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Skoraczyński G, Dittwald P, Miasojedow B, Szymkuć S, Gajewska EP, Grzybowski BA, Gambin A. Predicting the outcomes of organic reactions via machine learning: are current descriptors sufficient? Sci Rep 2017; 7:3582. [PMID: 28620199 PMCID: PMC5472585 DOI: 10.1038/s41598-017-02303-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/06/2017] [Indexed: 11/09/2022] Open
Abstract
As machine learning/artificial intelligence algorithms are defeating chess masters and, most recently, GO champions, there is interest - and hope - that they will prove equally useful in assisting chemists in predicting outcomes of organic reactions. This paper demonstrates, however, that the applicability of machine learning to the problems of chemical reactivity over diverse types of chemistries remains limited - in particular, with the currently available chemical descriptors, fundamental mathematical theorems impose upper bounds on the accuracy with which raction yields and times can be predicted. Improving the performance of machine-learning methods calls for the development of fundamentally new chemical descriptors.
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Affiliation(s)
- G Skoraczyński
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097, Warsaw, Poland
| | - P Dittwald
- DARPA Make-It Program & the Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - B Miasojedow
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097, Warsaw, Poland
| | - S Szymkuć
- DARPA Make-It Program & the Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - E P Gajewska
- DARPA Make-It Program & the Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - B A Grzybowski
- DARPA Make-It Program & the Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland. .,Center for Soft and Living Matter of Korea's Institute for Basic Science (IBS), Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
| | - A Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097, Warsaw, Poland.
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Caboni L, Gálvez-Llompart M, Gálvez J, Blanco F, Rubio-Martinez J, Fayne D, Lloyd DG. Molecular topology applied to the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a non-ligand-binding-pocket antiandrogen. J Chem Inf Model 2014; 54:2953-66. [PMID: 25233256 DOI: 10.1021/ci500324f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the discovery of 1-benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a novel non-ligand binding pocket (non-LBP) antagonist of the androgen receptor (AR) through the application of molecular topology techniques. This compound, validated through time-resolved fluorescence resonance energy transfer and fluorescence polarization biological assays, provides the basis for lead optimization and structure-activity relationship analysis of a new series of non-LBP AR antagonists. Induced-fit docking and molecular dynamics studies have been performed to establish a consistent hypothesis for the interaction of the new active molecule on the AR surface.
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Affiliation(s)
- Laura Caboni
- Molecular Design Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin , Dublin 2, Ireland
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Galvez J, Galvez-Llompart M, Zanni R, Garcia-Domenech R. Advances in the molecular modeling and quantitative structure–activity relationship-based design for antihistamines. Expert Opin Drug Discov 2013; 8:305-17. [DOI: 10.1517/17460441.2013.748745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Predicting Dyspnea Inducers by Molecular Topology. J CHEM-NY 2013. [DOI: 10.1155/2013/798508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
QSAR based on molecular topology (MT) is an excellent methodology used in predicting physicochemical and biological properties of compounds. This approach is applied here for the development of a mathematical model capable to recognize drugs showing dyspnea as a side effect. Using linear discriminant analysis, it was found a four-variable regression equations enabling a predictive rate of about 81% and 73% in the training and test sets of compounds, respectively. These results demonstrate that QSAR-MT is an efficient tool to predict the appearance of dyspnea associated with drug consumption.
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Gálvez-Llompart M, Gálvez J, García-Domenech R, Kier LB. Modeling Drug-Induced Anorexia by Molecular Topology. J Chem Inf Model 2012; 52:1337-44. [DOI: 10.1021/ci2006092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- María Gálvez-Llompart
- Molecular Connectivity and Drug
Design Research Unit, Faculty of Pharmacy, Department of Physical
Chemistry, University of Valencia Avd, V.A. Estellés, s/n 46100-Burjassot,
Valencia, Spain
| | - Jorge Gálvez
- Molecular Connectivity and Drug
Design Research Unit, Faculty of Pharmacy, Department of Physical
Chemistry, University of Valencia Avd, V.A. Estellés, s/n 46100-Burjassot,
Valencia, Spain
| | - Ramón García-Domenech
- Molecular Connectivity and Drug
Design Research Unit, Faculty of Pharmacy, Department of Physical
Chemistry, University of Valencia Avd, V.A. Estellés, s/n 46100-Burjassot,
Valencia, Spain
| | - Lemont B. Kier
- Center
for the Study of Biological
Complexity, Virginia Commonwealth University, P.O. Box 842030, Richmond,
Virginia 23284, United States
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Galvez-Llompart M, Zanni R, García-Domenech R. Modeling natural anti-inflammatory compounds by molecular topology. Int J Mol Sci 2011; 12:9481-503. [PMID: 22272145 PMCID: PMC3257142 DOI: 10.3390/ijms12129481] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 12/25/2022] Open
Abstract
One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into drugs for treating inflammatory diseases. Computer-aided drug design has proved to be a very useful tool for discovering new drugs and, specifically, Molecular Topology has become a good technique for such a goal. A topological-mathematical model, obtained by linear discriminant analysis, has been developed for the search of new anti-inflammatory natural compounds. An external validation obtained with the remaining compounds (those not used in building up the model), has been carried out. Finally, a virtual screening on natural products was performed and 74 compounds showed actual anti-inflammatory activity. From them, 54 had been previously described as anti-inflammatory in the literature. This can be seen as a plus in the model validation and as a reinforcement of the role of Molecular Topology as an efficient tool for the discovery of new anti-inflammatory natural compounds.
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Affiliation(s)
- María Galvez-Llompart
- Molecular Connectivity & Drug Design Research Unit, Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Avenida V.A. Estelles s/n, Burjasot, Valencia 46100, Spain; E-Mails: (M.G.-L.); (R.Z.)
| | - Riccardo Zanni
- Molecular Connectivity & Drug Design Research Unit, Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Avenida V.A. Estelles s/n, Burjasot, Valencia 46100, Spain; E-Mails: (M.G.-L.); (R.Z.)
- Department of Pharmacology, Faculty of Pharmacy, University of Bologna, Via Irnerio, Bologna 48-40126, Italy
| | - Ramón García-Domenech
- Molecular Connectivity & Drug Design Research Unit, Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Avenida V.A. Estelles s/n, Burjasot, Valencia 46100, Spain; E-Mails: (M.G.-L.); (R.Z.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-963544291; Fax: +34-963544892
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