EKO Approach To Find Small Molecules That Perturb Protein Protein Interaction

描述（由申请人提供）：制药行业的主要新领域之一是设计小分子来干扰蛋白质-蛋白质相互作用的PPIs。许多经过医学验证的蛋白质靶点都涉及PPIs，但总的来说，现有的方法不足以发现干扰这些靶点的小分子。小分子PPI模拟有限责任公司拥有知识产权，涵盖了设计可以干扰PPI的有机化合物的创新方法。这一方法的核心是两个计算协议。第一个是称为淬灭分子动力学（QMD）的程序，用于确定小分子的首选结构，第二个是称为探索关键方向（EKO）的专有算法，用于大规模地数据挖掘具有结构特征的ppi。Small Molecule PPI Mimics LLC建议通过以下方式产生收入来源：(i)识别可用于干扰PPI的可专利化学型，并出售该信息，或基于此进行合作；（ii）准备和测试公司将拥有的可专利化学型，然后出售或用于签订合作协议。要开发EKO的商业潜力，有几个步骤是必要的。第一个是开发一个不需要从商业供应商那里获得软件例程许可的QMD版本。其次，有必要调整软件，使其在标准台式计算机上运行得更快，具有更友好的界面和更少的命令行。第三，该软件需要通过实验数据进一步验证，以显示化合物可以结合与该过程相关的ppi。该应用程序将支持这三个领域的工作。

DESCRIPTION (provided by applicant): One of the major new frontiers in the pharmaceutical industry is the design of small molecules to perturb protein-protein interactions PPIs. Many medicinally validated protein targets involve PPIs, but the methods available to discover small molecules that perturb these are, on aggregate, inadequate. Small Molecule PPI Mimics LLC owns intellectual property covering an innovative new approach to designing organic compounds that can perturb PPIs. Two computational protocols are at the core of this approach. The first is a procedure called Quenched Molecular Dynamics (QMD) to determine preferred conformations of small molecules, and the second is a proprietary algorithm called Exploring Key Orientations (EKO) to data-mine structurally characterized PPIs on a massive scale. Small Molecule PPI Mimics LLC proposes to generate revenue streams by: (i) identifying patentable chemotypes that can be used to interfere with PPIs and selling this information, or entering into collaborations based on it; and, (ii) preparing and testing patentable chemotypes that the company will own, then sell or use to enter into collaborative agreements. Several steps are necessary to exploit the commercial potential of EKO. The first is to develop a version of QMD that is unencumbered by the need to license software routines from commercial vendors. Secondly, it is necessary to adapt the software so that it can be run faster, on a standard desktop computer with a more user-friendly interface with less command lines. Third, that software needs to be further validated with experimental data showing compounds can bind PPIs implicated in this process. This application is to support efforts in these three areas.