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Updated: Mar 28, 2026
Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
Published on: October 2, 2017
Crystal Structures of KPC-2 and SHV-1 β-Lactamases in Complex with the Boronic Acid Transition State Analog S02030
Nhu Q Nguyen1, Nikhil P Krishnan1, Laura J Rojas2
1Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, USA.
Abstract:
Resistance to expanded-spectrum cephalosporins and carbapenems has rendered certain strains of Klebsiella pneumoniae the most problematic pathogens infecting patients in the hospital and community. This broad-spectrum resistance to β-lactamases emerges in part via the expression of KPC-2 and SHV-1 β-lactamases and variants thereof. KPC-2 carbapenemase is particularly worrisome, as the genetic determinant encoding this β-lactamase is rapidly spread via plasmids. Moreover, KPC-2, a class A enzyme, is difficult to inhibit with mechanism-based inactivators (e.g., clavulanate). In order to develop new β-lactamase inhibitors (BLIs) to add to the limited available armamentarium that can inhibit KPC-2, we have structurally probed the boronic acid transition state analog S02030 for its inhibition of KPC-2 and SHV-1. S02030 contains a boronic acid, a thiophene, and a carboxyl triazole moiety. We present here the 1.54- and 1.87-Å resolution crystal structures of S02030 bound to SHV-1 and KPC-2 β-lactamases, respectively, as well as a comparative analysis of the S02030 binding modes, including a previously determined S02030 class C ADC-7 β-lactamase complex. S02030 is able to inhibit vastly different serine β-lactamases by interacting with the conserved features of these active sites, which includes (i) forming the bond with catalytic serine via the boron atom, (ii) positioning one of the boronic acid oxygens in the oxyanion hole, and (iii) utilizing its amide moiety to make conserved interactions across the width of the active site. In addition, S02030 is able to overcome more distantly located structural differences between the β-lactamases. This unique feature is achieved by repositioning the more polar carboxyl-triazole moiety, generated by click chemistry, to create polar interactions as well as reorient the more hydrophobic thiophene moiety. The former is aided by the unusual polar nature of the triazole ring, allowing it to potentially form a unique C-H…O 2.9-Å hydrogen bond with S130 in KPC-2.
Insights
This study reveals how the novel inhibitor S02030 effectively targets KPC-2 and SHV-1 beta-lactamases, crucial for combating antibiotic resistance. Its unique binding mechanism offers a promising strategy against problematic Klebsiella pneumoniae infections.
Area of Science:
- Structural Biology
- Medicinal Chemistry
- Antimicrobial Resistance
Background:
- Klebsiella pneumoniae strains exhibiting resistance to expanded-spectrum cephalosporins and carbapenems are major hospital-acquired and community pathogens.
- This resistance is often mediated by beta-lactamases, including KPC-2 and SHV-1, with KPC-2 being particularly concerning due to its rapid plasmid-mediated spread.
- Existing inhibitors like clavulanate are often ineffective against KPC-2.
Purpose of the Study:
- To structurally characterize the inhibition of KPC-2 and SHV-1 beta-lactamases by the boronic acid transition state analog S02030.
- To develop novel beta-lactamase inhibitors (BLIs) to combat resistance in Klebsiella pneumoniae.
- To understand the binding mode of S02030 across different classes of serine beta-lactamases.
Main Methods:
- Determined crystal structures of S02030 bound to SHV-1 and KPC-2 beta-lactamases at 1.54 Å and 1.87 Å resolution, respectively.
- Performed comparative analysis of S02030 binding modes, including a previously determined complex with ADC-7 beta-lactamase.
- Utilized click chemistry to generate the carboxyl-triazole moiety of S02030.
Main Results:
- S02030 effectively inhibits diverse serine beta-lactamases by engaging conserved active site features: boron atom bonding to catalytic serine, oxyanion hole interaction, and conserved amide moiety interactions.
- The inhibitor accommodates structural variations between beta-lactamases by repositioning its thiophene and carboxyl-triazole moieties.
- A unique C-H…O hydrogen bond between the triazole ring and S130 in KPC-2 was observed, contributing to binding affinity.
Conclusions:
- S02030 demonstrates broad-spectrum inhibition of serine beta-lactamases, including KPC-2 and SHV-1, by exploiting conserved active site features and adapting to structural differences.
- The inhibitor's design, incorporating a boronic acid, thiophene, and carboxyl triazole, provides a promising scaffold for developing new antibiotics against drug-resistant bacteria.
- Structural insights into S02030 binding pave the way for rational design of next-generation beta-lactamase inhibitors.
