Anti-plague agents targeting YopH of Yersinia Pestis

描述（由申请人提供）：根据美国国家过敏和传染病研究所的分类，鼠疫耶尔森氏菌是A类优先病原体。它是导致瘟疫的病原体。由于已经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，因此这项研究的长期目标是使用计算和实验方法的独特组合来加速发现和开发针对这种蛋白质的抗鼠疫药物。这项申请有三个具体目标。具体目标1侧重于优化铅对硝基儿茶酚硫酸盐（pNCS）。我们的计算研究已经产生了有用的见解，以改善pNCS对YopH的选择性结合。我们将进行更多的定量计算，以进一步阐述这些发现。然后，最有用的见解将指导重点化学库的构建，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侧重于识别具有不同化学支架的新电极导线。我们将首先使用计算方法来筛选化学库，以获得更易于管理的化合物数量，用于实验筛选。这些计算方法包括结合受体柔性的现代分子对接技术、用于评估clogP以与Lipinski规则一起使用以评估化合物是否为药物样的量子力学/Poisson- Boltzmann-Surface-Area模型，以及用于指导选择性药物开发的信息学方法。在实验方面，我们正在吸取我们以前在开发YopH，PTP 1B，PTPa和VHR体外测定方面的经验。我们还将确定YopH和一些最有前途的抑制剂之间的复合物的晶体结构，以帮助合理优化新药先导化合物。具体目标3侧重于对从具体目标2中获得的药物线索进行初步优化。计算化学修饰实验（使用我们的量子力学/分子力学/Poisson-Boltzmann-Surface-Area模型和统计力学微扰理论），YopH和整个人类蛋白磷酸酶家族的比较口袋分析，以及药物类似物的计算预测将被执行，以帮助建议值得合成的化合物进行实验测试。在当前的资助期内，我们的目标是鉴定Ki值小于50 nM的抑制剂，选择性为100倍，有利于YopH（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药物设计的现代计算方法提供一个很好的机会。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。它是导致瘟疫的病原体，可以被滥用为武器。这项研究旨在确定针对这种细菌的一种名为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.