Developing mass spectrometry to understand molecular mechanisms of antibacterial and antiviral drugs

细菌和病毒利用越来越新颖和巧妙的途径来感染人类和动物宿主。他们持续的“创造性”导致了当今两大最严重的健康威胁：耐药细菌和病毒流行病死灰复燃，如当前的COVID-19大流行。在这两种情况下，我们对药物机制的理解存在差距，这是取得进展的主要障碍。发现新抗生素的过程极其缓慢，设计新抗生素也很困难，因为我们对大多数现有抗生素的工作原理知之甚少。我们也缺乏对细菌如何获得耐药性的详细了解。与此同时，迫切需要更好地了解正在被重新用于治疗COVID-19感染的现有药物。在这项研究中，我们的目标是填补我们对抗生素和抗病毒药物的理解上的关键空白，包括那些对细菌和Covid-19都有一定疗效的药物。我们将研究这些药物起作用的地方的分子活动——细菌和病毒周围的膜。这一领域的一个挑战是膜研究的技术难度，但我们最近开发了专门的技术，使用质谱法，使这种研究成为可能。我们的研究将集中在Darobactin上，这是一种最近发现的抗生素。我们的目标是了解Darobactin（及其改良形式）如何进入细菌细胞，从而帮助设计新的抗生素。随着有效抗生素的范围缩小，另一个策略是重新设计我们已有的抗生素。例如，一种新版本的万古霉素（将两个万古霉素分子结合在一起）已被证明是有效的，我们预测其治疗感染的途径与传统的万古霉素不同。揭示这种新的作用模式是我们工作的另一个重点，并将为重新设计其他现有抗生素的努力提供信息。我们工作的另一个领域旨在确定新的抗生素靶点。它关注的是细菌膜上的酶，这些酶在细菌细胞周围建立和重塑了高度保护的壁。我们将监测细胞壁成分的合成和组装，探索削弱这些细菌防御的干预措施，并可能开发出新的抗生素。我们随后将讨论细菌抵抗抗生素治疗的一种方式——通过组装一个外排泵将抗生素排出细胞。一家名为AceI的泵出口氯己定，这是一种在低收入国家广泛使用的低成本抗菌剂，阻碍了这种在临床卫生方面非常有效的物质的使用。我们进一步的研究致力于寻找这种泵的抑制剂。我们还旨在发现其他复杂的药物外排泵是如何组装的，以及它们如何出口药物。如果成功，这一策略将使我们现有的许多抗生素得以继续使用。在将我们的方法应用于COVID-19的过程中，我们渴望提高对正在被重新用于感染治疗的药物的理解——它们的机制和靶点，以及将它们结合起来创造“药物鸡尾酒”（就像成功用于艾滋病毒一样）的潜力。我们还将研究如何协调和控制病毒的组装。随着COVID-19治疗的新药物靶点不断出现，我们将探索它们与细胞膜上其他分子结合的药物结合相互作用。这项研究计划将从多个角度调查细菌和病毒成分之间的相互作用，以及可以防止它们感染我们的药物。通过确定新的药物靶点、设计新药以及重新设计和重新利用现有药物，它们共同构成了一项强有力的战略，有助于寻找新的抗生素和应对COVID-19。

Bacteria and viruses exploit increasingly novel and ingenious pathways to infect their human and animal hosts. Their continued 'inventiveness' has led to two of today's most serious health threats: drug-resistant bacteria and resurgent viral epidemics such as the current COVID-19 pandemic. In both cases, gaps in our understanding of drug mechanisms pose a major barrier to progress. Discovering new antibiotics is painstakingly slow, and designing new ones is difficult because we have a poor grasp of how most existing antibiotics work. We also lack detailed insight into how bacteria achieve resistance. Meanwhile, there is a critical need to better understand existing drugs that are being repurposed to treat COVID-19 infections. In this research, we aim to fill in the critical gaps in our understanding of both antibiotic and antiviral drugs, including those showing some efficacy against both bacteria and Covid-19. We will study molecular activities taking place where these drugs act - in the membranes that surround bacteria and viruses. A challenge in this area has been the technical difficulty of membrane studies, but we have recently developed specialised techniques, using mass spectrometry, that make such studies possible. One strand of our research will focus on Darobactin, an antibiotic that was discovered recently. We aim to understand how Darobactin (and modified forms of it) enter bacterial cells - aiding the design of new antibiotics. As the range of effective antibiotics dwindles, another strategy is to re-engineer the antibiotics we already have. For example, a new version of the last-resort antibiotic vancomycin (with two vancomycin molecules joined together) has proven effective, and we predict its pathway for treating infection is different to that of traditional vancomycin. Uncovering this new mode of action is another focus of our work, and would inform efforts to re-engineer other existing antibiotics. Another area of our work aims to identify new antibiotic targets. It focuses on enzymes that sit in the membranes of bacteria, building and remodelling the highly protective wall that surrounds bacterial cells. We will monitor the synthesis and assembly of cell wall components, exploring interventions that weaken these bacterial defences and could be developed into new antibiotics. We will subsequently address one of the ways in which bacteria resist antibiotic treatment - by assembling an efflux pump to flush the antibiotic out of the cell. One pump, AceI, exports chlorhexidine, a low cost antimicrobial used widely in low-income countries - hindering use of what had been a highly effective substance for clinical hygiene. A further strand of our research is devoted to finding inhibitors for this pump. We also aim to discover how other complex drug efflux pumps are assembled, and how they export drugs. If successful, this strategy could enable the continued use of many of our existing antibiotics. In applying our approaches to COVID-19, we are keen to improve understanding of drugs that are being repurposed for infection treatment - their mechanisms and targets, and the potential to combine them to create 'drug cocktails' (as successfully employed for HIV). We will also investigate how assembly of the virus is coordinated and controlled. As new drug targets continue to emerge for COVID-19 therapies, we will explore their drug binding interactions in combination with other molecules that reside in the membranes of cells. This research programme will investigate, from multiple perspectives, the interactions between components of bacteria and viruses, and the drugs that can prevent them from infecting us. Together - through identification of new drug targets, design of new drugs and re-engineering and re-purposing of existing drugs - they represent a powerful strategy to help in the search for new antibiotics and to tackle COVID-19.