A close look onto structural models and primary ligands of metallo-β-lactamases

Abstract

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 In four cases, these models, prepared jointly with the authors of the original depositions, superseded the previous deposits.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.

Crystal structures of VIM‐1 complexes explain active site heterogeneity in VIM‐class metallo‐β‐lactamases

“…The active site view of the ML302F complex is shown in lighter, and meropenem in darker, shades. (C) Overlay of hydrolysed meropenem binding to VIM‐1 (darker colours) and NDM‐1 (pdb 5N0H ; lighter colours). (D) Overlay of available VIM crystal structures (details as Fig.…”

Investigation of Dipicolinic Acid Isosteres for the Inhibition of Metallo‐β‐Lactamases

“…The flexible active site of NDM-1, the diversity of relatedM BLs, al ack of understanding for inhibition mechanisms, and misinterpretation of structural data have all contributed to delayedi nhibitor development. [26,27] A survey of current NDM-1 inhibitors reveals al arge portion of inhibitors bear ac arboxylic acid motif. [25,26] In line with this, our lab previouslyu sed af ragment-based drugd iscovery( FBDD) approacht oi dentify dipicolinica cid (DPA) as al ead metalbinding pharmacophore (MBP) for NDM-1i nhibitor development.…”

“…[22][23][24] Unfortunately,e ven with the rapid spread of the bla NDM gene and the evolution of NDM variants,l ittle advancement has been made in inhibitor development. [26,27] A survey of current NDM-1 inhibitors reveals al arge portion of inhibitors bear ac arboxylic acid motif. The flexible active site of NDM-1, the diversity of relatedM BLs, al ack of understanding for inhibition mechanisms, and misinterpretation of structural data have all contributed to delayedi nhibitor development.…”

On the evolution of the quality of macromolecular models in the PDB

“…However, with the expansion of the Protein Data Bank (PDB) [5] from merely seven structures at its inception in 1971 to~160 000 today, it is inevitable that some of the macromolecular models will be subpar and sometimes even incorrect. Unfortunately, suboptimal structures have a tangible negative impact on biomedical research that relies on structural data [6]. However, crystallographers, who have always been in the forefront of structural biology, also in this regard seem to be setting example of how to deal with suboptimal or irreproducible science.…”