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Gantzer P, Creton B, Nieto-Draghi C. Inverse-QSPR for de novo Design: A Review. Mol Inform 2019; 39:e1900087. [PMID: 31682079 DOI: 10.1002/minf.201900087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
Abstract
The use of computer tools to solve chemistry-related problems has given rise to a large and increasing number of publications these last decades. This new field of science is now well recognized and labelled Chemoinformatics. Among all chemoinformatics techniques, the use of statistical based approaches for property predictions has been the subject of numerous research reflecting both new developments and many cases of applications. The so obtained predictive models relating a property to molecular features - descriptors - are gathered under the acronym QSPR, for Quantitative Structure Property Relationships. Apart from the obvious use of such models to predict property values for new compounds, their use to virtually synthesize new molecules - de novo design - is currently a high-interest subject. Inverse-QSPR (i-QSPR) methods have hence been developed to accelerate the discovery of new materials that meet a set of specifications. In the proposed manuscript, we review existing i-QSPR methodologies published in the open literature in a way to highlight developments, applications, improvements and limitations of each.
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Affiliation(s)
- Philippe Gantzer
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Benoit Creton
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Carlos Nieto-Draghi
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
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Designing High-Refractive Index Polymers Using Materials Informatics. Polymers (Basel) 2018; 10:polym10010103. [PMID: 30966141 PMCID: PMC6415069 DOI: 10.3390/polym10010103] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/17/2018] [Indexed: 11/16/2022] Open
Abstract
A machine learning strategy is presented for the rapid discovery of new polymeric materials satisfying multiple desirable properties. Of particular interest is the design of high refractive index polymers. Our in silico approach employs a series of quantitative structure⁻property relationship models that facilitate rapid virtual screening of polymers based on relevant properties such as the refractive index, glass transition and thermal decomposition temperatures, and solubility in standard solvents. Exploration of the chemical space is carried out using an evolutionary algorithm that assembles synthetically tractable monomers from a database of existing fragments. Selected monomer structures that were further evaluated using density functional theory calculations agree well with model predictions.
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Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. J Cheminform 2017; 9:64. [PMID: 29260340 PMCID: PMC5736515 DOI: 10.1186/s13321-017-0252-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/08/2017] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for. RESULTS Here, we showcase the use of the open source workflow RetroPath2.0. First, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. We then use this enumeration strategy to screen the chemical space around a set of monomers and predict their glass transition temperatures, as well as around aminoglycosides to search structures maximizing antibacterial activity. We also perform a screening around aminoglycosides with enzymatic reaction rules to ensure biosynthetic accessibility. We finally use our workflow on an E. coli model to complete E. coli metabolome, with novel molecules generated using promiscuous enzymatic reaction rules. These novel molecules are searched on the MS spectra of an E. coli cell lysate interfacing our workflow with OpenMS through the KNIME Analytics Platform. CONCLUSION We provide an easy to use and modify, modular, and open-source workflow. We demonstrate its versatility through a variety of use cases including molecular structure enumeration, virtual screening in the chemical space, and metabolome completion. Because it is open source and freely available on MyExperiment.org, workflow community contributions should likely expand further the features of the tool, even beyond the use cases presented in the paper.
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Affiliation(s)
- Mathilde Koch
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Thomas Duigou
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Pablo Carbonell
- SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. .,CNRS-UMR8030/Laboratoire iSSB, Université Paris-Saclay, 91000, Évry, France.
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Celiz AD, Smith JGW, Langer R, Anderson DG, Winkler DA, Barrett DA, Davies MC, Young LE, Denning C, Alexander MR. Materials for stem cell factories of the future. NATURE MATERIALS 2014; 13:570-9. [PMID: 24845996 DOI: 10.1038/nmat3972] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 03/31/2014] [Indexed: 05/10/2023]
Abstract
Polymeric substrates are being identified that could permit translation of human pluripotent stem cells from laboratory-based research to industrial-scale biomedicine. Well-defined materials are required to allow cell banking and to provide the raw material for reproducible differentiation into lineages for large-scale drug-screening programs and clinical use. Yet more than 1 billion cells for each patient are needed to replace losses during heart attack, multiple sclerosis and diabetes. Producing this number of cells is challenging, and a rethink of the current predominant cell-derived substrates is needed to provide technology that can be scaled to meet the needs of millions of patients a year. In this Review, we consider the role of materials discovery, an emerging area of materials chemistry that is in large part driven by the challenges posed by biologists to materials scientists.
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Affiliation(s)
- Adam D Celiz
- 1] Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK [2] Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts 02115, USA
| | - James G W Smith
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David A Winkler
- 1] CSIRO Materials Science and Engineering, Bag 10, Clayton South MDC 3169, Australia [2] Monash Institute of Pharmaceutical Sciences, 399 Royal Parade, Parkville 3052, Australia
| | - David A Barrett
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Martyn C Davies
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Lorraine E Young
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Chris Denning
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Morgan R Alexander
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
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Eriksson M, Chen H, Carlsson L, Nissink JWM, Cumming JG, Nilsson I. Beyond the Scope of Free-Wilson Analysis. 2: Can Distance Encoded R-Group Fingerprints Provide Interpretable Nonlinear Models? J Chem Inf Model 2014; 54:1117-28. [DOI: 10.1021/ci500075q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Mats Eriksson
- Chemistry Innovation Center, Discovery Sciences, ‡CVMD Innovative Medicines and §Computational Toxicology, Global Safety Assessment, AstraZeneca R&D, Mölndal 431 83, Sweden
- Oncology Innovative Medicines and ⊥Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Hongming Chen
- Chemistry Innovation Center, Discovery Sciences, ‡CVMD Innovative Medicines and §Computational Toxicology, Global Safety Assessment, AstraZeneca R&D, Mölndal 431 83, Sweden
- Oncology Innovative Medicines and ⊥Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Lars Carlsson
- Chemistry Innovation Center, Discovery Sciences, ‡CVMD Innovative Medicines and §Computational Toxicology, Global Safety Assessment, AstraZeneca R&D, Mölndal 431 83, Sweden
- Oncology Innovative Medicines and ⊥Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D, Alderley Park, Macclesfield SK10 4TG, U.K
| | - J. Willem M. Nissink
- Chemistry Innovation Center, Discovery Sciences, ‡CVMD Innovative Medicines and §Computational Toxicology, Global Safety Assessment, AstraZeneca R&D, Mölndal 431 83, Sweden
- Oncology Innovative Medicines and ⊥Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D, Alderley Park, Macclesfield SK10 4TG, U.K
| | - John G. Cumming
- Chemistry Innovation Center, Discovery Sciences, ‡CVMD Innovative Medicines and §Computational Toxicology, Global Safety Assessment, AstraZeneca R&D, Mölndal 431 83, Sweden
- Oncology Innovative Medicines and ⊥Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Ingemar Nilsson
- Chemistry Innovation Center, Discovery Sciences, ‡CVMD Innovative Medicines and §Computational Toxicology, Global Safety Assessment, AstraZeneca R&D, Mölndal 431 83, Sweden
- Oncology Innovative Medicines and ⊥Chemistry Innovation Center, Discovery Sciences, AstraZeneca R&D, Alderley Park, Macclesfield SK10 4TG, U.K
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Dai YM, Zhu ZP, Cao Z, Zhang YF, Zeng JL, Li X. Prediction of boiling points of organic compounds by QSPR tools. J Mol Graph Model 2013; 44:113-9. [PMID: 23792208 DOI: 10.1016/j.jmgm.2013.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
The novel electro-negativity topological descriptors of YC, WC were derived from molecular structure by equilibrium electro-negativity of atom and relative bond length of molecule. The quantitative structure-property relationships (QSPR) between descriptors of YC, WC as well as path number parameter P3 and the normal boiling points of 80 alkanes, 65 unsaturated hydrocarbons and 70 alcohols were obtained separately. The high-quality prediction models were evidenced by coefficient of determination (R(2)), the standard error (S), average absolute errors (AAE) and predictive parameters (Qext(2),RCV(2),Rm(2)). According to the regression equations, the influences of the length of carbon backbone, the size, the degree of branching of a molecule and the role of functional groups on the normal boiling point were analyzed. Comparison results with reference models demonstrated that novel topological descriptors based on the equilibrium electro-negativity of atom and the relative bond length were useful molecular descriptors for predicting the normal boiling points of organic compounds.
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Affiliation(s)
- Yi-min Dai
- School of Chemistry and Biological Engineering, Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, Changsha University of Science and Technology, Changsha 410004, China.
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Gombar VK, Hall SD. Quantitative Structure–Activity Relationship Models of Clinical Pharmacokinetics: Clearance and Volume of Distribution. J Chem Inf Model 2013; 53:948-57. [DOI: 10.1021/ci400001u] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vijay K. Gombar
- Lilly Research Laboratories, Drug Disposition & Toxicology, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Stephen D. Hall
- Lilly Research Laboratories, Drug Disposition & Toxicology, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
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