Structure–kinetic relationship analyses and identification of dominating interactions for optimization of lead compounds should ideally be based on intrinsic rate constants instead of the more easily accessible observed kinetic constants, which also account for binding-linked reactions. The intrinsic rate constants for sulfonamide inhibitors and pharmacologically relevant isoforms of carbonic anhydrase were determined by a novel surface plasmon resonance (SPR) biosensor-based approach, using chemodynamic analysis of binding-linked pH-dependent effects. The observed association rates (k_a^obs) were pH-dependent and correlated with the fraction of deprotonated inhibitor and protonated zinc-bound water molecule. The intrinsic association rate constants (k_a^intr) were pH independent and higher than k_a^obs. By contrast, the observed and intrinsic dissociation rate constants were identical and pH-independent, demonstrating that the observed association and dissociation mechanisms are inherently different. A model accounting for the differences between intrinsic and observed rate constants was developed, useful also for other interactions with binding-linked protonation reactions.

中文翻译：

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蛋白质-配体相互作用的内在动力学及其在药物设计中的意义

理想情况下，结构动力学分析和主要相互作用的识别以优化先导化合物应基于固有速率常数，而不是更容易获得的观察到的动力学常数，后者也说明了结合连接的反应。磺酰胺抑制剂和碳酸酐酶的药理学相关同工型的内在速率常数是通过基于结合表面的pH依赖效应的化学动力学分析的新型表面等离振子共振（SPR）生物传感器方法确定的。观察到的关联率（k _a ^obs）与pH有关，并且与去质子化的抑制剂和质子化的与锌结合的水分子的比例相关。固有的缔合速率常数（k _a ^intr）与pH无关，高于k _a ^obs。相比之下，观察到的和解离速率常数是相同的，并且与pH无关，这表明观察到的缔合和解离机理本质上是不同的。建立了一个模型，该模型解释了固有速率常数和观察到的速率常数之间的差异，该模型也可用于与结合连接的质子化反应的其他相互作用。