Computational Design of Inhibitor Specificity

描述（由申请人提供）：药物治疗的发展已成为治疗传染病和癌症的重要途径。某些感染因子和癌细胞的高出错复制率可在相对较短的时间内导致耐药性。该项目将寻求一种新的方法来开发不容易出现靶标抗性的酶抑制剂，即底物包膜假说，将开发和应用小分子配体的逆计算设计方法，并将通过与有机和药物化学、酶分析、蛋白质晶体学和病毒学。HIV蛋白酶之所以被选为案例研究，是因为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。底物包膜假说认为，存在于底物共享体积内的抑制剂不太容易受到抗性突变的影响，因为这种突变仍然必须翻转底物。通过我们的计算方法，我们将开发具有与抗性突变体面板强大结合特性的HIV蛋白酶抑制剂，通过协同工作，这些抑制剂将被合成，分析和表征。初步工作取得了一定的成功，并提出了一些关于底物包络假设的问题。拟议的项目涉及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，包括有效处理目标位点的灵活性，结合额外的隐式溶剂能量函数形式，以及实现更有效的搜索算法。拟议的项目将严格测试底物包膜假说，方法是通过对遵守底物包膜和不遵守底物包膜的抑制剂进行精细设计，包括通过设计遵守底物包膜的变体来挽救屈服于抗性突变和违反底物包膜的抑制剂。这些在粘附底物包膜方面存在差异但在其他方面相同的抑制剂的集合将是将抗性概况与包膜假设联系起来的关键资源，我将与我的实验合作者一起研究。拟议的项目还将设计和研究预计广泛结合一组抗性突变体的多个成员的抑制剂的特性，并将它们与预计仅与单个目标结合的抑制剂的特性进行比较。通过这种方式，可能会产生坚固粘合剂的新原理和基材包络假设的改进。像底物包膜假说这样的隐式设计方法的一个特殊优势是，它们不需要事先明确了解耐药性突变。

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.