Anticipating antimicrobial resistance: predicting the resistance-spectrum of emerging lactamase variants using atomistic simulation and experiment

不断上升的抗生素耐药性是人类健康的一个主要问题。内酰胺类抗生素是最重要的一类抗生素，对内酰胺类抗生素的耐药性通常是通过内酰胺酶（BL）分解而产生的。许多产生BL的细菌具有多重耐药性，可能导致无法治疗的感染。令人担忧的是，经常检测到赋予抗性的新BL变体。由于细菌通常具有多种BL，因此通常不清楚哪些BL引起对哪些内酰胺抗生素的耐药性，以及重要的是，如何引起耐药性。使用多尺度计算机模拟，我们先前计算了一些已知的BL的内酰胺酰基酶形成和分解的效率，从而预测它们是否以及如何赋予对特定内酰胺的抗性。临床分离株的基因组分析以及实验室实验可以鉴定新的BL变体，从而提供对具有增强的抗生素分解活性的BL的进化的见解。在这个原子模拟主导的多学科项目中，主要目标是了解新出现的BL对关键内酰胺类抗生素（例如头孢菌素类，碳青霉烯类）的活性增加，然后预测潜在的新变体。基于多尺度模拟的计算分析将用于评估1）最近发现的临床相关丝氨酸BL的酰基酶的形成和分解;和2）在实验室中获得的耐药性增加的丝氨酸BL（例如，由我们的国际合作者）。这是具有挑战性的，因为这些变体（与抗生素复合）的确切结构通常不可用，并且需要探索不同的反应机制。值得注意的是，我们将使用所获得的见解和开发的方案来预测新的推定的耐药赋予BL变异体，从关键位置的突变的计算筛选。然后通过内酰胺水解的实验测定来验证选定BL和变体对抗生素分解的计算预测。

Rising antibiotic resistance is a major problem for human health. Resistance to lactams, the single most important antibiotic class, usually arises through their breakdown by lactamases (BLs). Many BL producing bacteria are multi-drug resistant and may cause untreatable infections. Worryingly, new BL variants conferring resistance are detected frequently. As bacteria usually harbour multiple BLs, it is often not clear which BLs cause resistance against which lactam antibiotics, and, importantly, how. Using multi-scale computer simulations, we have previously calculated the efficiency of lactam acyl-enzyme formation and breakdown for a number of known BLs, thereby predicting whether and how they confer resistance to specific lactams. Genomic analysis of clinical isolates as well as lab experiments can identify new BL variants and thereby provide insights into the evolution of BLs with enhanced antibiotic breakdown activity. In this atomistic simulation-led multidisciplinary project, the main aim will be to understand increased activity of newly arising BLs against key lactam antibiotics (e.g. cephalosporins, carbapenems), and then predict potential new variants. Computational assays based on multi-scale simulations will be used to assess formation and breakdown of the acyl-enzymes of 1) recently discovered, clinically relevant serine BLs; and 2) serine BLs with increased resistance obtained in the lab (e.g. by our international collaborators). This is challenging, as exact structures of these variants (in complex with antibiotics) are often not available and different reaction mechanisms will need to be explored. Notably, we will use the insights gained and protocols developed to predict new putative resistance-conferring BL variants from computational screening of mutations at key positions. Computational predictions of antibiotic breakdown by selected BLs and variants will then be validated by experimental determination of lactam hydrolysis.