Structure-based discovery and design of novel class D beta-lactamase inhibitors

描述（由申请人提供）：内酰胺类，如青霉素和头孢菌素，是当今临床使用最广泛的抗生素处方类别。由于这些药物的广泛使用和滥用，耐药性不断发展，现已成为世纪最紧迫的公共卫生危机之一。许多耐药细菌表达β-内酰胺酶。这些酶水解限定的内酰胺环，使它们对它们的原始靶标（交联细菌细胞壁的转肽酶）无活性。基于序列相似性和作用机制，β-内酰胺酶分为四个不同的类别（A、B、C和D）。为了克服耐药性，已经开发了抑制剂来阻断这些酶的活性。特别值得关注的是D <$-内酰胺酶或苯唑西林酶（OXA），它们不受经典的<$-内酰胺类抑制剂（如克拉维酸）的抑制， 水解临床使用的几种最有效的β-内酰胺类（氧亚氨基头孢菌素和碳青霉烯类）。在某种程度上，耐药性来自于抑制剂与内酰胺本身的结构相似性：两者都含有内酰胺环。因此，迫切需要不类似于β-内酰胺底物的新型抑制剂。然而，大多数基于结构的设计工作依赖于对现有的内酰胺抗生素的修饰。我们的策略使用酶上存在的结合位点的共识图，并将其与分子对接配对，以发现D-内酰胺类酶的新型抑制剂。我们使用这种方法确定了两类抑制剂。第一种是通过分子对接鉴定的非共价片段，第二种是可逆的共价硼酸过渡态类似物。这两类化合物都为将这些化合物优化为具有所需药物样性质的可行先导化合物提供了极好的起点。随着D <$-内酰胺酶与每一类分子复合物的X射线晶体结构的掌握，我们准备将这些化合物开发成D <$-内酰胺酶的第一个临床抑制剂。

DESCRIPTION (provided by applicant): ¿-lactams, like penicillin and the cephalosporins, are the most widely prescribed class of antibiotics in clinical use today. In response to their extensive use and misuse, resistance has developed and is now one of the most pressing public health crises of the 21st century. Many resistant bacteria express ¿-lactamase enzymes. These enzymes hydrolyze the defining lactam ring, rendering them inactive toward their original target, the transpeptidases that crosslink the bacterial cell wall. ¿-lactamases are categorized into four, distinct classes (A, B, C, and D) based on sequence similarity and mechanism of action. In an effort to overcome resistance, inhibitors have been developed to block the activity of these enzymes. Of particular concern are the class D ¿-lactamases, or oxacillinases (OXAs), which are not inhibited by classic ¿-lactam-based inhibitors, like clavulanic acid, and are able to hydrolyze several of the most potent ¿-lactams in clinical use (the oxyimino cephalosporins and the carbapenems). In part, resistance derives from the structural similarity of the inhibitors to te ¿-lactams themselves: both contain a ¿-lactam ring. Therefore an urgent need exists for novel inhibitors that do not resemble the ¿-lactam substrates. However, most structure-based design efforts rely on modification of existing ¿-lactam antibiotics. Our strategy uses a consensus map of binding sites present on the enzyme and pairs this with molecular docking to discover novel inhibitors for the class D ¿-lactamases. We identified two classes of inhibitors using this approach. The first are non-covalent fragments that were identified via molecular docking, and the second are reversible, covalent boronic acid transition state analogs. Both classes provide an excellent starting point for optimization of these compounds into viable leads with desired drug-like properties. With X-ray crystal structures of class D ¿-lactamases in complexes with molecules from each class now in hand, we are poised to develop these compounds into the first clinical inhibitors for class D ¿-lactamases.