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计算蛋白质设计被重新用于探索酶活力并帮助预测抗生素耐药性。

Computational protein design repurposed to explore enzyme vitality and help predict antibiotic resistance.

作者信息

Michael Eleni, Saint-Jalme Rémy, Mignon David, Simonson Thomas

机构信息

Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Palaiseau, France.

出版信息

Front Mol Biosci. 2023 Jan 9;9:905588. doi: 10.3389/fmolb.2022.905588. eCollection 2022.

Abstract

In response to antibiotics that inhibit a bacterial enzyme, resistance mutations inevitably arise. Predicting them ahead of time would aid target selection and drug design. The simplest resistance mechanism would be to reduce antibiotic binding without sacrificing too much substrate binding. The property that reflects this is the enzyme "vitality", defined here as the difference between the inhibitor and substrate binding free energies. To predict such mutations, we borrow methodology from computational protein design. We use a Monte Carlo exploration of mutation space and vitality changes, allowing us to rank thousands of mutations and identify ones that might provide resistance through the simple mechanism considered. As an illustration, we chose dihydrofolate reductase, an essential enzyme targeted by several antibiotics. We simulated its complexes with the inhibitor trimethoprim and the substrate dihydrofolate. 20 active site positions were mutated, or "redesigned" individually, then in pairs or quartets. We computed the resulting binding free energy and vitality changes. Out of seven known resistance mutations involving active site positions, five were correctly recovered. Ten positions exhibited mutations with significant predicted vitality gains. Direct couplings between designed positions were predicted to be small, which reduces the combinatorial complexity of the mutation space to be explored. It also suggests that over the course of evolution, resistance mutations involving several positions do not need the underlying point mutations to arise all at once: they can appear and become fixed one after the other.

摘要

针对抑制细菌酶的抗生素,耐药性突变不可避免地会出现。提前预测这些突变将有助于靶点选择和药物设计。最简单的耐药机制是在不牺牲太多底物结合的情况下减少抗生素结合。反映这一特性的是酶的“活力”,这里定义为抑制剂与底物结合自由能之间的差异。为了预测此类突变,我们借鉴了计算蛋白质设计的方法。我们使用蒙特卡罗方法探索突变空间和活力变化,从而能够对数以千计的突变进行排序,并识别出可能通过所考虑的简单机制产生耐药性的突变。作为示例,我们选择了二氢叶酸还原酶,这是一种被多种抗生素靶向的关键酶。我们模拟了它与抑制剂甲氧苄啶和底物二氢叶酸的复合物。对20个活性位点位置进行单独突变,即“重新设计”,然后成对或四个一组进行突变。我们计算了由此产生的结合自由能和活力变化。在涉及活性位点位置的七个已知耐药性突变中,有五个被正确识别出来。有十个位置的突变显示预测的活力有显著增加。预测设计位置之间的直接耦合较小,这降低了要探索的突变空间的组合复杂性。这也表明在进化过程中,涉及多个位置的耐药性突变并不需要所有潜在的点突变同时出现:它们可以一个接一个地出现并固定下来。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c7/9868620/23df2784e0c0/fmolb-09-905588-g001.jpg

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