An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets
An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets
复制标题
SARS-CoV-2 靶点溶剂化热力学和结构图的在线存储库
DOI：
10.1007/s10822-020-00341-x
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发表时间：
2020
影响因子：
3.5
通讯作者：
Kurtzman, Tom
中科院分区：
文献类型：
--
作者：
Olson, Brian;Cruz, Anthony;Chen, Lieyang;Ghattas, Mossa;Ji, Yeonji;Huang, Kunhui;Ayoub, Steven;Luchko, Tyler;McKay, Daniel J.;Kurtzman, Tom
SARS-CoV-2最近跨越物种并通过人际传播迅速传播，导致COVID-19全球爆发。由于缺乏有效的疫苗，加上疾病的严重性，有必要尝试开发小分子药物来对抗病毒。COVID19_GIST_HSA是一个免费的在线资源库，提供COVID-19相关蛋白质小分子药物靶标的溶剂化热力学图。使用AmberTools cpptraj-GIST生成网格非均匀溶剂化理论图，使用AmberTools rism3d.snglpnt创建3D参考相互作用位点模型图，使用SSTMap代码创建水合位点分析图。所得数据可应用于药物设计工作：为对接的溶剂置换评分、合理的先导修饰、基于配体和蛋白质的药效团元件的优先级排序以及基于水的药效团的产生。在这里，我们演示了溶剂化热力学映射数据的使用。希望这些免费提供的数据将有助于小分子药物发现工作，以击败SARS-CoV-2。
SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid inhomogeneous solvation theory maps were generated using AmberTools cpptraj-GIST, 3D reference interaction site model maps were created with AmberTools rism3d.snglpnt and hydration site analysis maps were created using SSTMap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2.
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影响因子：
15
作者：
Abel, Robert;Young, Tom;Friesner, Richard A.
通讯作者：
Friesner, Richard A.
影响因子：
5.5
作者：
Kraml, Johannes;Kamenik, Anna S.;Liedl, Klaus R.
通讯作者：
Liedl, Klaus R.
影响因子：
5.5
作者：
Maier JA;Martinez C;Kasavajhala K;Wickstrom L;Hauser KE;Simmerling C
通讯作者：
Simmerling C
基于位点 3D-RISM 的分子重建方法以及与酶活性位点中 GIST 水合热力学图的比较
影响因子：
3.7
作者：
Nguyen, Crystal;Yamazaki, Takeshi;Kovalenko, Andriy;Case, David A.;Gilson, Michael K.;Kurtzman, Tom;Luchko, Tyler
通讯作者：
Luchko, Tyler
影响因子：
5.5
作者：
Luchko, Tyler;Gusarov, Sergey;Roe, Daniel R.;Simmerling, Carlos;Case, David A.;Tuszynski, Jack;Kovalenko, Andriy
通讯作者：
Kovalenko, Andriy