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Ji Y, Li R, Tian Y, Chen G, Yan A. Classification models and SAR analysis on thromboxane A 2 synthase inhibitors by machine learning methods. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:429-462. [PMID: 35678125 DOI: 10.1080/1062936x.2022.2078880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Thromboxane A2 synthase (TXS) is a promising drug target for cardiovascular diseases and cancer. In this work, we conducted a structure-activity relationship (SAR) study on 526 TXS inhibitors for bioactivity prediction. Three types of descriptors (MACCS fingerprints, ECFP4 fingerprints, and MOE descriptors) were utilized to characterize inhibitors, 24 classification models were developed by support vector machine (SVM), random forest (RF), extreme gradient boosting (XGBoost), and deep neural networks (DNN). Then we reduced the number of fingerprints according to the contribution of descriptors to the models, and constructed 16 extra models on simplified fingerprints. In general, Model_4D built by DNN algorithm and 67 bits MACCS fingerprints performs best. The prediction accuracy of the model on the test set is 0.969, and Matthews correlation coefficient (MCC) is 0.936. The distance between compound and model (dSTD-PRO) was used to characterize the application domain of the model. In the test set of Model_4D, dSTD-PRO of 91.5% compounds is lower than the corresponding training set threshold (threshold0.90 = 0.1055), and the accuracy of these compounds is 0.983. In addition, the important descriptors were summarized and further analyzed. It showed that aromatic nitrogenous heterocyclic groups were beneficial to improve the bioactivity of TXS inhibitors.
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Affiliation(s)
- Y Ji
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - R Li
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Y Tian
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
| | - G Chen
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - A Yan
- State Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical Engineering, Beijing University of Chemical Technology, Beijing, P. R. China
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Wagman AS, Boyce RS, Brown SP, Fang E, Goff D, Jansen JM, Le VP, Levine BH, Ng SC, Ni ZJ, Nuss JM, Pfister KB, Ramurthy S, Renhowe PA, Ring DB, Shu W, Subramanian S, Zhou XA, Shafer CM, Harrison SD, Johnson KW, Bussiere DE. Synthesis, Binding Mode, and Antihyperglycemic Activity of Potent and Selective (5-Imidazol-2-yl-4-phenylpyrimidin-2-yl)[2-(2-pyridylamino)ethyl]amine Inhibitors of Glycogen Synthase Kinase 3. J Med Chem 2017; 60:8482-8514. [DOI: 10.1021/acs.jmedchem.7b00922] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Allan S. Wagman
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Rustum S. Boyce
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sean P. Brown
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Eric Fang
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dane Goff
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Johanna M. Jansen
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Vincent P. Le
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Barry H. Levine
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Simon C. Ng
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Zhi-Jie Ni
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - John M. Nuss
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Keith B. Pfister
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Savithri Ramurthy
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Paul A. Renhowe
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - David B. Ring
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wei Shu
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sharadha Subramanian
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Xiaohui A. Zhou
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cynthia M. Shafer
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Stephen D. Harrison
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Kirk W. Johnson
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Dirksen E. Bussiere
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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Wallach DR, Chisholm JD. Alkylation of Sulfonamides with Trichloroacetimidates under Thermal Conditions. J Org Chem 2016; 81:8035-42. [PMID: 27487402 PMCID: PMC5010445 DOI: 10.1021/acs.joc.6b01421] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An intermolecular alkylation of sulfonamides with trichloroacetimidates is reported. This transformation does not require an exogenous acid, base, or transition metal catalyst; instead the addition occurs in refluxing toluene without additives. The sulfonamide alkylation partner appears to be only limited by sterics, with unsubstituted sulfonamides providing better yields than more encumbered N-alkyl sulfonamides. The trichloroacetimidate alkylating agent must be a stable cation precursor for the substitution reaction to proceed under these conditions.
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Affiliation(s)
- Daniel R. Wallach
- Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, NY 13244
| | - John D. Chisholm
- Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, NY 13244
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