1
|
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.
Collapse
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
| |
Collapse
|
3
|
Sanz F, Carrió P, López O, Capoferri L, Kooi DP, Vermeulen NPE, Geerke DP, Montanari F, Ecker GF, Schwab CH, Kleinöder T, Magdziarz T, Pastor M. Integrative Modeling Strategies for Predicting Drug Toxicities at the eTOX Project. Mol Inform 2015; 34:477-84. [DOI: 10.1002/minf.201400193] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/01/2015] [Indexed: 11/11/2022]
|
4
|
Schwöbel JAH, Bienfait B, Gasteiger J, Kleinöder T, Marusczyk J, Sacher O, Schwab CH, Tarkhov A, Terfloth L, Cronin MTD. Quantifying intrinsic chemical reactivity of molecular structural features for protein binding and reactive toxicity, using the MOSES chemoinformatics system. J Cheminform 2012. [PMCID: PMC3341280 DOI: 10.1186/1758-2946-4-s1-o8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
5
|
Zitha-Bovens E, Maas P, Wife D, Tijhuis J, Hu QN, Kleinöder T, Gasteiger J. COMDECOM: predicting the lifetime of screening compounds in DMSO solution. ACTA ACUST UNITED AC 2009; 14:557-65. [PMID: 19483143 DOI: 10.1177/1087057109336953] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The technological evolution of the 1990s in both combinatorial chemistry and high-throughput screening created the demand for rapid access to the compound deck to support the screening process. The common strategy within the pharmaceutical industry is to store the screening library in DMSO solution. Several studies have shown that a percentage of these compounds decompose in solution, varying from a few percent of the total to a substantial part of the library. In the COMDECOM (COMpound DECOMposition) project, the compound stability of screening compounds in DMSO solution is monitored in an accelerated thermal, hydrolytic, and oxidative decomposition program. A large database with stability data is collected, and from this database, a predictive model is being developed. The aim of this program is to build an algorithm that can flag compounds that are likely to decompose-information that is considered to be of utmost importance (e.g., in the compound acquisition process and when evaluation screening results of library compounds, as well as in the determination of optimal storage conditions).
Collapse
|
6
|
Zhang J, Kleinöder T, Gasteiger J. Prediction of pKa values for aliphatic carboxylic acids and alcohols with empirical atomic charge descriptors. J Chem Inf Model 2007; 46:2256-66. [PMID: 17125168 DOI: 10.1021/ci060129d] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two quantitative pKa prediction models for aliphatic carboxylic acids and for alcohols were developed by multiple linear-regression (MLR) analysis with empirical atomic descriptors. The acid and alcohol molecules were described by a set of five and four atomic descriptors, respectively. For the pKa model of 1122 aliphatic carboxylic acids, the squared correlation coefficient is 0.813 with a standard error of prediction of 0.423; for the pKa model of 288 alcohols, the squared correlation coefficient is 0.817 with a standard error of prediction of 0.755, respectively. The good predictive abilities of the models obtained were indicated by both cross-validation and by external validation. An atomic descriptor was developed to model the inductive effect of the neighboring atoms for a central atom in a molecule. The ability of the descriptor to measure the inductive effect of substituent groups was demonstrated by a good correlation of this descriptor with Taft sigma* constants in aliphatic carboxylic acids. It provides a new approach to estimate Taft sigma* constants directly from molecular structures. An algorithm using Kohonen neural networks for splitting a data set into a training set and a test set is also presented.
Collapse
Affiliation(s)
- Jinhua Zhang
- Computer-Chemie-Centrum and Institut für Organische Chemie, Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, D-91052, Erlangen, Germany
| | | | | |
Collapse
|
7
|
Gasteiger J, Bauerschmidt S, Burkard U, Hemmer MC, Herwig A, Von Homeyer A, Höllering R, Kleinöder T, Kostka T, Schwab C, Selzer P, Steinhauer L. Decision support systems for chemical structure representation, reaction modeling, and spectra simulation. SAR QSAR Environ Res 2002; 13:89-110. [PMID: 12074394 DOI: 10.1080/10629360290002253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The choice of an appropriate structure coding scheme is the secret to success in QSAR studies. Depending on the problem at hand, 2D or 3D descriptors have to be chosen; the consideration of electronic effects might be crucial, conformational flexibility has to be of special concern. Artificial neural networks, both with unsupervised and with supervised learning schemes, are powerful tools for establishing relationships between structure and physical, chemical, or biological properties. The EROS system for the simulation of chemical reactions is briefly presented and its application to the degradation of s-triazine herbicides is shown. It is further shown how the simulation of chemical reactions can be combined with the simulation of infrared spectra for the efficient identification of the structure of degradation products.
Collapse
Affiliation(s)
- J Gasteiger
- Computer-Chemie-Centrum and Institute of Organic Chemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|