Data from: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme

The CTX-M family of beta lactamases mediate broad-spectrum antibiotic resistance and present in the majority of drug-resistant gram-negative bacteria infections worldwide. Allosteric mutations that increase catalytic rates of these drug resistance enzymes have been identified in clinical isolates but are challenging to predict prospectively. We have used molecular dynamics simulations to predict allosteric mutants increasing CTX-M9 drug resistance, experimentally testing top mutants using multiple antibiotics. Purified enzymes show an increase in catalytic rate and efficiency, while mutant crystal structures show no detectable changes from wild-type CTX-M9. We hypothesize that increased drug resistance results from changes in the conformational ensemble of an acyl intermediate in hydrolysis. Machine-learning analyses on top-scoring mutants identify changes to the binding-pocket conformational ensemble by which these allosteric mutations transmit their effect. These findings show how molecular simulation can predict how allosteric mutations alter active-site conformational equilibria to increase catalytic rates and thus resistance against common clinically used antibiotics.

CTX-M家族β-内酰胺酶（β-lactamase）可介导广谱抗生素耐药性，在全球范围内多数耐药革兰氏阴性菌感染中均有检出。能够提升这类耐药酶催化速率的别构突变（allosteric mutation）已在临床分离株中被发现，但前瞻性预测此类突变仍颇具挑战。本研究借助分子动力学模拟（molecular dynamics simulations）预测了可提升CTX-M9耐药性的别构突变体，并采用多种抗生素对筛选出的优质突变体开展实验验证。纯化后的酶制剂的催化速率与催化效率均有所提升，而突变体的晶体结构与野生型CTX-M9相比未出现可检测到的变化。本研究推测，耐药性的提升源于水解过程中酰基中间体构象集合的改变。对高分突变体开展的机器学习分析表明，此类别构突变通过改变结合口袋的构象集合来传递其效应。本研究结果揭示了分子模拟可如何用于预测别构突变如何改变活性位点构象平衡，从而提升催化速率，进而增强对临床常用抗生素的耐药性。