Matthew Kalp

Inhibition of OXA-1 β-Lactamase by Penems

ABSTRACT The partnering of a β-lactam with a β-lactamase inhibitor is a highly effective strategy that can be used to combat bacterial resistance to β-lactam antibiotics mediated by serine β-lactamases (EC 3.2.5.6). To this end, we tested two novel penem inhibitors against OXA-1, a class D β-lactamase that is resistant to inactivation by tazobactam. The Ki of each penem inhibitor for OXA-1 was in the nM range (Ki of penem 1, 45 ± 8 nM; Ki of penem 2, 12 ± 2 nM). The first-order rate constant for enzyme and inhibitor complex inactivation of penems 1 and 2 for OXA-1 β-lactamase were 0.13 ± 0.01 s−1 and 0.11 ± 0.01 s−1, respectively. By using an inhibitor-to-enzyme ratio of 1:1, 100% inactivation was achieved in ≤900 s and the recovery of OXA-1 β-lactamase activity was not detected at 24 h. Covalent adducts of penems 1 and 2 (changes in molecular masses, +306 ± 3 and +321 ± 3 Da, respectively) were identified by electrospray ionization mass spectrometry (ESI-MS). After tryptic digestion of OXA-1 inactivated by penems 1 and 2, ESI-MS and matrix-assisted laser desorption ionization-time-of-flight MS identified the adducts of 306 ± 3 and 321 ± 3 Da attached to the peptide containing the active-site Ser67. The base hydrolysis of penem 2, monitored by serial 1H nuclear magnetic resonance analysis, suggested that penem 2 formed a linear imine species that underwent 7-endo-trig cyclization to ultimately form a cyclic enamine, the 1,4-thiazepine derivative. Susceptibility testing demonstrated that the penem inhibitors at 4 mg/liter effectively restored susceptibility to piperacillin. Penem β-lactamase inhibitors which demonstrate high affinities and which form long-lived acyl intermediates may prove to be extremely useful against the broad range of inhibitor-resistant serine β-lactamases present in gram-negative bacteria.

Efficient inhibition of class A and class D β-lactamases by Michaelis complexes

A 6-alkylidiene penam sulfone, SA-1-204, is an efficient inhibitor of both SHV-1 and OXA-1 β-lactamases with KI = 42 ± 4nm and 1.0 ± 0.1 μm, respectively. To gain insight into the reaction chemistry of SA-1-204, the reactions between this inhibitor and SHV-1 and OXA-1 were studied by Raman spectroscopy in single crystals and in solution. Raman signatures characteristic of the unreacted β-lactam ring show that in both phases the inhibitor binds as a noncovalent Michaelis-like complex. This complex is present as the major population for periods of up to an hour. On longer time scales, the Raman data show that β-lactam ring opening eventually leads to a complex mixture of reaction products. However, the data clearly demonstrate that the key species for inhibition on the time scale of bacterial half-lives is the noncovalent complex preceding acylation.

Carbapenems and SHV-1 β-Lactamase Form Different Acyl-Enzyme Populations in Crystals and Solution

The reactions between single crystals of the SHV-1 beta-lactamase enzyme and the carbapenems, meropenem, imipenem, and ertapenem, have been studied by Raman microscopy. Aided by quantum mechanical calculations, major populations of two acyl-enzyme species, a labile Delta (2)-pyrroline and a more tightly bound Delta (1)-pyrroline, have been identified for all three compounds. These isomers differ only in the position of the double bond about the carbapenem nucleus. This discovery is consonant with X-ray crystallographic findings that also identified two populations for meropenem bound in SHV-1: one with the acyl CO group in the oxyanion hole and the second with the acyl group rotated 180 degrees compared to its expected position [Nukaga, M., Bethel, C. R., Thomson, J. M., Hujer, A. M., Distler, A. M., Anderson, V. E., Knox, J. R., and Bonomo, R. A. (2008) J. Am. Chem. Soc. (in press)]. When crystals of the Delta (1)- and Delta (2)-containing acyl-enzymes were exposed to solutions with no carbapenem, rapid deacylation of the Delta (2) species was observed by kinetic Raman experiments. However, no change in the Delta (1) population was observed over 1 h, the effective lifetime of the crystal. These observations lead to the hypothesis that the stable Delta (1) species is due to the form seen by X-ray with the acyl carbonyl outside the oxyanion hole, while the Delta (2) species corresponds to the form with the carbonyl inside the oxyanion hole. Soak-in and soak-out Raman experiments also demonstrated that tautomeric exchange between the Delta (1) and Delta (2) forms does not occur on the crystalline enzyme. When meropenem or ertapenem was reacted with SHV-1 in solution, the Raman difference spectra demonstrated that only a major population corresponding to the Delta (1) acyl-enzyme could be detected. The 1003 cm (-1) mode of the phenyl ring positioned on the C3 side chain of ertapenem acts as an effective internal Raman intensity standard, and the ratio of its intensity to that of the 1600 cm (-1) feature of Delta (1) provides an estimate of the relative populations of Delta (1). In solution, I 1600/ I 1003 equals 2, and in the crystal, I 1600 /I 1003 equals 1. This is strong evidence that the Delta (1) and Delta (2) acyl-enzymes in the crystal are present in approximately equal amounts, in agreement with the X-ray data. However, in solution there are twice as many Delta (1) species per Phe group, and this represents approximately 100% of the active sites, which is consistent with the observed inhibition of the enzymes activity.

Role of E166 in the imine to enamine tautomerization of the clinical β-lactamase inhibitor sulbactam

Mechanism-based inhibitors of class A beta-lactamases, such as sulbactam, undergo a complex series of chemical reactions in the enzyme active site. Formation of a trans-enamine acyl-enzyme via a hydrolysis-prone imine is responsible for transient inhibition of the enzyme. Although the imine to enamine tautomerization is crucial to inhibition of the enzyme, there are no experimental data to suggest how this chemical transformation is catalyzed in the active site. In this report, we show that E166 acts as a general base to promote the imine to enamine tautomerization.

β-Lactamase Inhibition: Mechanistic Details and Novel Inhibitors

Bacteria that are resistant to β-lactam antibiotics by producing β-lactamases are a significant public health threat. These β-lactamases hydrolyze β-lactams and render them inactive. To combat these resistant strains, β-lactams are often administered with β-lactamase inhibitors. Unfortunately, β-lactamases are beginning to acquire mutations which confer resistance to these inhibitors as well. Therefore, a clear need exists to identify novel inhibitors to ensure continued antibiotic efficacy.We used a synergistic X-ray and Raman crystallographic approach to investigate the mechanisms of inhibitor binding and to further the development of new inhibitors of the β-lactamase SHV-1. To this end, we first engineered an acylation deficient mutant to capture the pre-acylation complex of β-lactamase and inhibitor. Our 1.45 A structure, as well Raman measurements, reveals an unreacted sulbactam species in the active site of the mutant SHV enzyme and represents the first pre-acylation structure between inhibitor and β-lactamase. The structure identifies key interactions that are made immediately before acylation.The second project involves a series of derivative compounds designed to improve upon the novel C2 penam sulfone inhibitor, SA2-13, which forms a stabilized trans-enamine conformation in the active site. Structures of the derivative compounds suggest that the C2 chain length is important in SA2-13 stabilization. Exploring a series of C2 derivatives by X-ray and Raman spectroscopy permitted deeper insight into more favorable inhibitor conformations.Understanding the interactions which occur in the steps immediately prior to and during covalent complex formation will allow for design of better β-lactamase inhibitors against these important drug targets. Using Raman and protein crystallography allow us to track and trap reaction intermediates inside protein crystals.