Design and Experimental Testing of New Docking Methods

新对接方法的设计和实验测试

• 批准号: 8204732
• 负责人: Brian K Shoichet
• 金额: $ 31.24万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-08-01 至 2013-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8204732
• 关键词: Adrenergic Receptor; Affinity; Algorithms; Binding; Biological Models; Blood Pressure; Crystallography; Development; Docking; Equilibrium; Experimental Designs; Experimental Models; Heart Rate; Infection; Lactamase; Learning; Libraries; Ligands; Malignant Neoplasms; Methods; Modeling; Molecular; Parasites; Pharmaceutical Preparations; Recording of previous events; Role; Screening procedure; Site; Solvents; System; Techniques; Testing; Thermodynamics; Work; drug discovery; high throughput screening; inhibitor/antagonist; molecular recognition; prospective; public health relevance; receptor; success

DESCRIPTION (provided by applicant): Molecular docking is now widely used for ligand discovery. The technique makes many approximations and though it has had noteworthy successes, it is neither fully reliable nor do we understand why it fails when it does. Here we develop well-controlled experimental systems to investigate specific problems in docking. These results inform development of new docking algorithms. The specific aims are: 1. Well-controlled model experimental systems to test docking algorithms. Extending work in the last period, we explore five new cavity sites to isolate specific terms in docking and molecular recognition. These cavities are entirely buried from solvent, dominated by single interactions, and bind multiple small ligands. We investigate the balance between ionic and polar interaction energies, desolvation, the role of bulk solvent, and the differences between recognition by aliphatic and aromatic groups. Predicted ligands are tested experimentally for binding and their geometries are determined by crystallography. These simple model systems only have impact if what we learn from them can be extended to biologically relevant sites. Also, some docking problems only emerge in such complicated sites. To investigate docking false negatives, we compare prospective docking and HTS campaigns targets. To investigate the role of library bias, we compare docking screens of fragment and drug-like libraries against two targets, ¿-lactamase and ¿2-adrenergic receptor. 2. New docking algorithms. We focus on methods that can be directly tested in the experimental systems. We investigate: i. ligand and receptor conformational energy strain in docking, which are thought to be critical but have been poorly treated. Because the cavities are small, these terms are much more tractable than they are in larger sites for larger ligands. The cavities are also well suited to evaluating ii. ligand and receptor desolvation in docking, which may be specifically tested in the polar and ionic perturbations in the model cavity sites. We also use iii. thermodynamic integration to calculate ligand-cavity affinities, leveraging these studies to isolate key missing terms in docking. Finally, we return to iv. formal calculations of bias in screening libraries, and its role in docking. PUBLIC HEALTH RELEVANCE: Computational docking is widely used in early drug discovery, even though it makes large errors. Here we develop experimental systems to investigate specific problems in the technique and use the results to guide the improvement of the methods. We extend these studies to biologically relevant targets, including those involved in parasite infections, cancer and blood pressure and heart rate control. These studies, in turn, inform our development of new methods.

描述（由申请人提供）：分子对接现在广泛用于配体发现。该技术进行了许多近似，虽然它取得了显著的成功，但它既不完全可靠，我们也不理解为什么它失败了。在这里，我们开发了控制良好的实验系统，以调查对接中的具体问题。这些结果通知新的对接算法的发展。具体目标是：1.良好控制的模型实验系统，以测试对接算法。在上一阶段的工作的延伸，我们探索了五个新的空腔网站，以隔离特定的条款对接和分子识别。这些空穴完全被溶剂掩埋，由单一相互作用主导，并结合多个小配体。我们调查离子和极性相互作用能之间的平衡，去溶剂化，散装溶剂的作用，以及识别脂肪族和芳香族基团之间的差异。预测配体的结合实验测试和它们的几何形状由晶体学确定。 这些简单的模型系统只有在我们从中学到的东西可以扩展到生物学相关的网站时才会产生影响。此外，一些对接问题只出现在这样复杂的网站。为了调查对接假阴性，我们比较了预期对接和HTS活动目标。为了研究文库偏倚的作用，我们比较了片段和药物样文库对两个靶点的对接筛选，<$-内酰胺酶和<$2-肾上腺素能受体。 2.新的对接算法。我们专注于可以在实验系统中直接测试的方法。我们调查：一。配体和受体的构象能应变对接，这被认为是至关重要的，但一直没有得到很好的处理。由于空穴很小，这些术语比在较大配体的较大位点中更容易处理。腔也非常适合于评估ii.对接中的配体和受体去溶剂化，这可以在模型腔位点中的极性和离子扰动中进行具体测试。我们也使用三。热力学积分来计算配体-腔亲和力，利用这些研究来分离对接中的关键缺失项。最后，我们回到IV。筛选文库中偏倚的正式计算及其在对接中的作用。 公共卫生相关性：计算对接广泛用于早期药物发现，尽管它会产生很大的错误。在这里，我们开发实验系统来调查技术中的具体问题，并使用结果来指导方法的改进。我们将这些研究扩展到生物学相关的目标，包括寄生虫感染，癌症和血压和心率控制。这些研究反过来又为我们开发新方法提供了信息。