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，会导致严重的神经系统疾病，如小头畸形症 新生儿和成人格林-巴利综合征。ZIKV也是一个全球威胁，在 热带和亚热带地区。此外，非媒介传播允许ZIKV感染人 全世界。目前既没有直接作用的抗病毒药物，也没有针对寨卡病毒的疫苗。ZIKV NS2B-NS3 蛋白水解酶是一个有吸引力的治疗靶点，因为它在病毒成熟过程中起着重要作用。海流 ZIKV蛋白水解酶的模拟多肽抑制剂细胞效价低，且非选择性抑制 人类的蛋白酶。这些模拟多肽抑制剂的局限性是由于它们的多肽支架和 共价弹头群过去用来提高它们的威力。因此，有必要发现临床上可行的方法。 蛋白酶抑制剂(PI)产生用于进一步药物开发的先导化合物。片剂类药物 设计(FBDD)是发现新支架的一种很有前途的方法，以克服 多肽仿生学。该项目旨在使用FBDD确定临床上可行的ZIKV PI。我假设联邦调查局 将导致有效的和选择性的ZIKV PI。此外，ZIKV蛋白酶如何识别不同的底物 仍然不为人知。其他病毒蛋白酶对不同底物识别的类似观察导致了 底物包络(SE)模型的发现，该模型表明良心体积的多样性 底物占据的活性部位是一种蛋白酶的识别方式。我假设SE 模型可以解释ZIKV蛋白酶对不同底物的识别。SE模型还解释了 这些病毒蛋白水解酶耐药的结构基础。在协商一致的卷内约束的PI 底物，即底物包膜，对耐药性不太敏感。耐药性是最大的 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面临的问题。因此， 耐药性问题必须在药物发现的早期阶段得到解决。这项提议允许 将ZIKV SE模型整合到FBDD方法中的独特机会，以抢先解决 抗药性问题。因此，ZIKV SE可以作为指导缓蚀剂设计的结构工具。至 研究这些假说，我将利用我在药物化学和结构生物学方面的专业知识来 合理设计、综合和评价ZKV绩效指标。我将依靠我在结晶学和 计算生物学解决ZIKV蛋白酶与抑制剂和底物的共晶结构， 分别进行了分析。从蛋白酶-底物的复合结构中，我将产生一种ZIKV蛋白酶SE。结果是 将提供对不同底物识别的结构基础的理解 ZIKV蛋白水解酶，并为进一步的药物开发产生临床上可行的PI。

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.