Structure-based design of beta-lactamase inhibitors. 1. Synthesis and evaluation of bridged monobactams.

Bridged monobactams are novel, potent, mechanism-based inhibitors of class C beta-lactamases, designed using X-ray crystal structures of the enzymes. They stabilize the acyl-enzyme intermediate by blocking access of water to the enzyme-inhibitor ester bond. Bridged monobactams are selective class C beta-lactamase inhibitors, with half-inhibition constants as low as 10 nM, and are less effective against class A and class B enzymes (half-inhibition constants > 100 microM) because of the different hydrolysis mechanisms in these classes of beta-lactamases. The stability of the acyl-enzyme complexes formed with class C beta-lactamases (half-lives up to 2 days were observed) enabled determination of their crystal structures. The conformation of the inhibitor moiety was close to that predicted by molecular modeling, confirming a simple reaction mechanism, unlike those of known beta-lactamase inhibitors such as clavulanic acid and penam sulfones, which involve secondary rearrangements. Synergy between the bridged monobactams and beta-lactamase-labile antibiotics could be observed when such combinations were tested against strains of Enterobacteriaceae that produce large amounts of class C beta-lactamases. The minimal inhibitory concentration of the antibiotic of more than 64 mg/L could be decreased to 0.25 mg/L in a 1:4 combination with the inhibitor.

Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis.

Beta-Lactamases (EC 3.5.2.6, 'penicillinases') are a family of enzymes that protect bacteria against the lethal effects of cell-wall synthesis of penicillins, cephalosporins and related antibiotic agents, by hydrolysing the beta-lactam antibiotics to biologically inactive compounds. Their production can, therefore, greatly contribute to the clinical problem of antibiotic resistance. Three classes of beta-lactamases--A, B and C--have been identified on the basis of their amino-acid sequence; class B beta-lactamases are metalloenzymes, and are clearly distinct from members of class A and C beta-lactamases, which both contain an active-site serine residue involved in the formation of an acyl enzyme with beta-lactam substrates during catalysis. It has been predicted that class C beta-lactamases share common structural features with D,D-carboxypeptidases and class A beta-lactamases, and further, suggested that class A and class C beta-lactamases have the same evolutionary origin as other beta-lactam target enzymes. We report here the refined three-dimensional structure of the class C beta-lactamase from Citrobacter freundii at 2.0-A resolution and confirm the predicted structural similarity. The refined structure of the acyl-enzyme formed with the monobactam inhibitor aztreonam at 2.5-A resolution defines the enzyme's active site and, along with molecular modelling, indicates a mechanism for beta-lactam hydrolysis. This leads to the hypothesis that Tyr 150 functions as a general base during catalysis.

Biochemical characterization of type A and type B beta-lactamase from Enterobacter cloacae.

Different types of chromosomally coded beta-lactamases are found in Enterobacter cloacae. E. cloacae M6300 produces beta-lactamase type A, which has an isoelectric point of 8.8, whereas E. cloacae 908 R produces beta-lactamase type B, which has an isoelectric point of 7.9. Both enzymes were purified to homogeneity by a procedure that included affinity chromatography on amino phenylboronic acid-modified Sepharose. The two enzymes were closely related as shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, kinetic constants with several substrates, amino acid composition, NH2-terminal amino acid sequence, and reaction with antisera. In addition to having different isoelectric points, the two enzymes migrated to slightly different positions on polyacrylamide gels and differed significantly in rate of catalysis for cephalothin, imipenem, and the penem Sch 34343. One of three antisera seemed to recognize an epitope that differs in the two enzymes. The diversity of cephalosporinases found in E. cloacae with respect to the evolution of novel beta-lactamases was considered.

Mechanism of inhibition of chromosomal beta-lactamases by third-generation cephalosporins.

The kinetic interactions of the beta-lactamase from Enterobacter cloacae 908 R with ceftriaxone, cefotaxime, and ceftazidime have been examined in detail. With all of these cephalosporins, there is an initial rapid reaction involving opening of the beta-lactam that then decreases to a slower steady-state rate (kss) of beta-lactam hydrolysis (at 37 degrees C: ceftriaxone, kss = 0.044 s-1; cefotaxime, kss = 0.033 s-1; ceftazidime, kss = 0.011 s-1). More than stoichiometric quantities of beta-lactam are cleaved during the rapid phase, during which there is accumulation of a transiently stable cephalosporin-enzyme complex whose rate of breakdown is slower than the overall rate of hydrolysis. Qualitatively similar behavior is observed with the E. cloacae M6300 beta-lactamase. These observations eliminate the possibility that the reaction follows a simple linear kinetic scheme. A branched kinetic scheme in which an initially formed acyl intermediate partitions between deacylation and elimination of the 3' substituent is proposed to explain the data. Investigations of the interaction of ceftriaxone with the chromosomally encoded beta-lactamases from Citrobacter freundii, Providencia rettgeri, Morganella morganii, Pseudomonas aeruginosa, and Escherichia coli show that the partitioning behavior of E. cloacae beta-lactamases is atypical. All of the data, however, clearly demonstrate that it is a physical impossibility for cephalosporin trapping to contribute to bacterial resistance phenotypes.

Poly(deoxyadenylic-deoxythymidylic acid) damage by radiolytically activated neocarzinostatin.

The anaerobic reaction of poly(deoxyadenylic-deoxythymidylic acid) with neocarzinostatin activated by the carboxyl radical CO2-, an electron donor generated from gamma-ray radiolysis of nitrous oxide saturated formate buffer, has been characterized. DNA damage includes base release and strand breaks. Few strand breaks are formed prior to alkaline treatment; they bear 3'-phosphoryl termini. In contrast, most (66%) of the base release occurs spontaneously. DNA damage is highly (95%) specific for thymidine sites. Neither DNA-drug covalent adduct nor nucleoside 5'-aldehyde, which are major products in the DNA-nicking reaction initiated by mercaptans and oxygen, is formed in this reaction. Data are presented to show that the CO2(-)-activated neocarzinostatin intermediate is a short-lived free radical able to abstract hydrogen atoms from the C-1' and C-5' positions of deoxyribose. Attack occurs mostly (68%) at the C-1' position, producing a lesion whose properties are consistent with those of (oxidized) apyrimidinic sites.

Neocarzinostatin abstracts a hydrogen during formation of nucleotide 5'-aldehyde on DNA.

The oxidative reaction of polydeoxyadenylic-deoxythymidylic acid [poly(dA-dT)] with neocarzinostatin that produces 5'-thymidine aldehyde esterified to the 5'-end of strand breaks proceeds with hydrogen abstraction. The abstracted hydrogen is covalently bound to the non-protein component of neocarzinostatin; only a small amount (5%) is washed out into solvent. These data rule out a peroxyl radical as the primary DNA damaging species involved in the production of the 5'-aldehyde group. In contrast to earlier reports, it is demonstrated that alpha-tocopherol is not an inhibitor of the reaction.

Inactivation of the RTEM beta-lactamase from Escherichia coli. Interaction of penam sulfones with enzyme.

The characteristics of the reaction of a number of mechanism-based inactivators of the RTEM beta-lactamase have suggested that a common mechanistic pathway may be followed by many of these compounds. These ideas have been tested by the synthesis and evaluation of some penam sulfones as beta-lactamase inactivators. The sulfones of poor beta-lactamase substrates are, as predicted, potent inactivators of the enzyme. A unique serin residue (Ser-70) is labeled by quinacillin sulfone, and it is likely that this serine acts nucleophilically in the normal hydrolytic reaction of the beta-lactamase to form an acyl-enzyme intermediate.

Inhibition of the RTEM beta-lactamase from Escherichia coli. Interaction of enzyme with derivatives of olivanic acid.

The interaction of the RTEM beta-lactamase with two derivatives of olivanic acid has been studied. The compound MM22382 (1) behaves simply as a good substrate for the enzyme and is a relatively ineffective inhibitor. In contrast, the sulfate ester MM13902 (2) is a poor substrate and an excellent inhibitor of the enzyme. The inhibition derives from a branching of the normal hydrolytic pathway of the enzyme. At long times, all the catalytic activity of the enzyme returns. Free sulfate ion is not produced during the interaction with the enzyme, which rules out a mechanistic pathway involving beta elimination between C-6 and C-8. The validity of a number of alternative schemes is assessed.

Inactivation of RTEM beta-lactamase from Escherichia coli by clavulanic acid and 9-deoxyclavulanic acid.

The interaction of the TEM-2 beta-lactamase with 9-deoxyclavulanic acid (3) and with both extensively labeled (2) and specifically labeled (1) clavulanic acid has been studied. The close similarity between 9-doexyclavulanate and clavulanate in kinetics, spectroscopic, and protein chemical terms show that the allyl alcohol group of clavulanate is irrelevant to its action as a beta-lactamase inactivator. Use of the radiolabeled samples of clavulanate shows that, of three irreversibly inactivated forms of the enzymes, two contain the whole clavulanate skeleton and the third only retains the carbon atoms of the original beta-lactam ring. These findings allow the complex interaction between clavulanic acid and the beta-lactamase to be defined more narrowly in chemical terms.

Beta-lactamase inactivation by mechanism-based reagents.

The mechanistic pathway followed by the E. coli RTEM beta-lactamase has been studied with a view to clarifying the mode of action of a number of recently discovered inactivators of the enzyme. There is clear evidence that the beta-lactamase-catalysed hydrolysis of the 7-alpha-methoxycephem, cefoxitin, proceeds via an acyl-enzyme intermediate. An analysis of the inactivation reactions of all the known beta-lactam derivatives that result in irreversible loss of enzyme activity permits the identification of three structural features required for a beta-lactamase inactivator. The application of these principles suggests a new group of mechanism-based inactivators of the enzyme: the sulphones of N-acyl derivatives of 6-beta-aminopenicillanic acid that are themselves poor substrates for the enzyme. These sulphones are powerful inactivators of the beta-lactamase.

Kinetic studies on the inactivation of Escherichia coli RTEM beta-lactamase by clavulanic acid.

The kinetic details of the irreversible inactivation of the Escherichia coli RTEM beta-lactamase by clavulanic acid have been elucidated. Clavulanate is destroyed by the enzyme and simultaneously inhibits it by producing two catalytically inactive forms. One of these is transiently stable and decomposes to free enzyme (k = 3.8 X 10(-3) S-1), while the other corresponds to an irreversibly inactivated form. The transient complex is formed from the Michaelis complex at a rate (k approximately 3 X 10(-2) S-1) which is some threefold faster than the rate of formation of the irreversibly inactivated complex. The transient complex is, therefore, the principle enzyme form present after short time periods. In the presence of excess clavulanate, however, all the enzyme accumulates into the irreversibly inactivated form. The number of clavulanate turnovers that occur prior to complete enzyme inactivation is 115.

Chemical studies on the inactivation of Escherichia coli RTEM beta-lactamase by clavulanic acid.

Incubation of clavulanic acid with the beta-lactamase from Escherichia coli RTEM leads to enzyme-catalyzed depletion of clavulanic acid, to transient inhibition, and to irreversible inactivation of the enzyme. Both the transiently inhibited and the irreversibly inactivated species show a marked increase in the absorbance at 281 nm that is proportional to the decrease in enzyme activity. Hydroxylamine treatment of irreversibly inactivated enzyme restores about one-third of the catalytic activity, with a concomitant decrease in absorbance at 281 nm. Polyacrylamide isoelectric focusing of the irreversibly inactivated enzyme shows three bands of approximately equal intensity, different from native enzyme. Upon hydroxylamine treatment, one of the three bands disappears and now focuses identically with native enzyme. It is evident that the irreversible inactivation of enzyme by an excess of clavulanic acid generates three products, one of which can be reactivated by hydroxylamine.