Discovery of Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries

项目概要/摘要 由于其有利的特性，β-内酰胺类占抗生素使用量的约60 国际吧然而，细菌对β-内酰胺类药物的耐药性一直在稳步增加， 对抗生素治疗的重大威胁。最常见的耐药机制是 β-内酰胺酶催化水解，使抗生素无效。一个特殊的领域 令人担忧的是由革兰氏阴性杆菌引起的多重耐药感染;几乎没有选择 治疗碳青霉烯类是一类β-内酰胺类抗生素，历史上 对β-内酰胺酶的作用敏感，并且使用量增加。越来越多的 然而，在医院环境中获得的细菌感染是由碳青霉烯耐药引起的， 肠球菌（CRE）病原体。肠杆菌科经常对碳青霉烯耐药 通过获得被称为碳青霉烯酶的质粒编码的β-内酰胺酶来获得抗生素。三个最 在全世界的诊所中经常遇到的碳青霉烯酶是KPC-2、NDM-1和OXA-48。的 本申请的目的是利用DNA编码的化学文库技术来发现小的 这些酶的分子抑制剂。这种方法涉及创建药物样蛋白库， 分子共价连接到一个独特的DNA条形码，使识别的结合剂， 在一个大的化合物池的目标。DNA编码的化学文库已经在 贝勒医学院的药物发现中心编码了超过20亿种化合物， 允许筛选宽化学空间的新的，非β-内酰胺抑制剂，这些重要的 耐药酶在初步研究中，我们通过以下方式证明了该方法的可行性： 使用DNA编码的化学文库鉴定CDD-97，其抑制OXA-48，Ki为600 nM。 OXA-48与CDD-97复合物的X射线结构显示，它与 活性位点残基和药物化学研究已经确定了结构-活性关系， 分子。DNA编码的化学文库筛选将扩展到OXA-48、NDM-1和 KPC-2 β-内酰胺酶和已鉴定的抑制剂将在以下方面进行表征： 抑制、X-射线结构、抑制光谱和对细菌的生物活性。此外，本发明还提供了一种方法， 药物化学方法将用于优化抑制剂的效力和积累， 细菌所提出的实验有可能产生新的非β-内酰胺抑制剂， 提供了有利于与β-内酰胺酶相互作用的化学支架的见解。

Project Summary/Abstract Because of their favorable characteristics, β-lactams make up approximately 60% of antibiotic usage worldwide. Bacterial resistance to β-lactam drugs, however, has been steadily increasing, posing a significant threat to antibiotic therapy. The most common mechanism of resistance is β-lactamase-catalyzed hydrolysis, which renders the antibiotics ineffective. An area of particular concern is multi-drug resistant infections caused by Gram-negative rods; leaving few options for treatment. Carbapenems are a class of β-lactam antibiotics that historically have been less susceptible to the action of β-lactamases and have seen increased usage. A rising number of bacterial infections acquired in hospital settings, however, are caused by carbapenem resistant Enterobactericiae (CRE) pathogens. Enterobacteriaceae frequently become resistant to carbapenem antibiotics by acquiring plasmid-encoded β-lactamases named carbapenemases. The three most frequently encountered carbapenemases in clinics worldwide are KPC-2, NDM-1, and OXA-48. The objective of this application is to utilize DNA-encoded chemical library technology to discover small molecule inhibitors of these enzymes. This approach involves the creation of libraries of drug-like molecules covalently attached to a unique DNA barcode that enables identification of binders for a target in a large pool of compounds. DNA-encoded chemical libraries have been constructed at the Center for Drug Discovery at Baylor College of Medicine that encode over 2 billion compounds, allowing a screen of wide chemical space for novel, non-β-lactam inhibitors of these important drug-resistance enzymes. In preliminary studies, we demonstrated the feasibility of the approach by using a DNA-encoded chemical library to identify CDD-97, which inhibits OXA-48 with a Ki of 600 nM. The X-ray structure of OXA-48 in complex with CDD-97 revealed it makes key interactions with active site residues and medicinal chemistry studies have defined structure-activity relationships for the molecule. DNA-encoded chemical library screens will be extended for the OXA-48, NDM-1 and KPC-2 β-lactamases and identified inhibitors will be characterized with respect to potency of inhibition, X-ray structure, spectrum of inhibition, and bioactivity versus bacteria. In addition, medicinal chemistry methods will be used to optimize potency and accumulation of inhibitors in bacteria. The proposed experiments have the potential to yield new, non-β-lactam, inhibitors and provide insights into chemical scaffolds that are favorable for interaction with β-lactamases.