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Zhang H, Shen C, Zhang HR, Chen WX, Luo QQ, Ding L. Discovery of novel DGAT1 inhibitors by combination of machine learning methods, pharmacophore model and 3D-QSAR model. Mol Divers 2021; 25:1481-1495. [PMID: 34160713 DOI: 10.1007/s11030-021-10247-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/03/2021] [Indexed: 02/05/2023]
Abstract
DGAT1 plays a crucial controlling role in triglyceride biosynthetic pathways, which makes it an attractive therapeutic target for obesity. Thus, development of DGAT1 inhibitors with novel chemical scaffolds is desired and important in the drug discovery. In this investigation, the multistep virtual screening methods, including machine learning methods and common feature pharmacophore model, were developed and used to identify novel DGAT1 inhibitors from BioDiversity database with 30,000 compounds. 531 compounds were predicted as DGAT1 inhibitors by combination of machine learning methods comprising of SVM, NB and RP models. Then, 12 agents were filtered from 531 compounds by using the common feature pharmacophore model. The 3D chemical structures of the 12 hits coordinated with surface charges and isosurface have been carefully analyzed by the established 3D-QSAR model. Finally, 8 compounds with desired properties were retained from the final hits and have been assigned to another research group to complete the follow-up compound synthesis and biologic evaluation.
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Affiliation(s)
- Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
| | - Chen Shen
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Hong-Rui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Wen-Xuan Chen
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Qing-Qing Luo
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Lan Ding
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
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Kumar P, Kumar A, Sindhu J. In silico design of diacylglycerol acyltransferase-1 (DGAT1) inhibitors based on SMILES descriptors using Monte-Carlo method. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:525-541. [PMID: 31331203 DOI: 10.1080/1062936x.2019.1629998] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
Diabetes, obesity and other diseases related to metabolism are worldwide health problems. These syndromes can be well treated when a particular enzyme-based therapy is developed. Diacylglycerol acyltransferase (DGAT; EC 2.3.1.20) is a microsomal enzyme which is responsible for the synthesis of triglycerides from 1,2-diacylglycerol by catalyzing the acyl-CoA-dependent acylation. The obesity and type-II diabetes can be checked by the inhibition of DGAT1 enzyme. Quantitative structure-activity relationship (QSAR) modelling is an essential technique in drug design and development. To study the aspect of DGAT1 inhibitors, Monte-Carlo method-based QSAR was developed for 197 DGAT1 inhibitors. QSAR models were derived by using the optimal descriptor based on SMILES notation. Different statistical parameters including the novel index of ideality of correlation were applied to validate the generated QSAR models. Four random splits were prepared from the data set. The statistical criteria r2 = 0.8129, CCC = 0.8979 and Q2 = 0.7962 of the validation set of split 1 were the best; therefore, the developed QSAR model of split 1 was decided to be the leading model. The molecular fragments, which were promoter of endpoint increase or decrease were also determined. Thirteen new DGAT1 inhibitors were designed from the lead compound DGAT011.
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Affiliation(s)
- P Kumar
- Department of Chemistry, Kurukshetra University , Kurukshetra , India
| | - A Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science and Technology , Hisar , India
| | - J Sindhu
- Department of Chemsitry, COBS&H CCS Haryana Agriculture University , Hisar , India
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Jo M, Won SW, Lee DG, Yun J, Kim S, Kwak YS. Facile ring opening reaction of oxazolone enables efficient amidation for aminoisobutyric acid. Arch Pharm Res 2018; 41:481-489. [PMID: 29696569 DOI: 10.1007/s12272-018-1031-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 04/13/2018] [Indexed: 11/29/2022]
Abstract
4,4-Dimethyloxazolones derived from N-protected aminoisobutyric acid (AIB) are particularly known as poor electrophiles due to the steric hindrance around the carbonyl and not employed as useful intermediates for amidation whereas numerous examples have been reported to support the utility of other oxazolones in amidation. AIB is an important and strategical synthon in medicinal chemistry but the peptide bond formation of the N-protected urethane derivatives of AIB is known to be often unproductive due to the rapid formation of the stable 4,4-dimethyloxazolone via an intramolecular cyclization. We discovered that the 4,4-dimethyloxazolone of an AIB urethane is in fact an excellent electrophile that enables efficient amidation even with weakly reactive nucleophiles. The 4,4-dimethyloxazolone can be stored in a pure form and used as a reagent offering an efficient and convenient synthetic tool for generating AIB-peptide analogs.
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Affiliation(s)
- Minmi Jo
- College of Pharmacy, Korea University, Sejong, 30019, Korea
| | - Sun-Woo Won
- College of Pharmacy, Korea University, Sejong, 30019, Korea
| | - Dong Guk Lee
- College of Pharmacy, Korea University, Sejong, 30019, Korea
| | - Jungeon Yun
- College of Pharmacy, Korea University, Sejong, 30019, Korea
| | - Sunhong Kim
- Disease Target Structure Research Center and Department of Bioscience, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology, Daejeon, 34141, Korea
| | - Young-Shin Kwak
- College of Pharmacy, Korea University, Sejong, 30019, Korea.
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Abstract
Unusual amino acids are fundamental building blocks of modern medicinal chemistry. The combination of readily functionalized amine and carboxyl groups attached to a chiral central core along with one or two potentially diverse side chains provides a unique three-dimensional structure with a high degree of functionality. This makes them invaluable as starting materials for syntheses of complex molecules, highly diverse elements for SAR campaigns, integral components of peptidomimetic drugs, and potential drugs on their own. This Perspective highlights the diversity of unnatural amino acid structures found in hit-to-lead and lead optimization campaigns and clinical stage and approved drugs, reflecting their increasingly important role in medicinal chemistry.
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Affiliation(s)
- Mark A T Blaskovich
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland Australia 4072
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