Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
Molecules. 2018 Aug 31;23(9):2217. doi: 10.3390/molecules23092217.
Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an Asp-Gly-Arg (DGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur via the five-membered ring succinimide intermediate. Recently, we computationally showed by the B3LYP density functional theory method, that inorganic phosphate and the Arg side chain can catalyze the NGR deamidation using a cyclic peptide, c[CH₂CO⁻NGRC]⁻NH₂. In this previous study, the tetrahedral intermediate of the succinimide formation was assumed to be readily protonated at the nitrogen originating from the Asn side chain by the solvent water before the release of an NH₃ molecule. In the present study, we found a new mechanism for the decomposition of the tetrahedral intermediate that does not require the protonation by an external proton source. The computational method is the same as in the previous study. In the new mechanism, the release of an NH₃ molecule occurs after a proton exchange between the peptide and the phosphate and conformational changes. The rate-determining step of the overall reaction course is the previously reported first step, i.e., the cyclization to form the tetrahedral intermediate.
天冬酰胺-甘氨酸-精氨酸（NGR）基序中的自发脱酰胺作用会产生天冬氨酸-甘氨酸-精氨酸（DGR）序列，由于可能应用于双重肿瘤靶向，该序列最近引起了相当大的关注。众所周知，肽链中天冬酰胺的脱酰胺反应是通过五元环琥珀酰亚胺中间体进行的。最近，我们通过 B3LYP 密度泛函理论方法计算表明，无机磷酸盐和精氨酸侧链可以通过环状肽 c[CH₂CO⁻NGRC]⁻NH₂ 催化 NGR 脱酰胺。在之前的研究中，假设在释放氨分子之前，溶剂水分子容易将琥珀酰亚胺形成的四面体型中间体质子化，生成源自天冬酰胺侧链的氮原子。在本研究中，我们发现了一种不需要外部质子源质子化的四面体中间体分解的新机制。计算方法与之前的研究相同。在新机制中，在肽和磷酸盐之间发生质子交换以及构象变化后，氨分子释放。整个反应过程的速率决定步骤是之前报道的第一步，即形成四面体中间体的环化。
