The behaviour of substrate mimetics in mediating the acceptance of nonspecific acyl moieties by proteases has been investigated as a direct function of their site-specific ester leaving groups. In this contribution we report on a computational approach to rationalise this interplay and to predict the power of a potential ester moiety to act as a suitable substrate mimetic for a given enzyme by means of an automated docking procedure. Investigations with seven distinct substrate mimetics and two proteases, subtilisin and chymotrypsin, show a clear correlation between the theoretically calculated binding energies ΔE and the specificity constants kcatKM−1 obtained from parallel hydrolysis kinetic studies. These results prove the general function of the docking approach as a rational model not only in predicting the general acceptance of a substrate mimetic in a qualitative manner, but also to provide reliable information on its individual specificity towards proteases.
基于底物拟态物在介导
蛋白酶接受非特异性酰基基团中的行为,我们研究了其位点特异性酯离去基团的直接影响。在本文中,我们报告了一种计算方法,以合理化这种相互作用,并通过自动对接程序预测潜在酯基团作为特定酶合适底物拟态物的能力。对七种不同的底物拟态物和两种
蛋白酶(苏布替酶和胰
蛋白酶)的研究表明,理论计算的结合能ΔE与通过平行
水解动力学研究获得的特异性常数kcatKM−1之间存在明显的相关性。这些结果证明了对接方法作为一种合理模型的普遍适用性,不仅能以定性方式预测底物拟态物的一般接受程度,还能提供其对
蛋白酶的个体特异性方面的可靠信息。