β-Lactamases are hydrolytic enzymes capable of opening the β-lactam ring of antibiotics such as penicillin, thus endowing the bacteria that produce them with antibiotic resistance. Of particular medical concern are metallo-β-lactamases (MBLs), with an active site built around coordinated Zn cations. MBLs are pan-reactive enzymes that can break down almost all classes of β-lactams, including such last-resort antibiotics as carbapenems. They are not only broad-spectrum-reactive but are often plasmid-borne (e.g., the New Delhi enzyme, NDM), and can spread horizontally even among unrelated bacteria. Acquired MBLs are encoded by mobile genetic elements, which often include other resistance genes, making the microbiological situation particularly alarming. There is an urgent need to develop MBL inhibitors in order to rescue our antibiotic armory. A number of such efforts have been undertaken, most notably using the 3D structures of various MBLs as drug-design targets. Structure-guided drug discovery depends on the quality of the structures that are collected in the Protein Data Bank (PDB) and on the consistency of the information in dedicated β-lactamase databases. We conducted a careful review of the crystal structures of class B β-lactamases, concluding that the quality of these structures varies widely, especially in the regions where small molecules interact with the macromolecules. In a number of examples the interpretation of the bound ligands (e.g., inhibitors, substrate/product analogs) is doubtful or even incorrect, and it appears that in some cases the modeling of ligands was not supported by electron density. For ten MBL structures, alternative interpretations of the original diffraction data could be proposed and the new models have been deposited in the PDB. In four cases, these models, prepared jointly with the authors of the original depositions, superseded the previous deposits. This review emphasizes the importance of critical assessment of structural models describing key drug design targets at the level of the raw experimental data. Since the structures reviewed here are the basis for ongoing design of new MBL inhibitors, it is important to identify and correct the problems with ambiguous crystallographic interpretations, thus enhancing reproducibility in this highly medically relevant area.

β-内酰胺酶是一种水解酶，能够打开青霉素等抗生素的β-内酰胺环，从而赋予产生它们的细菌对抗生素的耐药性。医学上特别关注的是金属-β-内酰胺酶（MBL），其活性位点围绕配位的锌阳离子构建。 MBL 是泛反应酶，可以分解几乎所有类别的 β-内酰胺，包括碳青霉烯类等最后手段的抗生素。它们不仅具有广谱反应性，而且通常是质粒传播的（例如新德里酶，NDM），甚至可以在不相关的细菌中水平传播。获得性 MBL 由移动遗传元件编码，这些元件通常包括其他抗性基因，使得微生物状况尤其令人担忧。为了拯救我们的抗生素库，迫切需要开发 MBL 抑制剂。已经开展了许多此类工作，最引人注目的是使用各种 MBL 的 3D 结构作为药物设计目标。结构引导的药物发现取决于蛋白质数据库 (PDB) 中收集的结构的质量以及专用 β-内酰胺酶数据库中信息的一致性。我们对 B 类 β-内酰胺酶的晶体结构进行了仔细审查，得出的结论是这些结构的质量差异很大，特别是在小分子与大分子相互作用的区域。在许多例子中，对结合配体（例如，抑制剂、底物/产物类似物）的解释是值得怀疑的，甚至是不正确的，并且在某些情况下，配体的建模似乎不受电子密度的支持。对于十个 MBL 结构，可以提出原始衍射数据的替代解释，并且新模型已存储在 PDB 中。 在四个案例中，这些模型是与原始证词的作者共同准备的，取代了之前的证词。本综述强调了在原始实验数据水平上对描述关键药物设计目标的结构模型进行严格评估的重要性。由于此处审查的结构是新型 MBL 抑制剂持续设计的基础，因此识别和纠正晶体学解释不明确的问题非常重要，从而提高这一高度医学相关领域的可重复性。