdis C, Albang R, Anastasova V, Anderson N, Bachert C, Ballereau S, Ballester F, Basagana X, Bedbrook A, Bergstrom A, Berg A, Brunekreef B, Burte E, Carlsen KH, Chatzi L, Coquet JM, Curin M, Demoly P, Eller E, Fantini MP, Gerhard B, Hammad H, Hertzen L, Hovland V, Jacquemin B, Just J, Keller T, Kerkhof M, Kiss R, Kogevinas M, Koletzko S, Lau S, Lehmann I, Lemonnier N, McEachan R, Mäkelä M, Mestres J, Minina E, Mowinckel P, Nadif R, Nawijn M, Oddie S, Pellet J, Pin I, Porta D, Rancière F, Rial‐Sebbag A, Saeys Y, Schuijs MJ, Siroux V, Tischer CG, Torrent M, Varraso R, De Vocht J, Wenger K, Wieser S, Xu C. Paving the way of systems biology and precision medicine in allergic diseases: the MeDALL success story: Mechanisms of the Development of ALLergy; EU FP7-CP-IP; Project No: 261357; 2010-2015. Allergy 2016; 71:1513-1525. [PMID: 26970340 PMCID: PMC5248602 DOI: 10.1111/all.12880] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 01/06/2023]
Abstract
MeDALL (Mechanisms of the Development of ALLergy; EU FP7-CP-IP; Project No: 261357; 2010-2015) has proposed an innovative approach to develop early indicators for the prediction, diagnosis, prevention and targets for therapy. MeDALL has linked epidemiological, clinical and basic research using a stepwise, large-scale and integrative approach: MeDALL data of precisely phenotyped children followed in 14 birth cohorts spread across Europe were combined with systems biology (omics, IgE measurement using microarrays) and environmental data. Multimorbidity in the same child is more common than expected by chance alone, suggesting that these diseases share causal mechanisms irrespective of IgE sensitization. IgE sensitization should be considered differently in monosensitized and polysensitized individuals. Allergic multimorbidities and IgE polysensitization are often associated with the persistence or severity of allergic diseases. Environmental exposures are relevant for the development of allergy-related diseases. To complement the population-based studies in children, MeDALL included mechanistic experimental animal studies and in vitro studies in humans. The integration of multimorbidities and polysensitization has resulted in a new classification framework of allergic diseases that could help to improve the understanding of genetic and epigenetic mechanisms of allergy as well as to better manage allergic diseases. Ethics and gender were considered. MeDALL has deployed translational activities within the EU agenda.
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Affiliation(s)
- J. Bousquet
- University Hospital Montpellier France
- MACVIA‐LR Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc‐Roussillon European Innovation Partnership on Active and Healthy Ageing Reference Site France
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - J. M. Anto
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - M. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - C. Auffray
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - T. Keil
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Berlin Germany
- Institute for Clinical Epidemiology and Biometry University of Wuerzburg Wuerzburg Germany
| | - I. Momas
- Department of Public Health and Health Products Paris Descartes University‐Sorbonne Paris Cité Paris France
- Paris Municipal Department of Social Action, Childhood, and Health Paris France
| | - D.S. Postma
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - R. Valenta
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Wickman
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - A. Cambon‐Thomsen
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - T. Haahtela
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - B. N. Lambrecht
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - K. C. Lodrup Carlsen
- Department of Paediatrics Faculty of Medicine Institute of Clinical Medicine Oslo University Hospital University of Oslo Oslo Norway
| | - G. H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - J. Sunyer
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - T. Zuberbier
- Secretary General of the Global Allergy and Asthma European Network (GALEN) Allergy‐Centre‐Charité at the Department of Dermatology Charité–Universitätsmedizin Berlin Berlin Germany
| | | | - A. Arno
- Onmedic Networks Barcelona Spain
| | - C. Bindslev‐Jensen
- Department of Dermatology and Allergy Centre Odense University Hospital Odense Denmark
| | - G. De Carlo
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - F. Forastiere
- Department of Epidemiology Regional Health Service Lazio Region Rome Italy
| | - J. Heinrich
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - M. L. Kowalski
- Department of Immunology, Rheumatology and Allergy Medical University of Lodz Lodz Poland
| | - D. Maier
- Biomax Informatics AG Munich Germany
| | - E. Melén
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
- Stockholm County Council Centre for Occupational and Environmental Medicine Stockholm Sweden
| | - S. Palkonen
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - H. A. Smit
- Julius Center of Health Sciences and Primary Care University Medical Center Utrecht University of Utrecht Utrecht the Netherlands
| | - M. Standl
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - J. Wright
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - A. Asarnoj
- Clinical Immunology and Allergy Unit Department of Medicine Solna Karolinska Institutet Stockholm Sweden
- Astrid Lindgren Children's Hospital Department of Pediatric Pulmonology and Allergy Karolinska University Hospital Stockholm Sweden
| | - M. Benet
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - N. Ballardini
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- St John's Institute of Dermatology King's College London London UK
| | - J. Garcia‐Aymerich
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - U. Gehring
- Institute for Risk Assessment Sciences Utrecht University Utrecht the Netherlands
| | - S. Guerra
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - C. Hohman
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Germany
| | - I. Kull
- Sachs’ Children and Youth Hospital, Södersjukhuset Stockholm and Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Clinical Science and Education, Södersjukhuset Karolinska InstitutetStockholm Sweden
| | - C. Lupinek
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Pinart
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - I. Skrindo
- Department of Paediatrics Faculty of Medicine Institute of Clinical Medicine Oslo University Hospital University of Oslo Oslo Norway
| | - M. Westman
- Department of Clinical Science, Intervention and Technology Karolinska Institutet Stockholm Sweden
- Department of ENT Diseases Karolinska University Hospital Stockholm Sweden
| | | | - C. Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF) University of Zurich Davos Switzerland
| | - R. Albang
- Biomax Informatics AG Munich Germany
| | - V. Anastasova
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - N. Anderson
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - C. Bachert
- ENT Department Ghent University Hospital Gent Belgium
| | - S. Ballereau
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - F. Ballester
- Environment and Health Area Centre for Public Health Research (CSISP) CIBERESP Department of Nursing University of Valencia Valencia Spain
| | - X. Basagana
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - A. Bedbrook
- MACVIA‐LR Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc‐Roussillon European Innovation Partnership on Active and Healthy Ageing Reference Site France
| | - A. Bergstrom
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - A. Berg
- Research Institute Department of Pediatrics Marien‐Hospital Wesel Germany
| | - B. Brunekreef
- Julius Center of Health Sciences and Primary Care University Medical Center Utrecht University of Utrecht Utrecht the Netherlands
| | - E. Burte
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - K. H. Carlsen
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - L. Chatzi
- Department of Social Medicine Faculty of Medicine University of Crete Heraklion Crete Greece
| | - J. M. Coquet
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - M. Curin
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - P. Demoly
- Department of Respiratory Diseases Montpellier University Hospital France
| | - E. Eller
- Department of Dermatology and Allergy Centre Odense University Hospital Odense Denmark
| | - M. P. Fantini
- Department of Medicine and Public Health Alma Mater Studiorum–University of Bologna Bologna Italy
| | | | - H. Hammad
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - L. Hertzen
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - V. Hovland
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - B. Jacquemin
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
| | - J. Just
- Allergology Department Centre de l'Asthme et des Allergies Hôpital d'Enfants Armand‐Trousseau (APHP) Sorbonne Universités Institut Pierre Louis d'Epidémiologie et de Santé Publique Paris France
| | - T. Keller
- Institute of Social Medicine, Epidemiology and Health Economics Charité–Universitätsmedizin Berlin Germany
| | - M. Kerkhof
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - R. Kiss
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - M. Kogevinas
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- IMIM (Hospital del Mar Research Institute) Barcelona Spain
- CIBER Epidemiología y Salud Pública (CIBERESP) Barcelona Spain
- Universitat Pompeu Fabra (UPF) Barcelona Spain
| | - S. Koletzko
- Division of Paediatric Gastroenterology and Hepatology Ludwig Maximilians University of Munich Munich Germany
| | - S. Lau
- Department for Pediatric Pneumology and Immunology Charité Medical University Berlin Germany
| | - I. Lehmann
- Department of Environmental Immunology/Core Facility Studies Helmholtz Centre for Environmental Research, UFZ Leipzig Germany
| | - N. Lemonnier
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - R. McEachan
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - M. Mäkelä
- Skin and Allergy Hospital Helsinki University Hospital Helsinki Finland
| | - J. Mestres
- Chemotargets SL and Chemogenomics Laboratory GRIB Unit IMIM‐Hospital del Mar and University Pompeu Fabra Barcelona Catalonia Spain
| | - E. Minina
- Biomax Informatics AG Munich Germany
| | - P. Mowinckel
- Department of Paediatrics Oslo University Hospital University of Oslo Oslo Norway
| | - R. Nadif
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - M. Nawijn
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
| | - S. Oddie
- Bradford Institute for Health Research Bradford Royal Infirmary Bradford UK
| | - J. Pellet
- European Institute for Systems Biology and Medicine CNRS‐ENS‐UCBL Université de Lyon Lyon France
| | - I. Pin
- Département de Pédiatrie CHU de Grenoble Grenoble Cedex 9 France
| | - D. Porta
- Department of Epidemiology Regional Health Service Lazio Region Rome Italy
| | - F. Rancière
- Department of Public Health and Health Products Paris Descartes University‐Sorbonne Paris Cité Paris France
| | - A. Rial‐Sebbag
- UMR Inserm U1027 and Université de Toulouse III Paul Sabatier Toulouse France
| | - Y. Saeys
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | - M. J. Schuijs
- VIB Inflammation Research Center Ghent University Ghent Belgium
| | | | - C. G. Tischer
- Institute of Epidemiology I German Research Centre for Environmental Health Helmholtz Zentrum München Neuherberg Germany
| | - M. Torrent
- Centre for Research in Environmental Epidemiology (CREAL) ISGLoBAL Barcelona Spain
- ib‐salut Area de Salut de Menorca Spain
| | - R. Varraso
- INSERM VIMA: Ageing and Chronic Diseases, Epidemiological and Public Health Approaches UVSQ Université Versailles St‐Quentin‐en‐Yvelines Paris France
| | - J. De Vocht
- EFA European Federation of Allergy and Airways Diseases Patients’ Associations Brussels Belgium
| | - K. Wenger
- Biomax Informatics AG Munich Germany
| | - S. Wieser
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - C. Xu
- Department of Pulmonary Medicine and Tuberculosis GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen the Netherlands
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Ferruz N, Harvey MJ, Mestres J, De Fabritiis G. Correction to Insights from Fragment Hit Binding Assays by Molecular Simulations. J Chem Inf Model 2016; 56:2123. [DOI: 10.1021/acs.jcim.6b00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Remez N, Garcia-Serna R, Vidal D, Mestres J. The In Vitro Pharmacological Profile of Drugs as a Proxy Indicator of Potential In Vivo Organ Toxicities. Chem Res Toxicol 2016; 29:637-48. [PMID: 26952164 DOI: 10.1021/acs.chemrestox.5b00470] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The potential of a drug to cause certain organ toxicities is somehow implicitly contained in its full pharmacological profile, provided the drug reaches and accumulates at the various organs where the different interacting proteins in its profile, both targets and off-targets, are expressed. Under this assumption, a computational approach was implemented to obtain a projected anatomical profile of a drug from its in vitro pharmacological profile linked to protein expression data across 47 organs. It was observed that the anatomical profiles obtained when using only the known primary targets of the drugs reflected roughly the intended organ targets. However, when both known and predicted secondary pharmacology was considered, the projected anatomical profiles of the drugs were able to clearly highlight potential organ off-targets. Accordingly, when applied to sets of drugs known to cause cardiotoxicity and hepatotoxicity, the approach is able to identify heart and liver, respectively, as the organs where the proteins in the pharmacological profile of the corresponding drugs are specifically expressed. When applied to a set of drugs linked to a risk of Torsades de Pointes, heart is again the organ clearly standing out from the rest and a potential protein profile hazard is proposed. The approach can be used as a proxy indicator of potential in vivo organ toxicities.
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Affiliation(s)
- Nikita Remez
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomèdica , Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain.,Chemotargets SL, Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain
| | - Ricard Garcia-Serna
- Chemotargets SL, Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain
| | - David Vidal
- Chemotargets SL, Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomèdica , Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain.,Chemotargets SL, Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain
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34
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Baumann K, Ecker GF, Mestres J, Schneider G. Molecular Informatics
: From Models to Systems and Beyond. Mol Inform 2016; 35:2. [DOI: 10.1002/minf.201680133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Antolin AA, Workman P, Mestres J, Al-Lazikani B. Polypharmacology in Precision Oncology: Current Applications and Future Prospects. Curr Pharm Des 2016; 22:6935-6945. [PMID: 27669965 PMCID: PMC5403974 DOI: 10.2174/1381612822666160923115828] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/19/2016] [Indexed: 02/08/2023]
Abstract
Over the past decade, a more comprehensive, large-scale approach to studying cancer genetics and biology has revealed the challenges of tumor heterogeneity, adaption, evolution and drug resistance, while systems-based pharmacology and chemical biology strategies have uncovered a much more complex interaction between drugs and the human proteome than was previously anticipated. In this mini-review we assess the progress and potential of drug polypharmacology in biomarker-driven precision oncology. Polypharmacology not only provides great opportunities for drug repurposing to exploit off-target effects in a new single-target indication but through simultaneous blockade of multiple targets or pathways offers exciting opportunities to slow, overcome or even prevent inherent or adaptive drug resistance. We highlight the many challenges associated with exploiting known or desired polypharmacology in drug design and development, and assess computational and experimental methods to uncover unknown polypharmacology. A comprehensive understanding of the intricate links between polypharmacology, efficacy and safety is urgently needed if we are to tackle the enduring challenge of cancer drug resistance and to fully exploit polypharmacology for the ultimate benefit of cancer patients.
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Affiliation(s)
- Albert A. Antolin
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Jordi Mestres
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
| | - Bissan Al-Lazikani
- Cancer Research UK Cancer Therapeutics Unit, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
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Rubio-Perez C, Tamborero D, Schroeder MP, Antolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N. Abstract A1-45: In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities. Cancer Res 2015. [DOI: 10.1158/1538-7445.transcagen-a1-45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The development of targeted therapies against altered driver proteins holds the promise of selectively and efficiently eliminating cancer cells. However, high intertumor heterogeneity is a major obstacle to develop and apply therapeutic targeted agents to treat most cancer patients. Here, we present the first large-scale therapeutic landscape of cancer as it stands today in a 6.792 sample cohort covering 28 tumor types.
To pursue this goal, we developed a three-step in silico drug prescription strategy. 1) To discover actionable driver events, we first comprehensively identified mutational cancer driver genes by detecting complementary signals of positive selection in the pattern of their mutations across the tumor cohorts. We also identified actionable copy number alteration (CNA) and fusion cancer driver genes. Second, we detected which of these driver genes would have an oncogenic role in the tumor and which ones would lose their function. With these two steps we generated the Drivers Database. 2) Next, we systematically gathered all information available on therapeutic agents; FDA approved and in clinical or pre-clinical stages. We considered three different types of targeting strategies for the cancer driver genes: direct targeting, indirect targeting and gene therapies in clinical trials. Moreover, we designed a set of rules for assigning therapeutic agents to specific genomic alterations beard for the driver genes. By doing this last step, we generated the Drivers Actionability Database. 3) Finally, by combining data of Drivers Database, Drivers Actionability Database and sample data, we developed in silico drug prescription, a novel approach to determine which of the drugs could benefit each of the tumor individuals.
In all, in the Driver Database we identified 460 mutational cancer driver genes acting in one or more of the tumor types along with 39 driver genes acting via CNAs or fusions. Fifty of these cancer driver genes are targeted by FDA approved agents, 63 by molecules currently in clinical trials and 74 are bound by pre-clinical ligands. We also identified 81 therapeutically unexploited targetable cancer genes. Lastly, by applying in silico drug prescription we found that only 6.7% of the patients could be treated following clinical guidelines, and were concentrated in only 6 tumor types. Moreover, considering repurposing strategies the fraction of patients that could benefit from FDA approved drugs would increase up to 40%, increasing remarkably the fraction of targetable patients in some tumor types like glioblastoma and thyroid cancer, and up to 72% if considering targeted therapies in clinical trials.
In summary, the in silico drug prescription based on Drivers and Drivers Actionability Databases was tested on one of the largest cohorts of tumor samples currently collected for research. The main result highlights the current scope of targeted anti-cancer therapies and its prospects for growth in view of the drugs that are currently in clinical trials or at pre-clinical stages. Additionally, another important output of this work is a ranked list of novel target opportunities for anticancer drug development. Continuous update of drug-target interactions information, and the application of the strategy to larger cohorts, will improve the in silico prescription rules contained within the two databases, thus enhancing its usefulness within personalized cancer medicine.
Citation Format: Carlota Rubio-Perez, David Tamborero, Michael P. Schroeder, Albert A. Antolín, Jordi Deu-Pons, Christian Perez-Llamas, Jordi Mestres, Abel Gonzalez-Perez, Nuria Lopez-Bigas. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-45.
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Affiliation(s)
- Carlota Rubio-Perez
- 1Biomedical Genomics Group, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain,
| | - David Tamborero
- 1Biomedical Genomics Group, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain,
| | - Michael P. Schroeder
- 1Biomedical Genomics Group, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain,
| | - Albert A. Antolín
- 2Systems Pharmacology, Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Deu-Pons
- 1Biomedical Genomics Group, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain,
| | - Christian Perez-Llamas
- 1Biomedical Genomics Group, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain,
| | - Jordi Mestres
- 2Systems Pharmacology, Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Abel Gonzalez-Perez
- 1Biomedical Genomics Group, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain,
| | - Nuria Lopez-Bigas
- 1Biomedical Genomics Group, Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain,
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Affiliation(s)
- Noelia Ferruz
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003 Barcelona, Barcelona, Spain
| | - Matthew J. Harvey
- Acellera, Barcelona
Biomedical Research Park (PRBB), Doctor
Aiguader 88, 08003, Barcelona, Barcelona, Spain
| | - Jordi Mestres
- Systems
Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Barcelona, Catalonia, Spain
| | - Gianni De Fabritiis
- Computational
Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Doctor Aiguader 88, 08003 Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Barcelona, Spain
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Abstract
The recent explosion of data linking drugs, proteins, and pathways with safety events has promoted the development of integrative systems approaches to large-scale predictive drug safety. The added value of such approaches is that, beyond the traditional identification of potentially labile chemical fragments for selected toxicity end points, they have the potential to provide mechanistic insights for a much larger and diverse set of safety events in a statistically sound nonsupervised manner, based on the similarity to drug classes, the interaction with secondary targets, and the interference with biological pathways. The combined identification of chemical and biological hazards enhances our ability to assess the safety risk of bioactive small molecules with higher confidence than that using structural alerts only. We are still a very long way from reliably predicting drug safety, but advances toward gaining a better understanding of the mechanisms leading to adverse outcomes represent a step forward in this direction.
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Affiliation(s)
- Ricard Garcia-Serna
- Chemotargets SL , Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain
| | - David Vidal
- Chemotargets SL , Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain
| | - Nikita Remez
- Chemotargets SL , Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain.,Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra , Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Chemotargets SL , Parc Científic de Barcelona, Baldiri Reixac 4 (TI-05A7), 08028 Barcelona, Catalonia, Spain.,Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra , Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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Rubio-Perez C, Tamborero D, Schroeder MP, Antolin AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N. Abstract 2983: In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent advances in DNA sequencing technologies provide unprecedented capacity to comprehensively identify the alterations, genes, and pathways involved in the tumorigenic process, raising the hope of extending targeted therapies against the drivers of cancer from a few successful examples to a broader personalized medicine strategy. However, high intertumor heterogeneity is a major obstacle to develop and apply therapeutic targeted agents to treat most cancer patient. In addition, advances in our ability to precisely assign the most effective targeted therapy to each patient based on the genome events driving the tumor are urgently needed.
The present study offers the first comprehensive assessment of the scope of targeted drugs in a large pan-cancer cohort. To pursue this goal, we developed a three-step in silico drug prescription strategy. We first identified the driver genes acting across 6792 tumor samples from 28 different cancer types via an integrated analysis of their mutations, copy number alterations and gene fusions. All information pertaining these driver genes has been compiled in a publicly available Drivers Database. Next, following the rationale that targeted therapies are effective only if they are administered to treat tumors driven by the alterations they are aimed at, we collected all therapeutic agents capable of targeting altered driver genes either directly, indirectly or through gene therapies. The catalog of available therapeutic agents and ancillary information on their application, referred here as Drivers Actionability Database, included FDA (Foods and Drugs Administration Agency) approved drugs, agents undergoing clinical trials, and ligands in pre-clinical stages. Finally, based on the driver alterations in each tumor in the cohort and the rules in the Drivers Actionability Database, we connected each patient to all targeted therapies that could benefit them, thus producing the landscape of utility of targeted therapeutic agents in the cohort.
We found that only a minority of patients could benefit from approved targeted therapy interventions following clinical guidelines (5.9%), while up to 40% could benefit from different types of repurposing opportunities of approve drugs, and up to 78% considering treatments currently under investigation. In addition, we identified 16 therapeutically unexploited cancer genes targeted by small molecules currently in pre-clinical stages, and 66 others structurally suitable for small molecule binding or accessible by antibody targeting. These results highlight the current scope of targeted anti-cancer therapies and its prospects for growth. The application of the strategy to larger cohorts and the continuous update of drug-target interactions information, will improve the in silico prescription rules contained within the two databases, thus enhancing its usefulness within personalized cancer medicine.
Citation Format: Carlota Rubio-Perez, David Tamborero, Michael P. Schroeder, Albert A. Antolin, Jordi Deu-Pons, Christian Perez-Llamas, Jordi Mestres, Abel Gonzalez-Perez, Nuria Lopez-Bigas. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2983. doi:10.1158/1538-7445.AM2015-2983
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Affiliation(s)
| | | | | | | | | | | | - Jordi Mestres
- 2Hospital del Mar Medical Research Institute, Barcelona, Spain
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Rubio-Perez C, Tamborero D, Schroeder MP, Antolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell 2015; 27:382-96. [PMID: 25759023 DOI: 10.1016/j.ccell.2015.02.007] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/21/2014] [Accepted: 02/17/2015] [Indexed: 12/12/2022]
Abstract
Large efforts dedicated to detect somatic alterations across tumor genomes/exomes are expected to produce significant improvements in precision cancer medicine. However, high inter-tumor heterogeneity is a major obstacle to developing and applying therapeutic targeted agents to treat most cancer patients. Here, we offer a comprehensive assessment of the scope of targeted therapeutic agents in a large pan-cancer cohort. We developed an in silico prescription strategy based on identification of the driver alterations in each tumor and their druggability options. Although relatively few tumors are tractable by approved agents following clinical guidelines (5.9%), up to 40.2% could benefit from different repurposing options, and up to 73.3% considering treatments currently under clinical investigation. We also identified 80 therapeutically targetable cancer genes.
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Affiliation(s)
- Carlota Rubio-Perez
- Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - David Tamborero
- Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Michael P Schroeder
- Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Albert A Antolín
- Systems Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Jordi Deu-Pons
- Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Christian Perez-Llamas
- Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Systems Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Abel Gonzalez-Perez
- Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Nuria Lopez-Bigas
- Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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Abstract
Small molecules are essential tool compounds to probe the role of proteins in biology and advance toward more efficient therapeutics. However, they are used without a complete knowledge of their selectivity across the entire proteome, at risk of confounding their effects due to unknown off-target interactions. Current state-of-the-art computational approaches to predicting the affinity profile of small molecules offer a means to anticipate potential nonobvious selectivity liabilities of chemical probes. The application of in silico target profiling on the full set of chemical probes from the NIH Molecular Libraries Program (MLP) resulted in the identification of biologically relevant in vitro affinities for proteins distantly related to the primary targets of ML006, ML123, ML141, and ML204, helping to lower the risk of their further use in chemical biology.
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Affiliation(s)
- Albert A. Antolín
- Systems
Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Systems
Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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Abstract
PARP inhibitors hold promise as a novel class of targeted anticancer drugs. However, their true mechanism of action is still not well understood following recent reports that show marked differences in cellular effects. Here, we demonstrate that three PARP drug candidates, namely, rucaparib, veliparib, and olaparib, have a clearly different in vitro affinity profile across a panel of diverse kinases selected using a computational approach that relates proteins by ligand similarity. In this respect, rucaparib inhibits nine kinases with micromolar affinity, including PIM1, PIM2, PRKD2, DYRK1A, CDK1, CDK9, HIPK2, CK2, and ALK. In contrast, olaparib does not inhibit any of the sixteen kinases tested. In between, veliparib inhibits only two, namely, PIM1 and CDK9. The differential kinase pharmacology observed among PARP inhibitors provides a plausible explanation to their different cellular effects and offers unexplored opportunities for this drug class, but alerts also on the risk associated to transferring directly both preclinical and clinical outcomes from one PARP drug candidate to another.
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Affiliation(s)
- Albert A Antolín
- Systems Pharmacology, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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Schmidt F, Amberg A, Mulliner D, Stolte M, Matter H, Hessler G, Dietrich A, Remez N, Vidal D, Mestres J, Czich A. Computational prediction of off-target related safety liabilities of molecules: Cardiotoxicity, hepatotoxicity and reproductive toxicity. Toxicol Lett 2014. [DOI: 10.1016/j.toxlet.2014.06.564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Horvath D, Lisurek M, Rupp B, Kühne R, Specker E, von Kries J, Rognan D, Andersson CD, Almqvist F, Elofsson M, Enqvist PA, Gustavsson AL, Remez N, Mestres J, Marcou G, Varnek A, Hibert M, Quintana J, Frank R. Design of a general-purpose European compound screening library for EU-OPENSCREEN. ChemMedChem 2014; 9:2309-26. [PMID: 25044981 DOI: 10.1002/cmdc.201402126] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Indexed: 01/08/2023]
Abstract
This work describes a collaborative effort to define and apply a protocol for the rational selection of a general-purpose screening library, to be used by the screening platforms affiliated with the EU-OPENSCREEN initiative. It is designed as a standard source of compounds for primary screening against novel biological targets, at the request of research partners. Given the general nature of the potential applications of this compound collection, the focus of the selection strategy lies on ensuring chemical stability, absence of reactive compounds, screening-compliant physicochemical properties, loose compliance to drug-likeness criteria (as drug design is a major, but not exclusive application), and maximal diversity/coverage of chemical space, aimed at providing hits for a wide spectrum of drugable targets. Finally, practical availability/cost issues cannot be avoided. The main goal of this publication is to inform potential future users of this library about its conception, sources, and characteristics. The outline of the selection procedure, notably of the filtering rules designed by a large committee of European medicinal chemists and chemoinformaticians, may be of general methodological interest for the screening/medicinal chemistry community. The selection task of 200K molecules out of a pre-filtered set of 1.4M candidates was shared by five independent European research groups, each picking a subset of 40K compounds according to their own in-house methodology and expertise. An in-depth analysis of chemical space coverage of the library serves not only to characterize the collection, but also to compare the various chemoinformatics-driven selection procedures of maximal diversity sets. Compound selections contributed by various participating groups were mapped onto general-purpose self-organizing maps (SOMs) built on the basis of marketed drugs and bioactive reference molecules. In this way, the occupancy of chemical space by the EU-OPENSCREEN library could be directly compared with distributions of known bioactives of various classes. This mapping highlights the relevance of the selection and shows how the consensus reached by merging the five different 40K selections contributes to achieve this relevance. The approach also allows one to readily identify subsets of target- or target-class-oriented compounds from the EU-OPENSCREEN library to suit the needs of the diverse range of potential users. The final EU-OPENSCREEN library, assembled by merging five independent selections of 40K compounds from various expert groups, represents an excellent example of a Europe-wide collaborative effort toward the common objective of building best-in-class European open screening platforms.
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Affiliation(s)
- Dragos Horvath
- Laboratoire de Chémoinformatique, UMR 7140 CNRS (LCS) - Université de Strasbourg, 1 rue Blaise Pascal, 6700 Strasbourg (France).
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Spitzmüller A, Mestres J. Identification of host interactions for phenotypic antimalarial hits. J Cheminform 2014; 6:O12. [PMID: 24765110 PMCID: PMC3980065 DOI: 10.1186/1758-2946-6-s1-o12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Andreas Spitzmüller
- Chemotargets SL and Systems Pharmacology Group, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia Spain
| | - Jordi Mestres
- Chemotargets SL and Systems Pharmacology Group, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia Spain
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Garcia-Reyero N, Escalon BL, Prats E, Stanley JK, Thienpont B, Melby NL, Barón E, Eljarrat E, Barceló D, Mestres J, Babin PJ, Perkins EJ, Raldúa D. Effects of BDE-209 contaminated sediments on zebrafish development and potential implications to human health. Environ Int 2014; 63:216-23. [PMID: 24317228 DOI: 10.1016/j.envint.2013.11.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/06/2013] [Accepted: 11/14/2013] [Indexed: 06/02/2023]
Abstract
Polybrominated diphenyl ethers are compounds widely used as flame-retardants, which are of increasing environmental concern due to their persistence, and potential adverse effects. This study had two objectives. First, we assessed if BDE-209 in sediment was bioavailable and bioaccumulated into zebrafish embryos. Secondly, we assessed the potential impact on human and environmental health of bioavailable BDE-209 using human in vitro cell assays and zebrafish embryos. Zebrafish were exposed from 4h to 8days post-fertilization to sediments spiked with 12.5mg/kg of BDE-209. Zebrafish larvae accumulated ten fold more BDE-209 than controls in unspiked sediment after 8days. BDE-209 impacted expression of neurological pathways and altered behavior of larvae, although BDE-209 had no visible affect on thyroid function or motoneuron and neuromast development. Zebrafish data and in silico predictions suggested that BDE-209 would also interact with key human transcription factors and receptors. We therefore tested these predictions using mammalian in vitro assays. BDE-209 activated human aryl hydrocarbon receptor, peroxisome proliferator activating receptors, CF/b-cat, activator protein 1, Oct-MLP, and the estrogen receptor-related alpha (ERRα) receptor in cell-based assays. BDE-209 also inhibited human acetylcholinesterase activity. The observation that BDE-209 can be bioaccumulated from contaminated sediment highlights the need to consider this as a potential environmental exposure route. Once accumulated, our data also show that BDE-209 has the potential to cause impacts on both human and environmental health.
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Affiliation(s)
- Natàlia Garcia-Reyero
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA.
| | - B Lynn Escalon
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Eva Prats
- Centro de Investigación y Desarrollo, CID-CSIC, Barcelona, Catalonia, Spain
| | - Jacob K Stanley
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Benedicte Thienpont
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalonia, Spain
| | - Nicolas L Melby
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Enrique Barón
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalonia, Spain
| | - Ethel Eljarrat
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalonia, Spain
| | - Damià Barceló
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Chemotargets, IMIM-Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Patrick J Babin
- Maladies Rares: Génétique et Métabolism, Université Bordeaux, Talence, France
| | - Edward J Perkins
- Environmental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS, USA
| | - Demetrio Raldúa
- Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalonia, Spain
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Jalencas X, Mestres J. Identification of Similar Binding Sites to Detect Distant Polypharmacology. Mol Inform 2013; 32:976-90. [PMID: 27481143 DOI: 10.1002/minf.201300082] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 07/29/2013] [Indexed: 01/19/2023]
Abstract
The ability of small molecules to interact with multiple proteins is referred to as polypharmacology. This property is often linked to the therapeutic action of drugs but it is known also to be responsible for many of their side effects. Because of its importance, the development of computational methods that can predict drug polypharmacology has become an important line of research that led recently to the identification of many novel targets for known drugs. Nowadays, the majority of these methods are based on measuring the similarity of a query molecule against the hundreds of thousands of molecules for which pharmacological data on thousands of proteins are available in public sources. However, similarity-based methods are inherently biased by the chemical coverage offered by the active molecules present in those public repositories, which limits significantly their capacity to predict interactions with proteins structurally and functionally unrelated to any of the already known targets for drugs. It is in this respect that structure-based methods aiming at identifying similar binding sites may offer an alternative complementary means to ligand-based methods for detecting distant polypharmacology. The different existing approaches to binding site detection, representation, comparison, and fragmentation are reviewed and recent successful applications presented.
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Affiliation(s)
- Xavier Jalencas
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute & University Pompeu Fabra, Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain fax: +34 93 3160550
| | - Jordi Mestres
- Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute & University Pompeu Fabra, Parc de Recerca Biomèdica, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain fax: +34 93 3160550.
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Abstract
Malaria is still one of the most devastating infectious diseases, affecting hundreds of millions of patients worldwide. Even though there are several established drugs in clinical use for malaria treatment, there is an urgent need for new drugs acting through novel mechanisms of action due to the rapid development of resistance. Resistance emerges when the parasite manages to mutate the sequence of the drug targets to the extent that the protein can still perform its function in the parasite but can no longer be inhibited by the drug, which then becomes almost ineffective. The design of a new generation of malaria drugs targeting multiple essential proteins would make it more difficult for the parasite to develop full resistance without lethally disrupting some of its vital functions. The challenge is then to identify which set of Plasmodium falciparum proteins, among the millions of possible combinations, can be targeted at the same time by a given chemotype. To do that, we predicted first the targets of the close to 20,000 antimalarial hits identified recently in three independent phenotypic screening campaigns. All targets predicted were then projected onto the genome of P. falciparum using orthologous relationships. A total of 226 P. falciparum proteins were predicted to be hit by at least one compound, of which 39 were found to be significantly enriched by the presence and degree of affinity of phenotypically active compounds. The analysis of the chemically compatible target combinations containing at least one of those 39 targets led to the identification of a priority set of 64 multi-target profiles that can set the ground for a new generation of more robust malaria drugs.
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Affiliation(s)
- Andreas Spitzmüller
- Chemotargets SL and Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
| | - Jordi Mestres
- Chemotargets SL and Systems Pharmacology, Research Programme on Biomedical Informatics (GRIB), IMIM Hospital del Mar Research Institute and Universitat Pompeu Fabra, Parc de Recerca Biomèdica, Barcelona, Catalonia, Spain
- * E-mail:
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