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Liu XQ, Yi YJ, Kong Y, Yu P, Zhao LG, Li DD. Consensus scoring model: A novel approach to the study of EGFR kinase inhibitors. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Yu P, Li D, Ni J, Zhao L, Ding G, Wang Z, Xiao W. Predictive QSAR modeling study on berberine derivatives with hypolipidemic activity. Chem Biol Drug Des 2017; 91:867-873. [DOI: 10.1111/cbdd.13150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/11/2017] [Accepted: 09/13/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Pan Yu
- Co-Innovation Center for Sustainable Forestry in Southern China; Nanjing Forestry University; Nanjing China
- College of Chemical Engineering; Nanjing Forestry University; Nanjing China
| | - Dongdong Li
- Co-Innovation Center for Sustainable Forestry in Southern China; Nanjing Forestry University; Nanjing China
- College of Chemical Engineering; Nanjing Forestry University; Nanjing China
| | - Junjun Ni
- College of Chemical Engineering; Nanjing Forestry University; Nanjing China
| | - Linguo Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China; Nanjing Forestry University; Nanjing China
- College of Chemical Engineering; Nanjing Forestry University; Nanjing China
| | - Gang Ding
- Jiangsu Kanion Pharmaceutical Co., Ltd.; Lianyungang Jiangsu Province China
| | - Zhenzhong Wang
- Jiangsu Kanion Pharmaceutical Co., Ltd.; Lianyungang Jiangsu Province China
| | - Wei Xiao
- Jiangsu Kanion Pharmaceutical Co., Ltd.; Lianyungang Jiangsu Province China
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Li DD, Meng XF, Wang Q, Yu P, Zhao LG, Zhang ZP, Wang ZZ, Xiao W. Consensus scoring model for the molecular docking study of mTOR kinase inhibitor. J Mol Graph Model 2017; 79:81-87. [PMID: 29154212 DOI: 10.1016/j.jmgm.2017.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 12/22/2022]
Abstract
The discovery of mammalian target of rapamycin (mTOR) kinase inhibitors has always been a research hotspot of antitumor drugs. Consensus scoring used in the docking study of mTOR kinase inhibitors usually improves hit rate of virtual screening. Herein, we attempt to build a series of consensus scoring models based on a set of the common scoring functions. In this paper, twenty-five kinds of mTOR inhibitors (16 clinical candidate compounds and 9 promising preclinical compounds) are carefully collected, and selected for the molecular docking study used by the Glide docking programs within the standard precise (SP) mode. The predicted poses of these ligands are saved, and revaluated by twenty-six available scoring functions, respectively. Subsequently, consensus scoring models are trained based on the obtained rescoring results by the partial least squares (PLS) method, and validated by Leave-one-out (LOO) method. In addition, three kinds of ligand efficiency indices (BEI, SEI, and LLE) instead of pIC50 as the activity could greatly improve the statistical quality of build models. Two best calculated models 10 and 22 using the same BEI indice have following statistical parameters, respectively: for model 10, training set R2=0.767, Q2=0.647, RMSE=0.024, and for test set R2=0.932, RMSE=0.026; for model 22, raining set R2=0.790, Q2=0.627, RMSE=0.023, and for test set R2=0.955, RMSE=0.020. These two consensus scoring model would be used for the docking virtual screening of novel mTOR inhibitors.
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Affiliation(s)
- Dong-Dong Li
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China.
| | - Xiang-Feng Meng
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Qiang Wang
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Pan Yu
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Lin-Guo Zhao
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Zheng-Ping Zhang
- Chia Tai Tianqing Pharmaceutical Group Co., Ltd., 369 South Yuzhou Road, Haizhou District, Lianyungang 222062, Jiangsu Province, China.
| | - Zhen-Zhong Wang
- Jiangsu Kanion Pharmaceutical Co., Ltd., 58 Haichang South Road, Lianyungang 222001, Jiangsu Province, China
| | - Wei Xiao
- Jiangsu Kanion Pharmaceutical Co., Ltd., 58 Haichang South Road, Lianyungang 222001, Jiangsu Province, China.
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Meirson T, Samson AO, Gil-Henn H. An in silico high-throughput screen identifies potential selective inhibitors for the non-receptor tyrosine kinase Pyk2. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:1535-1557. [PMID: 28572720 PMCID: PMC5441678 DOI: 10.2147/dddt.s136150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The non-receptor tyrosine kinase proline-rich tyrosine kinase 2 (Pyk2) is a critical mediator of signaling from cell surface growth factor and adhesion receptors to cell migration, proliferation, and survival. Emerging evidence indicates that signaling by Pyk2 regulates hematopoietic cell response, bone density, neuronal degeneration, angiogenesis, and cancer. These physiological and pathological roles of Pyk2 warrant it as a valuable therapeutic target for invasive cancers, osteoporosis, Alzheimer’s disease, and inflammatory cellular response. Despite its potential as a therapeutic target, no potent and selective inhibitor of Pyk2 is available at present. As a first step toward discovering specific potential inhibitors of Pyk2, we used an in silico high-throughput screening approach. A virtual library of six million lead-like compounds was docked against four different high-resolution Pyk2 kinase domain crystal structures and further selected for predicted potency and ligand efficiency. Ligand selectivity for Pyk2 over focal adhesion kinase (FAK) was evaluated by comparative docking of ligands and measurement of binding free energy so as to obtain 40 potential candidates. Finally, the structural flexibility of a subset of the docking complexes was evaluated by molecular dynamics simulation, followed by intermolecular interaction analysis. These compounds may be considered as promising leads for further development of highly selective Pyk2 inhibitors.
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Affiliation(s)
- Tomer Meirson
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Abraham O Samson
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Hava Gil-Henn
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
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Sheridan RP. Debunking the Idea that Ligand Efficiency Indices Are Superior to pIC50 as QSAR Activities. J Chem Inf Model 2016; 56:2253-2262. [DOI: 10.1021/acs.jcim.6b00431] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert P. Sheridan
- Modeling and Informatics Department, Merck & Co. Inc., Rahway, New Jersey 07065, United States
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