Multiple Protein Structures in Computational Drug Design

描述(由申请人提供)：这项建议侧重于通过使用蛋白质构象(多蛋白质结构，MPS)的集合来代表固有的灵活性，将蛋白质的灵活性纳入药物开发。这种方法已被证明克服了传统对接刚性结构的一些限制，导致更高的命中率和更大的已识别缓蚀剂的化学多样性。更重要的是，目前的目标发展了这样一种想法，即蛋白质的构象行为可以用来识别新的抑制模式。这项工作的长期目标是通过开发更准确地对目标蛋白质进行建模并结合结构蛋白质组学提供的大量信息的方法来改进基于结构的药物发现(SBDD)领域。这项研究被很好地整合，提供了方法学发展和对关键生物医学重要性的系统的实际应用，以证明技术的总体实用性。第一个目标(SA1)审查了对MPS方法的各种改进。将使用MPS的替代来源。混合溶剂模拟被提出以增强蛋白质表面的映射。来自多个溶剂晶体结构的基准数据将确定哪些算法策略在许多蛋白质中执行得最好。本课程将考察变构中心的适用性。SA2和SA3分别进行蛋白质动力学的计算研究，以推动发现HIV-1蛋白酶(HIVP)和b-分泌酶(BACE1)的新抑制剂。这两种蛋白质都是天冬氨酸蛋白酶，它们的高度柔韧性极大地影响了配体的结合和抑制。事实证明，MPS方法对于具有大的暴露的结合位点的系统是有利的，这对传统的对接是有问题的。针对HIVP的新抑制模式有望减少艾滋病治疗中的耐药性。我们对抑制BACE1的替代模式的追求将集中在识别更有可能跨越血脑屏障的较小的先导化合物；这种药代动力学特性对于治疗阿尔茨海默病绝对必要，但文献中缺乏大多数抑制剂。MPS方法的实验验证是后面目标的关键组成部分，包括分析潜在的缓蚀剂，并通过氢交换、结晶学和核磁共振进行关键的结构研究。 与公共卫生相关：将开发改进的计算机辅助药物发现技术。计算机将被用来了解蛋白质的灵活性，并找到抑制HIV-1蛋白酶和b-分泌酶的新方法。需要具有新机制的抑制剂来克服艾滋病的耐药性和治疗阿尔茨海默病的药代动力学障碍。

DESCRIPTION (provided by applicant): This proposal focuses on incorporating protein flexibility into drug discovery by using ensembles of protein conformations (multiple protein structures, MPS) to represent inherent flexibility. This approach has been shown to overcome some limitations of traditional docking to rigid structures, resulting in higher hit rates and greater chemical diversity of identified inhibitors. More importantly, the current aims evolve the idea that a protein's conformational behavior can be used to identify new modes of inhibition. The long-term goal of this work is to improve the field of structure-based drug discovery (SBDD) by developing methods that more accurately model target proteins and incorporate the vast information available from structural proteomics. This study is well integrated, providing both methodological development and practical application to systems of critical biomedical importance to prove overall utility of the techniques. The first aim (SA1) examines various improvements to the MPS methodology. Alternative sources of MPS will be used. Mixed solvent simulations are proposed to enhance mapping the protein surface. Benchmark data from multiple solvent crystal structures will identify which algorithmic strategies perform best across many proteins. Applicability to allosteric sites will be examined. SA2 and SA3 conduct computational studies of protein dynamics to drive the discovery of new inhibitors for HIV-1 protease (HIVp) and b-secretase (BACE1), respectively. Both proteins are aspartyl proteases, and their large degree of flexibility greatly affects ligand binding and inhibition. The MPS approach has proven advantageous for systems with large, exposed binding sites that are problematic for traditional docking. Targeting new modes of inhibition for HIVp has the promise of reducing drug resistance in AIDS treatment. Our pursuit of alternative modes of inhibiting BACE1 will focus on identifying smaller lead compounds that are more likely to cross the blood-brain barrier; this pharmacokinetic property is absolutely essential to treat Alzheimer's disease but is lacking in most inhibitors in the literature. Experimental verification of the MPS methodology is a key component of the later aims, including assaying potential inhibitors and performing key structural studies by deuterium exchange, crystallography, and NMR. PUBLIC HEALTH RELEVANCE: Improved techniques for computer-aided drug discovery will be developed. Computers will be used to understand protein flexibility and find new ways to inhibit HIV-1 protease and b-secretase. Inhibitors with new mechanisms are needed to overcome drug resistance in AIDS and pharmacokinetic barriers in treating Alzheimer's disease, respectively.