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一套集成的建模工具,可助力科学家进行基于结构和性质的药物设计。

An integrated suite of modeling tools that empower scientists in structure- and property-based drug design.

作者信息

Feng Jianwen A, Aliagas Ignacio, Bergeron Philippe, Blaney Jeff M, Bradley Erin K, Koehler Michael F T, Lee Man-Ling, Ortwine Daniel F, Tsui Vickie, Wu Johnny, Gobbi Alberto

机构信息

Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA,

出版信息

J Comput Aided Mol Des. 2015 Jun;29(6):511-23. doi: 10.1007/s10822-015-9845-4. Epub 2015 Apr 29.

Abstract

Structure- and property-based drug design is an integral part of modern drug discovery, enabling the design of compounds aimed at improving potency and selectivity. However, building molecules using desktop modeling tools can easily lead to poor designs that appear to form many favorable interactions with the protein's active site. Although a proposed molecule looks good on screen and appears to fit into the protein site X-ray crystal structure or pharmacophore model, doing so might require a high-energy small molecule conformation, which would likely be inactive. To help scientists make better design decisions, we have built integrated, easy-to-use, interactive software tools to perform docking experiments, de novo design, shape and pharmacophore based database searches, small molecule conformational analysis and molecular property calculations. Using a combination of these tools helps scientists in assessing the likelihood that a designed molecule will be active and have desirable drug metabolism and pharmacokinetic properties. Small molecule discovery success requires project teams to rapidly design and synthesize potent molecules with good ADME properties. Empowering scientists to evaluate ideas quickly and make better design decisions with easy-to-access and easy-to-understand software on their desktop is now a key part of our discovery process.

摘要

基于结构和性质的药物设计是现代药物发现不可或缺的一部分,有助于设计旨在提高效力和选择性的化合物。然而,使用桌面建模工具构建分子很容易导致设计不佳,这些设计似乎与蛋白质的活性位点形成许多有利的相互作用。尽管一个提议的分子在屏幕上看起来不错,并且似乎适合蛋白质位点的X射线晶体结构或药效团模型,但这样做可能需要一个高能的小分子构象,而这很可能是无活性的。为了帮助科学家做出更好的设计决策,我们构建了集成的、易于使用的交互式软件工具,用于进行对接实验、从头设计、基于形状和药效团的数据库搜索、小分子构象分析和分子性质计算。结合使用这些工具可帮助科学家评估设计的分子具有活性并具有理想的药物代谢和药代动力学性质的可能性。小分子发现的成功需要项目团队快速设计和合成具有良好ADME性质的强效分子。让科学家能够在桌面上使用易于访问和理解的软件快速评估想法并做出更好的设计决策,现在已成为我们发现过程的关键部分。

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