Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge
文献类型：期刊论文
| 作者 | Peng, Cheng2,3; Wang, Jinan2; Yu, Yuqi2,3; Wang, Guimin2,3; Chen, Zhaoqiang2,3; Xu, Zhijian2 ; Cai, Tingting2; Shao, Qiang2; Shi, Jiye4; Zhu, Weiliang1,2,3
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| 刊名 | FUTURE MEDICINAL CHEMISTRY
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| 出版日期 | 2019-02-01 |
| 卷号 | 11期号:4页码:303-321 |
| 关键词 | atomic charge binding-free energy electrostatic polarization semiempirical quantum mechanics solvated interaction energy |
| ISSN号 | 1756-8919 |
| DOI | 10.4155/fmc-2018-0207 |
| 通讯作者 | Wang, Jinan(jawang@simm.ac.cn) ; Zhu, Weiliang(wlzhu@simm.ac.cn) |
| 英文摘要 | Aim: It is a challenge to predict binding-free energy (Delta G) accurately. Methodology/results: For accurate Delta G prediction, a new strategy combining solvated interaction energy (SIE) or molecular mechanics/generalized Born surface area (MM/GBSA) approach with the Coulson charge of both protein and ligand calculated by semiempirical quantum mechanics (SQM), named SIE-SQMPC or MM/GBSA-SQMPC approach, was developed and tested on 50 protein-ligand complexes. Both approaches achieved higher correlation (R-2) between experimental and predicted Delta G than that with Amber-ff03 charge, even for ligands with highly different scaffolds. But, SIE-SQMPC is computationally much faster than MM/GBSA-SQMPC. Conclusion: SIE-SQMPC provided an effective alternative to predict Delta G of protein-ligand binding (R-2 = 0.66-0.94 for SIE-AM1; R-2 = 0.59-0.98 for SIE-PM7), which has the potential of high-throughput processing for molecular docking and drug design. |
| WOS关键词 | SOLVATED INTERACTION ENERGY ; POLARIZABLE FORCE-FIELD ; BOUNDARY-ELEMENT METHOD ; ELECTROSTATIC POLARIZATION ; MOLECULAR-MECHANICS ; NDDO APPROXIMATIONS ; DYNAMICS ; DOCKING ; SURFACE ; OPTIMIZATION |
| 资助项目 | National Key R&D Programs of China[2016YFA0502301] ; National Key R&D Programs of China[2017YFB0202601] ; National Natural Science Foundation of China[81573350] ; Special Program for Applied Research on Super Computation of the NSFCGuangdong Joint Fund[U1501501] |
| WOS研究方向 | Pharmacology & Pharmacy |
| 语种 | 英语 |
| WOS记录号 | WOS:000465358000005 |
| 出版者 | FUTURE SCI LTD |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/289961]  |
| 专题 | 中国科学院上海药物研究所 |
| 通讯作者 | Wang, Jinan; Zhu, Weiliang |
| 作者单位 | 1.Pilot Natl Lab Marine Sci & Technol Qingdao, Open Studio Druggabil Res Marine Nat Prod, 1 Wenhai Rd, Qingdao 266237, Shandong, Peoples R China 2.Chinese Acad Sci, Drug Discovery & Design Ctr, CAS Key Lab Receptor Res, Shanghai Inst Mat Med, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China 3.Univ Chinese Acad Sci, Sch Pharm, 19A Yuquan Rd, Beijing 100049, Peoples R China 4.UCB Biopharma SPRL, Chemin Foriest, Braine Lalleud, Belgium |
| 推荐引用方式 GB/T 7714 | Peng, Cheng,Wang, Jinan,Yu, Yuqi,et al. Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge[J]. FUTURE MEDICINAL CHEMISTRY,2019,11(4):303-321. |
| APA | Peng, Cheng.,Wang, Jinan.,Yu, Yuqi.,Wang, Guimin.,Chen, Zhaoqiang.,...&Zhu, Weiliang.(2019).Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge.FUTURE MEDICINAL CHEMISTRY,11(4),303-321. |
| MLA | Peng, Cheng,et al."Improving the accuracy of predicting protein-ligand binding-free energy with semiempirical quantum chemistry charge".FUTURE MEDICINAL CHEMISTRY 11.4(2019):303-321. |
入库方式： OAI收割
来源：上海药物研究所
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