Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance

Abstract

β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis. Although nucleophilic serine-β-lactamases have long been clinically important, most broad-spectrum β-lactamases employ one or two metal ions (likely Zn2+) in catalysis. To date, potent and clinically useful inhibitors of these metallo-β-lactamases (MBLs) have not been available, exacerbating their negative impact on healthcare. MBLs are categorised into three subgroups: B1, B2, and B3 MBLs, depending on their sequence similarities, active site structures, interactions with metal ions, and substrate preferences. The majority of MBLs associated with the spread of antibiotic resistance belong to the B1 subgroup. Most characterized B3 MBLs have been discovered in environmental bacteria, but they are increasingly identified in clinical samples. B3-type MBLs display greater diversity in their active sites than other MBLs. Furthermore, at least one of the known B3-type MBLs is inhibited by the serine-β-lactamase inhibitor clavulanic acid, an observation that may promote the design of derivatives active against a broader range of MBLs. In this Mini Review, recent advances in structure-function relationships of B3-type MBLs will be discussed, with a view to inspiring inhibitor development to combat the growing spread of β-lactam resistance.

Novel Metallo-β-Lactamase blaCVI-1 Isolated from a Chromobaterium violaceum Clinical Strain Resistant to Colistin

“…Our analysis confirmed the presence of key conserved residues, including Glu69, Gly84, and Asn220, which are essential for the catalytic activity of these enzymes. Additionally, the presence of one Zn2+ binding site (Asn116, His118, and His196) was identified, consistent with previous reports [ 7 ]. Notably, instead of the typical cysteine residue (Cys221), a lysine residue was found at that position.…”

“…Notably, instead of the typical cysteine residue (Cys221), a lysine residue was found at that position. B2 metalloenzymes are characterized by their NHH/DCH active site motif, corresponding to the Zn1 and Zn2 sites, respectively; however, only one zinc ion, in the Zn 2 site, is required for catalysis [ 7 ]. Consequently, CVI-1 still exhibited carbapenem hydrolysis capacity, although further studies are needed to fully understand its enzymatic activity.…”

“…This finding highlights the evolutionary lineage of CVI-1 within the diversity of metallo-β-lactamases. Previous studies found that Subclass B1 + B2 share an evolutionary origin distinct from that of the B3 subclass, although the β -lactam-hydrolysing function evolved independently within each group [ 7 , 18 ]. The identification and characterization of bla CVI-1 as a subclass B2 metallo-β-lactamase in C. violaceum contribute to our understanding of the genetic mechanisms underlying β-lactam resistance in this pathogen.…”

“…Additionally, the genome revealed the presence of various β-lactamase precursors, including a probable B2 class metallo-β-lactamase [ 5 ]. B2-type metallo-β-lactamases exhibit a phylogenetic relationship with the B1 subclass enzymes, which include enzymes such as NDM-1, IMP-1, and VIM-2 [ 7 ]. However, B2 enzymes are distinct in their high degree of substrate selectivity within the metallo-β-lactamase group, specifically demonstrating effective inactivation of carbapenems [ 7 ].…”

“…B2-type metallo-β-lactamases exhibit a phylogenetic relationship with the B1 subclass enzymes, which include enzymes such as NDM-1, IMP-1, and VIM-2 [ 7 ]. However, B2 enzymes are distinct in their high degree of substrate selectivity within the metallo-β-lactamase group, specifically demonstrating effective inactivation of carbapenems [ 7 ]. In addition, the B2-enzymes constitute the smallest Class B subgroup, of which the best-known member is CphA.…”