COMPUTATIONAL STUDIES OF LIGAND BINDING TO ENZYMES

拟议的研究将使用理论计算方法来 在一个详细的原子上研究酶的分子特异性 水平。特异性靶标酶/底物体系为牛酶 胰酶和一系列取代的苯甲酰胺类抑制剂。该项目 将包括三个阶段，旨在获得全面的 酶的特异性图片，从扩散方法的 配基-酶对形成非共价络合物 酶的特异性部位的抑制物。 在第一阶段中，开发了用于建模的经验势能函数 详细的原子水平上的蛋白质将被用来确定最佳 一系列取代苯甲酰胺的结构和结合能 与胰酶结合的抑制剂，并评估结合能和结构 氢键、静电、范德华和 其他互动。之间的近似结合常数差 通过这种静态方法计算的各种抑制剂将与 确定研究有效性的实验结合常数数据 它们忽略了明显的溶剂和熵效应。在第二阶段 分子动力学方法，模拟了原子的热运动 一种蛋白质/抑制剂复合体，将用于计算真正的热力学 与该系列抑制剂结合的胰酶的结合常数。这些 计算将考虑与溶剂的详细相互作用 分子和熵贡献。在第三阶段中，布朗动力学 将使用一种方法来研究扩散相遇的动力学 酶/配体反应的阶段。这种方法是基于随机的 模拟酶/配体对在溶剂介质中的运动。这 运动受到一系列复杂的分子间相互作用的影响。 建议的研究将证明使用模型的可行性。 确定酶对各种底物亲和力的计算 并确定必须包括哪些功能才能理解 酶的专一性。这最终将在预测中发挥实际作用。 修饰后的合成药物或酶的生物活性 预选任务。

The proposed study will employ theoretical computational methods to investigate the molecular specificity of enzymes on a detailed atomic level. The specific target enzyme/substrate system is the enzyme bovine trypsin and a series of substituted benzamidine inhibitors. The project will consist of three phases directed towards gaining a comprehensive picture of enzyme specificity, from the diffusional approach of the ligand-enzyme pair to the formation of a non-covalent complex of the inhibitor at the specificity site of the enzyme. In Phase I an empirical potential energy function developed for modeling proteins on a detailed atomic level will be used to determine optimum structures and binding energies for a series of substituted benzamidine inhibitors bound to trypsin, and to evaluate binding energy and structural differences in terms of hydrogen bonding, electrostatic, van der Waals and other interactions. Approximate binding constant differences between various inhibitors calculated by this static approach will be compared with experimental binding constant data to determine the validity of studies which ignore explicit solvent and entropy effects. In Phase II the molecular dynamics approach, which simulates the thermal atomic motions in a protein/inhibitor complex, will be used to calculate true thermodynamic binding constants for trypsin bound to the series of inhibitors. These calculations will take into account the detailed interactions with solvent molecules and entropic contributions. In Phase III a Brownian dynamics approach will be used to study the dynamics of the diffusional encounter stage of enzyme/ligand reactions. This approach is based on a stochastic simulation of motion of enzyme/ligand pairs in a solvent medium. This motion is influenced by a complicated range of intermolecular interactions. The proposed studies will demonstrate the feasibility of using model calculations to determine the affinity of enzymes for various substrates and to determine what features must be included in order to understand enzyme specificity. This will ultimately be of practical use in predicting the biological activity of synthetic drugs or enzymes modified to carry out preselected tasks.