Inhibition of Klebsiella β-Lactamases (SHV-1 and KPC-2) by Avibactam: A Structural Study.
β-Lactamase inhibition is an important clinical strategy in overcoming β-lactamase-mediated resistance to β-lactam antibiotics in Gram negative bacteria. A new β-lactamase inhibitor, avibactam, is entering the clinical arena and promising to be a major step forward in our antibiotic armamentarium. Avibactam has remarkable broad-spectrum activity in being able to inhibit classes A, C, and some class D β-lactamases. We present here structural investigations into class A β-lactamase inhibition by avibactam as we report the crystal structures of SHV-1, the chromosomal penicillinase of Klebsiella pneumoniae, and KPC-2, an acquired carbapenemase found in the same pathogen, complexed with avibactam. The 1.80 Å KPC-2 and 1.42 Å resolution SHV-1 β-lactamase avibactam complex structures reveal avibactam covalently bonded to the catalytic S70 residue. Analysis of the interactions and chair-shaped conformation of avibactam bound to the active sites of KPC-2 and SHV-1 provides structural insights into recently laboratory-generated amino acid substitutions that result in resistance to avibactam in KPC-2 and SHV-1. Furthermore, we observed several important differences in the interactions with amino acid residues, in particular that avibactam forms hydrogen bonds to S130 in KPC-2 but not in SHV-1, that can possibly explain some of the different kinetic constants of inhibition. Our observations provide a possible reason for the ability of KPC-2 β-lactamase to slowly desulfate avibactam with a potential role for the stereochemistry around the N1 atom of avibactam and/or the presence of an active site water molecule that could aid in avibactam desulfation, an unexpected consequence of novel inhibition chemistry.
Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America.
Nikhil P
NP
Krishnan
Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America.
Nhu Q
NQ
Nguyen
Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH, 44106, United States of America.
Krisztina M
KM
Papp-Wallace
Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America; Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH, 44106, United States of America; Department of Medicine, Case Western Reserve University, Cleveland, OH, United States of America; Department of Pharmacology, Case Western Reserve University, Cleveland, OH, United States of America; Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, United States of America.
Robert A
RA
Bonomo
Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, United States of America.
Focco
F
van den Akker
D019943:Amino Acid Substitution; D000900:Anti-Bacterial Agents / Q000737:chemistry* / Q000494:pharmacology; D053961:Azabicyclo Compounds / Q000737:chemistry* / Q000494:pharmacology; D020134:Catalytic Domain; D002876:Chromosomes, Bacterial / Q000737:chemistry; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D007700:Kinetics; D007711:Klebsiella pneumoniae / Q000737:chemistry / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics; D008024:Ligands; D008826:Microbial Sensitivity Tests; D008958:Models, Molecular; D011485:Protein Binding; D013237:Stereoisomerism; D014867:Water / Q000737:chemistry; D018440:beta-Lactam Resistance / Q000235:genetics; D001618:beta-Lactamases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
D000900:Anti-Bacterial Agents; D053961:Azabicyclo Compounds; D008024:Ligands; D014867:Water; C543519:avibactam; C491478:beta-lactamase KPC-2; C054882:beta-lactamase PIT-2; D001618:beta-Lactamases