Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation,Journal of Chemical Information and Modeling

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Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2018-03-09 00:00:00 , DOI: 10.1021/acs.jcim.8b00043
Dušan Petrović ₁ , Ansgar Bokel ₂ , Matthew Allan _{1,

3} , Vlada B. Urlacher ₂ , Birgit Strodel _{1,

4}

Affiliation

Engineering high chemo-, regio-, and stereoselectivity is a prerequisite for enzyme usage in organic synthesis. Cytochromes P450 can oxidize a broad range of substrates, including macrocycles, which are becoming popular scaffolds for therapeutic agents. However, a large conformational space explored by macrocycles not only reduces the selectivity of oxidation but also impairs computational enzyme design strategies based on docking and molecular dynamics (MD) simulations. We present a novel design workflow that uses enhanced-sampling Hamiltonian replica exchange (HREX) MD and focuses on quantifying the substrate binding for suggesting the mutations to be made. This computational approach is applied to P450 BM3 with the aim to shift regioselectively toward one of the numerous possible positions during β-cembrenediol oxidation. The predictions are experimentally tested and the resulting product distributions validate our design strategy, as single mutations led up to 5-fold regioselectivity increases. We thus conclude that the HREX-MD-based workflow is a promising tool for the identification of positions for mutagenesis aiming at P450 enzymes with improved regioselectivity.

中文翻译：

用于化学和区域选择性大环氧化的细胞色素P450的模拟指导设计

设计高化学选择性，区域选择性和立体选择性是在有机合成中使用酶的先决条件。细胞色素P450可以氧化多种底物，包括大环化合物，它们已成为治疗剂的常用支架。然而，大环所探索的大构象空间不仅降低了氧化的选择性，而且还损害了基于对接和分子动力学（MD）模拟的计算酶设计策略。我们提出了一种新颖的设计工作流程，该流程使用增强采样的汉密尔顿副本交换（HREX）MD，并着重于定量底物结合以暗示拟进行的突变。这种计算方法应用于P450 BM3，目的是在β-脑二醇氧化期间将区域选择性地移向众多可能的位置之一。这些预测经过实验检验，最终的产品分布验证了我们的设计策略，因为单个突变导致区域选择性提高了5倍。因此，我们得出的结论是，基于HREX-MD的工作流程是一种有前途的工具，可用于确定诱变的目标，目的是针对具有提高的区域选择性的P450酶。

更新日期：2018-03-09

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