Computational Design of Inhibitor Specificity

描述(由申请人提供)：药物疗法的发展一直是治疗传染病和癌症的基本方法。某些感染性病原体和癌细胞容易错误复制的高比率可能导致在相对较短的时间范围内产生耐药性。该项目将寻求一种新的方法来开发不太容易出现靶标耐药性的酶抑制剂，即底物包膜假说，将开发和应用小分子配体的反向计算设计方法，并将通过与有机化学和药物化学、酶分析、蛋白质结晶学和病毒学专家的实验小组的合作，在HIV-1蛋白酶的背景下广泛测试底物包膜假说。由于在临床化合物的选择压力下，在患者群体和细胞培养中选择了大量关于耐药突变的先验信息，因此HIV蛋白酶被选为一个案例研究。底物包膜假说认为，位于底物共享体积内的抑制剂对耐药性突变不太敏感，因为这样的突变体仍然必须翻转底物。通过我们的计算方法，我们将开发与耐药突变株具有强大结合性能的HIV蛋白酶抑制剂，并通过合作工作合成、分析和表征这些抑制剂。初步工作已经证明了一些成功，并提出了一些关于底物包膜假说的问题。拟议的项目包括进一步发展我们的计算配体设计方法以实现当前工作的目标，但这些发展具有广泛的适用性，包括有效地处理目标位置的灵活性，加入额外的隐式溶剂能量函数形式，以及实施更有效的搜索算法。拟议的项目将通过对不尊重底物包膜和不尊重底物包膜的抑制剂的精细设计来严格测试底物包膜假说，包括通过设计尊重底物包膜的变体来拯救屈服于耐药性突变和违反底物包膜的抑制剂的测试。这些与底物包膜粘附性不同的完全相同的抑制剂的集合将是将耐药性曲线与包膜假说联系起来的关键资源，我将与我的实验合作者一起研究包膜假说。这项拟议的项目还将设计和研究预计将广泛结合到一组耐药突变株的多个成员上的抑制剂的性质，并将它们与预计仅与单一靶点结合的抑制剂的性质进行比较。这样，就有可能产生用于坚固粘结剂的新原理和对底物包络假设的改进。像底物包膜假说这样的隐式设计方法的一个特别优点是，它们不需要事先明确了解耐药突变。 与公共卫生相关：目前针对传染病和癌症的药物治疗受到耐药性的出现的限制，在这种情况下，以前有效的治疗方法往往通过靶点突变而失去效力。该项目旨在研究开发新疗法的方法，以防止或至少显著延缓耐药性的出现。最初的工作将针对艾滋病毒蛋白水解酶，这是目前一些疗法的目标，但耐药株的出现仍然是一个重大问题。

DESCRIPTION (provided by applicant): The development of drug therapies has been an essential approach to the treatment of infectious disease and cancer. High rates of error-prone replication for certain infectious agents and cancer cells can lead to drug resistance on a relatively short time scale. This project will pursue a new approach to the development of enzyme inhibitors that are less prone to the emergence of target resistance, namely the substrate envelope hypothesis, will develop and apply inverse computational design methods for small-molecule ligands, and will test the substrate envelope hypothesis extensively in the context of HIV-1 protease through a collaborative effort with experimental groups expert in organic and medicinal chemistry, enzyme assays, protein crystallography, and virology. HIV protease has been selected as a case study due to the large amount of prior information regarding resistance mutations that have been selected in patient populations and cell culture under the selective pressure of clinical compounds. The substrate envelope hypothesis maintains that inhibitors that reside within the volume shared by substrates are less susceptible to resistance mutations, because such mutants must still turn over substrates. Through our computational approaches we will develop inhibitors for HIV protease with robust binding properties to panels of resistance mutants, and through collaborative work these inhibitors will be synthesized, assayed, and characterized. Preliminary work has demonstrated some success and raised some questions regarding the substrate envelope hypothesis. The proposed project involves the further development of our computational ligand design methodology to achieve the goals of the current work, but the developments are of broad applicability, including the efficient treatment of target site flexibility, the incorporation of additional implicit solvent energy function forms, and the implementation of more efficient search algorithms. The proposed project will stringently test the substrate envelope hypothesis through the fine- scale design of inhibitors that do and do not respect the substrate envelope, including tests to rescue inhibitors that succumb to resistance mutations and that violate the substrate envelope, through the design of variants that respect the envelope. This collection of otherwise identical inhibitors that differ in their adherence to the substrate envelope will be a crucial resource for relating resistance profiles to the envelope hypothesis, which I will study with my experimental collaborators. The proposed project will also design and study the properties of inhibitors predicted to bind broadly to multiple members of a panel of resistance mutants, and compare them to properties of inhibitors predicted to bind narrowly to a single target. In this way, new principles for robust binders and improvements to the substrate envelope hypothesis are likely to result. A particular advantage to implicit design approaches like the substrate envelope hypothesis is that they do not require prior explicit knowledge of drug resistance mutations. PUBLIC HEALTH RELEVANCE: Current medical drug therapy for infectious disease and cancer is limited by the emergence of resistance, in which a previously effective therapy loses its effectiveness, often through mutations in the target. This project aims to study methods for developing new therapies that prevent, or at least significantly delay, the emergence of resistance. Initial work will target the HIV protease, which is the target of some current therapies, but for which the emergence of resistant strains remains a significant problem.