Fragment-based drug design and substrate envelope model of the Zika virus protease

项目摘要 寨卡病毒（ZIKV）是一种蚊媒病毒，可导致严重的神经系统疾病，如小头畸形， 新生儿和成人格林-巴利综合征。ZIKV也是一个全球性的威胁， 热带和亚热带地区。此外，非媒介传播使ZIKV能够感染人 国际吧没有直接作用的抗病毒药物或疫苗可用于寨卡病毒。ZIKV NS2B-NS3 蛋白酶由于其在病毒成熟中的重要作用而成为有吸引力的治疗靶点。当前 ZIKV蛋白酶的肽模拟物抑制剂具有差的细胞效力和非选择性抑制ZIKV蛋白酶的能力。 人蛋白酶。这些肽模拟物抑制剂的局限性是其肽支架的结果， 共价弹头基团用于增加其效力。因此，需要发现临床上可行的 蛋白酶抑制剂（PI），以产生先导化合物，用于进一步的药物开发。片段药物 设计（FBDD）是一种很有前途的方法，用于发现新的支架，以克服 肽模拟物该项目旨在使用FBDD鉴定临床上可行的ZIKV PI。我假设FBDD 将产生有效的和选择性的ZIKV PI。此外，ZIKV蛋白酶如何识别不同的底物， 仍然未知。其他病毒蛋白酶对不同底物识别的类似观察导致了 发现的基板信封（SE）模型，其中指出，良心体积的多样性 底物占据蛋白酶的活性位点是识别模式。我假设SE 该模型可以解释ZIKV蛋白酶的不同底物识别。SE模型还解释了 这些病毒蛋白酶耐药性的结构基础。结合在聚合物的共有体积内的PI 底物（即底物包膜）不太容易产生耐药性。耐药性最大 针对其他高度变异病毒的病毒蛋白酶的直接作用抗病毒药物所面临的问题。因此 抗药性问题必须在药物发现的早期阶段加以解决。该提案允许 将ZIKV SE模型纳入FBDD方法的独特机会，以抢先解决 抗药性问题。因此，ZIKV SE可以是指导抑制剂设计的结构工具。到 调查这些假设，我将利用我在药物化学和结构生物学方面的专业知识， 合理设计、合成和评价ZIKV PI。我将依靠我在晶体学方面的经验， 计算生物学来解决ZIKV蛋白酶与抑制剂和底物的共晶体结构， 分别从蛋白酶-底物复合物结构，我将产生ZIKV蛋白酶SE。结果 从这个项目将提供一个不同的基板识别的结构基础的理解， ZIKV蛋白酶，并且还产生临床上可行的PI用于进一步的药物开发。

Project Summary Zika virus (ZIKV) is a mosquito-borne virus that causes severe neurological diseases such as microcephaly in neonates and Guillain-Barre syndrome in adults. ZIKV is also a global threat with a large at-risk population in the tropical and subtropical regions. Furthermore, non-vector borne transmission allows ZIKV to infect people worldwide. There are neither direct-acting antivirals nor vaccines available against Zika. The ZIKV NS2B-NS3 protease is an attractive therapeutic target because of its essential role in viral maturation. The current peptidomimetic inhibitors of the ZIKV protease suffer from poor cellular potency and nonselective inhibition of human proteases. The limitations of these peptidomimetic inhibitors are a result of their peptide scaffold and covalent warhead groups used to increase their potency. Hence, there is a need to discover clinically viable protease inhibitors (PIs) to generate lead compounds for further drug development. Fragment-based drug design (FBDD) is a promising approach for discovering novel scaffolds to overcome the limitations of peptidomimetics. This project aims to identify clinically viable ZIKV PIs using FBDD. I hypothesize that FBDD will result in potent and selective ZIKV PIs. Moreover, how the ZIKV protease recognizes diverse substrates remains unknown. Similar observations of diverse substrates recognition by other viral proteases led to the discovery of the substrate envelope (SE) model, which states that the conscience volume the diverse substrates occupy within the active site of a protease is the mode of recognition. I hypothesize that the SE model can explain diverse substrate recognition by the ZIKV protease. The SE model also explained the structural basis of drug resistance for those viral proteases. PIs that bind within the consensus volume of the substrates, i.e. the substrate envelope, are less susceptible to drug resistance. Drug resistance is the biggest problem facing direct-acting antivirals targeting viral proteases of other highly mutating viruses. Therefore, the problem of drug resistance must be addressed at the early stages of drug discovery. This proposal allows the unique opportunity to incorporate the ZIKV SE model into the FBDD approach to preemptively address the problem of drug resistance. Hence, the ZIKV SE can be a structural tool to guide inhibitor design. To investigate these hypotheses, I will leverage my expertise in medicinal chemistry and structural biology to rationally design, synthesize and evaluate the ZIKV PIs. I will rely on my experience in crystallography and computational biology to solve co-crystal structures of the ZIKV protease with inhibitors and substrates, respectively. From the protease-substrate complex structures, I will generate a ZIKV protease SE. The results from this project will provide an understanding of the structural basis of diverse substrate recognition by the ZIKV protease, and also generate clinically viable PIs for further drug development.