Structural and mechanistic insights into oxidative biaryl coupling to form the arylomycin core by an engineered CYP450†

IF 3.5 3区 化学 Q2 CHEMISTRY, INORGANIC & NUCLEAR
Vandana Kardam, Vaibhav Bhatt and Kshatresh Dutta Dubey
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Abstract

Arylomycin, a potent antibiotic targeting bacterial signal peptidase, is difficult to synthesize experimentally due to its poor to moderate yields and the formation of a mixture of compounds. A recent experimental bioengineering work shows that the core of arylomycin can be efficiently synthesized by engineering the cytochrome P450 enzyme from Streptomyces sp.; however, the mechanism of the same was not elucidated. Herein, we have thoroughly investigated the mechanism behind the evolution of the enzyme for the synthesis of the arylomycin core via C–C bond formation in the CYP450 enzyme using hybrid QM/MM calculations, MD simulations, and DFT calculations. We show that strategic mutations such as (a) G-101 → A facilitate biaryl coupling by subtly pushing the substrate and (b) the Q-306 → H mutation creates a strong pi–pi interaction with the substrate that brings the two phenol rings of the substrate closer to undergo C–C coupling. Importantly, our QM/MM calculations show that for efficient C–C formation, the reaction should proceed via the biradical mechanism rather than hydroxylation.

Abstract Image

通过工程化 CYP450 氧化双酰偶联形成芳基霉素核心的结构和机理透视
红霉素(Arylomycin)是一种针对细菌信号肽酶的强效抗生素,但由于其产量较低且会形成混合物,因此很难通过实验合成。最近的一项生物工程实验工作表明,通过工程化细胞色素 P450 酶链霉菌(Streptomyces sp)可以高效合成 Arylomycin 的核心,但其机制尚未阐明。在此,我们利用 QM/MM 混合计算、MD 模拟和 DFT 计算,深入研究了通过 CYP450 酶中的 C-C 键形成合成红霉素核心的酶进化机制。我们的研究表明,战略突变(如 a) G-101A 突变)通过巧妙地推动底物而促进了双芳基偶联;b) Q-306→H 突变与底物产生了强烈的 pi-pi 相互作用,使底物的两个酚环更接近于发生 C-C 偶联。重要的是,我们的 QM/MM 计算表明,为了有效地形成 C-C,反应应该通过双辐射机制而不是羟基化机制进行。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Dalton Transactions
Dalton Transactions 化学-无机化学与核化学
CiteScore
6.60
自引率
7.50%
发文量
1832
审稿时长
1.5 months
期刊介绍: Dalton Transactions is a journal for all areas of inorganic chemistry, which encompasses the organometallic, bioinorganic and materials chemistry of the elements, with applications including synthesis, catalysis, energy conversion/storage, electrical devices and medicine. Dalton Transactions welcomes high-quality, original submissions in all of these areas and more, where the advancement of knowledge in inorganic chemistry is significant.
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