A new approach to solvent determination in QM/MM-based X-ray crystallographic refinement

基于 QM/MM 的 X 射线晶体学精修中溶剂测定的新方法

• 批准号: 8834159
• 负责人: Lance M Westerhoff
• 金额: $ 14.11万
• 依托单位: QUANTUMBIO, INC.
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-12-01 至 2016-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8834159
• 关键词: Active Sites; Address; Affinity; Agreement; Algorithms; Benchmarking; Binding; Chemicals; Collaborations; Communities; Complex; Computer software; Coupled; Crystallography; Data; Databases; Docking; Drug Design; Drug Industry; Drug Interactions; Experimental Models; Failure; Grant; Hand; Health; Human; Hydration status; Hydrogen Bonding; Industry; Industry Collaborators; Laboratories; Lead; Letters; Ligands; Literature; Macromolecular Complexes; Manuals; Maps; Measures; Mediating; Metals; Methodology; Methods; Michigan; Modeling; Muramidase; Nuclear Magnetic Resonance; Phase; Play; Population; Positioning Attribute; Probability; Proteins; Protocols documentation; Publishing; Quantum Mechanics; R-factor; Reporting; Research; Resolution; Resources; Roentgen Rays; Role; Running; Scientist; Services; Site; Small Business Innovation Research Grant; Solvents; Structure; System; Techniques; Time; Universities; Validation; Water; Weight; Work; X-Ray Crystallography; base; cofactor; density; drug discovery; electron density; human disease; improved; innovation; insight; novel strategies; novel therapeutics; protein complex; protein structure; public health relevance; quantum; receptor; research study; resistance factors; restraint; statistics; success; three dimensional structure

DESCRIPTION (provided by applicant): Success in structure based drug design (SBDD) and fragment based drug design are ultimately largely dependent upon the quality of the three-dimensional (3D) structure of protein:ligand and protein:protein complexes that is the core structural technique. Both nuclear magnetic resonance (NMR) and X-ray crystallography are used to determine experimental models pertaining to these structures. Through a previous project, QuantumBio Inc. improved the quality of the X-ray refinement through integration of the Company's quantum mechanics (QM) based DivCon Discovery Suite with the PHENIX crystallographic package. This natural synergy brings the power and accuracy of quantum mechanics to the field of X-ray refinement as it plays to the core strengths of QM methods (e.g. no atom types, support for more "exotic" chemical systems, metals, and so on). This early success has led to an expanded commercial offering that was released in February 2014. The present proposal is focused on a further improvement the accuracy of the X-ray refinement protocol by incorporating improved explicit solvent structure determination. It is quite clear - an there is a growing body of evidence that indicates - that the influences of solvent have significant impact on the ligand and receptor structure as well as on the energetics of the binding. Very often exploration of an active site - such as in lead discovery and optimization - is a question of whether or not additional "unseen" waters are mediating the interactions between ligand, protein, cofactor, and so on. An intrinsic problem in macromolecular X-ray crystallography is that only a partial number of solvent molecules can be unambiguously revealed due to the resolution limitations. Unlike approaches such as WaterMap, conventional 3D-RISM, and SZMAP, which are used to predict waters regardless of their agreement with experiment, the key innovation of this method is through the use of an advanced explicit water determination algorithm to filter crystallographic data and generate the complete, experimental solvent structure within the macromolecular complex. In preliminary studies performed with our partners, the evidence that this approach is applicable to the problem at hand is quite compelling. Specifically, the results for the 2.5 A lysozyme crystal structure 2EPE have shown that the application of the new solvation methodology leads to twice as many waters or a 100% improvement in the hydration shell for the low-resolution lysozyme structure accompanied by the improvement of the overall crystallographic statistics. The method also successfully found key, crystallographic "bridging" waters along with active site pocket stabilization waters when executed on the protein:ligand complex represented in PDBid:3ERQ. Together, these preliminary results are quite encouraging, and completion of this SBIR will allow us to completely generalize and validate the method and prepare it for commercial deployment.

描述（由申请人提供）：基于结构的药物设计（SBDD）和基于碎片的药物设计的成功最终取决于蛋白质的三维（3D）结构的质量：配体和蛋白质：蛋白质络合物：蛋白质络合物是核心结构技术。核磁共振（NMR）和X射线晶体学均用于确定与这些结构有关的实验模型。通过以前的项目，Quantumbio Inc.通过将基于公司的量子力学（QM）Divcon Discovery Suite与Phenix Crystallographic套件的集成来提高X射线细化的质量。这种自然的协同作用将量子力学的力量和准确性带入了X射线改进的领域，因为它可以发挥QM方法的核心优势（例如，没有原子类型，支持更多“外来”化学系统，金属等）。这一早期成功导致了2014年2月发布的扩展商业产品。本提案通过纳入改进的显式溶剂结构的确定来进一步提高X射线改进协议的准确性。很明显 - 越来越多的证据表明 - 溶剂的影响对配体和受体结构以及结合的能量学具有重大影响。经常探索活动站点（例如铅发现和优化中）是 一个问题是否介导了配体，蛋白质，辅因子等之间的相互作用。大分子X射线晶体学中的一个固有问题是，由于分辨率的局限性，只能明确揭示一部分数量的溶剂分子。与水图，常规3D-rism和SZMAP等方法不同，这些方法用于预测水，无论其与实验的一致如何，这种方法的关键创新是通过使用先进的显式水测定算法来筛选晶体学数据并生成完整的实验性溶剂结构。在与我们的合作伙伴进行的初步研究中，这种方法适用于手头问题的证据非常令人信服。具体而言，2.5 A溶菌酶晶体结构2EPE的结果表明，新溶剂化方法的应用导致水合壳的两倍或100％改善的水合溶菌酶结构，并伴随着整体晶体学统计的改善，伴随着低分辨率的溶菌酶结构。该方法还成功地找到了关键，当在蛋白质上执行时，晶体学“桥接”水以及活跃的位点袋稳定水：PDBID中表示的配体配合物：3erq。总之，这些初步结果令人鼓舞，该SBIR的完成将使我们能够完全概括和验证该方法并为商业部署做准备。