Devof a elopment new simulation-guided approach to design antimicrobial peptides with high selectivity towards individual bacterial species

该项目的目标是开发新的基于分子动力学（MD）模拟的肽设计方法，并将其应用于设计和优化新型抗菌肽（AMP），以高选择性靶向单个细菌物种。开发新的抗菌药物以应对快速上升的抗生素耐药性是最紧迫和关键的未满足的卫生保健需求之一。这反映在英国的抗菌素耐药性战略中，该战略是BBSRC重点领域的一部分。AMP是非常有前途的药效团，但它们的化学多样性，灵活的性质，和禁止数量的可能的配置，加上缺乏合适的设计和优化工具，阻碍了他们的翻译到临床。我和我的团队一直致力于开发定量准确的实验验证的分子模拟方法来设计膜活性肽超过15年。该提案建立在这种专业知识的基础上，将提供新的实验验证的物理模拟方法，用于合理设计和优化新的AMP。由于耐药菌株的出现，目前的抗生素越来越失败。与此同时，制药业正在从新抗生素的开发中撤退。这是因为开发新抗生素的极高成本无法收回，因为任何新药都需要储备以治疗耐药性感染。因此，不仅存在开发新抗生素疗法的关键未满足的需求，而且还需要降低抗菌药效团设计和验证成本的方法。抗菌肽是最有前途的一类抗菌药效团。它们比抗生素更能抵抗抗菌素耐药性的形成，易于生产和修改，并提供了一个近乎无限的化学和结构水库，这在很大程度上尚未开发。在我们的初步工作（专利申请中）中，我们表明AMP可以被设计为提供下一代抗菌剂所需的关键特征：精确和排他性地靶向特定的病原微生物，而不伤害共生细菌或人体组织。在这里，我们将在这项工作的基础上开发新的模拟指导方法，以设计具有高选择性的靶向特定细菌物种的AMP。首先，我们应用无偏的原子细节肽分区MD模拟设计序列，有效地结合到细菌和人类细胞的特定膜模型。接下来，我们将结合联合收割机遗传算法和分子组装模拟，将成孔突变引入这些膜靶向序列。我们开发的这些模拟方法利用复杂的算法和方法，使我们能够迭代模拟数万个序列突变，以积极选择在特定膜中以高选择性分配和形成孔的肽。然后，这些设计的功能序列将用作使用组合肽文库方法进行实验优化的模板。这种结合了模拟引导设计和实验优化的方法相当于筛选数百万个肽序列，而成本和时间只是一小部分。我们将通过对活细菌和人类细胞系的体外筛选来验证所设计的AMP的功能特性和靶向抗菌活性。这里开发的方法不仅将提供急需的设计工具来实现AMP作为药效团的潜力，而且还将从根本上推进我们对特定肽序列如何靶向具有特定脂质组成的双层的理解，并为细胞膜中肽孔形成的分子机制提供了新的线索。

The goal of this project is to develop new molecular dynamics (MD) simulation based peptide-design methods and apply them to design and optimize novel antimicrobial peptides (AMPs) that target individual bacterial species with high selectivity. Developing new antibacterials to tackle rapidly rising antibiotic resistance is one of the most pressing and critical unmet health care needs. This is reflected by the UK's Antimicrobial Resistance Strategy, which is part of a BBSRC focus area. AMPs are extremely promising pharmacophores, but their chemical diversity, flexible nature, and prohibitive number of possible configurations, combined with the lack of suitable design and optimization tools has hindered their translation into the clinic. My group and I have been working on developing quantitatively accurate experimentally validated molecular simulation methods to design membrane-active peptide for over 15 years. This proposal builds on this expertise and will deliver new experimentally validated physical simulation methods for rational design and optimization of new AMPs. Current antibiotics are increasingly failing due to the emergence of drug-resistant bacterial strains. At the same time the pharmaceutical industry is retreating from the development of new antibiotics. This is because the extremely high cost of developing new antibiotics cannot be recuperated, as any new drugs will need to be held in reserve to treat drug-resistant infections. Hence there is not only a critical unmet need to develop new antibiotic therapies, but also a need for methods that bring down the cost of antibacterial pharmacophore design and validation. AMPs present one of the most promising classes of antimicrobial pharmacophores. They are more resilient than antibiotics against antimicrobial resistance formation, easy to produce and modify, and offer a near-infinite chemical and structural reservoir, which remains largely untapped. In our preliminary work (patent pending), we show that AMPs can be designed to provide a key feature desirable for next-generation antimicrobials: precise and exclusive targeting of specific pathogenic microbes without harming symbiotic bacteria or human tissues. Here we will build on this work to develop new simulation-guided methods to design AMPs that target specific bacterial species with high selectivity. First we apply unbiased atomic detail peptide partitioning MD simulations to design sequences that bind efficiently to specific membrane models of bacteria and human cells. Next we will combine genetic algorithms and molecular assembly simulations to introduce pore-forming mutations into these membrane-targeting sequences. These simulation approaches, developed by us, utilize sophisticated algorithms and methodologies that will allow us to iteratively simulate tens of thousands of sequence mutations to actively select for peptides that partition and form pores in specific membranes with high selectivity. These designed functional sequences will then serve as templates for experimental optimization using a combinatorial peptide library approach. This combined simulation-guided design and experimental optimization approach is equivalent to screening millions of peptide sequences, in a fraction of the cost and time. We will validate the functional characteristics and targeted antibacterial activity of the designed AMPs by in vitro screening against live bacteria and human cell lines.The methods developed here will not only provide urgently needed design tools to realize the potential of AMPs as pharmacophores, but also fundamentally advance our understanding of how specific peptide sequences target bilayers with particular lipid compositions, and shed new light on the molecular mechanisms driving the formation of peptide pores in cellular membranes.