Anti-plague agents targeting YopH of Yersinia Pestis

描述（申请人提供）：根据美国国家过敏和传染病研究所的分类，鼠疫耶尔森菌是a类优先药剂。它是引起鼠疫的病原体。由于已有证据表明阻断这种细菌的蛋白酪氨酸磷酸酶YopH可以消除这种细菌的致病作用，因此本研究的长期目标是使用一种独特的计算和实验相结合的方法来加速发现和开发针对这种蛋白的抗鼠疫剂。这个应用程序有三个特定的目标。具体目标1侧重于对硝基儿茶酚硫酸铅（pNCS）的优化。我们的计算研究已经为改进pNCS选择性结合YopH产生了有用的见解。我们将进行更多的定量计算来进一步阐述这些发现。最有用的见解将指导重点化学文库的构建，用于实验筛选和计算机辅助设计化合物的合成，用于实验测试。具体目标2侧重于识别不同化学支架的新线索。我们将首先使用计算方法筛选化学文库，以提出更易于管理的化合物数量进行实验筛选。这些计算方法包括结合受体灵活性的现代分子对接技术，用于评估clogP的量子力学/泊松-玻尔兹曼-表面积模型，用于与Lipinski规则一起评估化合物是否具有药物样性，以及用于指导选择性药物开发的信息学方法。在实验方面，我们正在借鉴我们以前在开发YopH， PTP1B， PTPa和VHR的体外检测方面的经验。我们还将确定YopH与一些最有希望的抑制剂之间复合物的晶体结构，以帮助合理优化新药先导。Specific Aim 3侧重于对从Specific Aim 2获得的药物先导物进行初步优化。计算化学修饰实验（使用我们的量子力学/分子力学/泊松-玻尔兹曼-表面积模型和统计力学摄动理论），YopH和整个人类蛋白磷酸酶家族的比较口袋分析，以及药物可能性的计算预测将进行，以帮助建议值得合成用于实验测试的化合物。在目前的资助期内，我们的目标是鉴定Ki值小于50 nM、选择性为YopH 100倍的抑制剂（与上述其他PTPases相比）。计算实验室和实验实验室之间的紧密合作也将为更彻底地验证用于药物设计的现代计算方法提供良好的机会。根据美国国家过敏和传染病研究所的分类，鼠疫耶尔森氏菌是a类优先病原体。它是引起鼠疫的病原体，可被误用为武器。这项研究旨在确定针对这种细菌中一种叫做YopH的蛋白质的抗鼠疫药物。

DESCRIPTION (provided by applicant): Yersinia pestis is a Category A priority agent according to the classification by the National Institute of Allergy and Infectious Diseases. It is the pathogen that causes plague. Because there are already evidences that blocking the protein tyrosine phosphatase YopH of this bacterium can remove the pathogenic effects of this bacterium, the long-term goal of this research is to use a unique blend of computational and experimental methods to speed up the discovery and development of anti-plague agents targeting this protein. There are three specific aims for this application. Specific Aim 1 focuses on optimizing the lead p-nitrocatechol sulfate (pNCS). Our computational studies have already generated useful insights into improving pNCS for selective binding towards YopH. We will perform more quantitative calculations to further elaborate these findings. The most useful insights will then guide the construction of focused chemical libraries for experimental screening and the synthesis of computer-aided designed compounds for experimental testing. Specific Aim 2 focuses on identifying new leads with different chemical scaffolds. We will first use computational approaches to screen chemical libraries to come up with a more manageable number of compounds for experimental screening. These computational approaches include modern molecular docking technology incorporating receptor flexibility, a Quantum Mechanics/Poisson- Boltzmann-Surface-Area model for evaluating clogP to use with Lipinski's Rules to assess whether compounds are drug-like, and informatics approach for guiding the development of selective drugs. On the experimental side, we are drawing our previous experiences on developing in vitro assays of YopH, PTP1B, PTPa and VHR. We will also determine the crystal structure of complexes between YopH and some of the most promising inhibitors to aid rational optimization of the new drug leads. Specific Aim 3 focuses on performing preliminary optimization of the drug leads obtained from Specific Aim 2. Computational chemical modification experiments (using our Quantum Mechanics/Molecular Mechanics/Poisson-Boltzmann-Surface-Area model and statistical mechanical perturbation theory), comparative pocket analysis of YopH and the whole family of human protein phosphatases, and computational prediction of drug-likeliness will be performed to help suggest compounds that are worthwhile to synthesize for experimental testing. For the current funding period we have set our goal of identifying inhibitors with Ki values of less than 50 nM and a selectivity of 100-fold in favor of YopH (versus the other PTPases noted above). The tight collaboration between a computational and an experimental laboratory will also provide a good opportunity to more thoroughly validate modern computational methods for drug design. Yersinia pestis is a Category A priority agent according to the classification by the National Institute of Allergy and Infectious Diseases. It is the pathogen that causes plague and can be misused as a weapon. This research aims at identifying anti-plague agents that target a protein called YopH of this bacterium.