Structure-Activity Relationship of 6-Methylidene Penems Bearing 6,5 Bicyclic Heterocycles as Broad-Spectrum β-Lactamase Inhibitors:  Evidence for 1,4-Thiazepine Intermediates with C7 R Stereochemistry by Computational Methods

Venkatesan, Aranapakam M.; Agarwal, Atul; Abé, Takao; Ushirogochi, Hideki; Yamamura, Itsuka; Ado, Mihira; Tsuyoshi, Takasaki; Santos, Osvaldo Dos; Gu, Yansong; Sum, Fuk‐Wah; Li, Zhong; Francisco, Gerry; Lin, Yang‐I; Petersen, Peter J.; Yang, Youjun; Kumagai, Toshio; Weiss, Jason; Shlaes, David M.; Knox, James R.; Mansour, Tarek S.

doi:10.1021/jm060021p

Cited by 38 publications

(29 citation statements)

References 32 publications

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“…The bicyclic heterocycles are synthesized as 6-methylidene penems attached to thiophene, imidazole, and pyrazole rings (428). Extension of the second heterocyclic ring yields the tricyclic derivatives, which show improved stability in solution and increased lipophilicity in in vivo studies (429).…”

Section: Brl 42715 Derivativesmentioning

confidence: 99%

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Three Decades of β-Lactamase Inhibitors

Drawz¹,

2010

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SUMMARYSince the introduction of penicillin, β-lactam antibiotics have been the antimicrobial agents of choice. Unfortunately, the efficacy of these life-saving antibiotics is significantly threatened by bacterial β-lactamases. β-Lactamases are now responsible for resistance to penicillins, extended-spectrum cephalosporins, monobactams, and carbapenems. In order to overcome β-lactamase-mediated resistance, β-lactamase inhibitors (clavulanate, sulbactam, and tazobactam) were introduced into clinical practice. These inhibitors greatly enhance the efficacy of their partner β-lactams (amoxicillin, ampicillin, piperacillin, and ticarcillin) in the treatment of seriousEnterobacteriaceaeand penicillin-resistant staphylococcal infections. However, selective pressure from excess antibiotic use accelerated the emergence of resistance to β-lactam-β-lactamase inhibitor combinations. Furthermore, the prevalence of clinically relevant β-lactamases from other classes that are resistant to inhibition is rapidly increasing. There is an urgent need for effective inhibitors that can restore the activity of β-lactams. Here, we review the catalytic mechanisms of each β-lactamase class. We then discuss approaches for circumventing β-lactamase-mediated resistance, including properties and characteristics of mechanism-based inactivators. We next highlight the mechanisms of action and salient clinical and microbiological features of β-lactamase inhibitors. We also emphasize their therapeutic applications. We close by focusing on novel compounds and the chemical features of these agents that may contribute to a “second generation” of inhibitors. The goal for the next 3 decades will be to design inhibitors that will be effective for more than a single class of β-lactamases.

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Section: Brl 42715 Derivativesmentioning

confidence: 99%

“…Extension of the second heterocyclic ring yields the tricyclic derivatives, which show improved stability in solution and increased lipophilicity in in vivo studies (429). As a group, these compounds have proven to be potent inhibitors of class A, C, and D ␤-lactamases (25,156,335,428,441).…”

Section: Brl 42715 Derivativesmentioning

confidence: 99%

Three Decades of β-Lactamase Inhibitors

Drawz¹,

2010

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“…1). These penems demonstrate similar levels of in vivo efficacy in mice and have been shown to be effective inhibitors of several class A, C, and D ␤-lactamases (4,43,(46)(47)(48)52).…”

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confidence: 92%

Inhibitor Resistance in the KPC-2 β-Lactamase, a Preeminent Property of This Class A β-Lactamase

Papp-Wallace

Bethel

Distler

et al. 2010

Antimicrob Agents Chemother

171

190

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As resistance determinants, KPC ␤-lactamases demonstrate a wide substrate spectrum that includes carbapenems, oxyimino-cephalosporins, and cephamycins. In addition, clinical strains harboring KPC-type ␤-lactamases are often identified as resistant to standard ␤-lactam-␤-lactamase inhibitor combinations in susceptibility testing. The KPC-2 carbapenemase presents a significant clinical challenge, as the mechanistic bases for KPC-2-associated phenotypes remain elusive. Here, we demonstrate resistance by KPC-2 to ␤-lactamase inhibitors by determining that clavulanic acid, sulbactam, and tazobactam are hydrolyzed by KPC-2 with partition ratios (k cat /k inact ratios, where k inact is the rate constant of enzyme inactivation) of 2,500, 1,000, and 500, respectively. Methylidene penems that contain an We also demonstrate that penems 1 and 2 are mechanism-based inactivators, having partition ratios (k cat /k inact ratios) of 250 and 50, respectively. To understand the mechanism of inhibition by these penems, we generated molecular representations of both inhibitors in the active site of KPC-2. These models (i) suggest that penem 1 and penem 2 interact differently with active site residues, with the carbonyl of penem 2 being positioned outside the oxyanion hole and in a less favorable position for hydrolysis than that of penem 1, and (ii) support the kinetic observations that penem 2 is the better inhibitor (k inact /K m ‫؍‬ 6.5 ؎ 0.6 M ؊1 s ؊1 ). We conclude that KPC-2 is unique among class A ␤-lactamases in being able to readily hydrolyze clavulanic acid, sulbactam, and tazobactam. In contrast, penem-type ␤-lactamase inhibitors, by exhibiting unique active site chemistry, may serve as an important scaffold for future development and offer an attractive alternative to our current ␤-lactamase inhibitors.In Klebsiella pneumoniae, ␤-lactam resistance is mediated predominantly by class A SHV, TEM, and CTX-M ␤-lactamases (7, 35). Single amino acid substitutions in the SHV and TEM ␤-lactamases can drastically alter the substrate profiles of the enzymes and confer resistance to extended-spectrum cephalosporins and ␤-lactamase inhibitors (5,12,34,36). ␤-Lactamases with altered substrate profiles (i.e., extended-spectrum or inhibitor-resistant ␤-lactamases) have significantly challenged the clinician's approach to the treatment of serious infectious diseases (36). Thus, the search for effective mechanism-based inhibitors of novel ␤-lactamases merits significant effort (8,9,32).First identified in K. pneumoniae, KPC class A ␤-lactamases threaten the use of all current ␤-lactam antibiotics (57). These ␤-lactamase enzymes are present in an increasing number of bacterial genera, becoming the major carbapenemase expressed by Gram-negative pathogens (e.g., Enterobacter spp., Escherichia coli, Citrobacter freundii, Pseudomonas spp., Serratia marcescens, Proteus mirabilis, and Salmonella enterica) in the United States (3,10,11,16,17,25,37,45,49,53,59). Moreover, KPC ␤-lactamases are becoming geographically widespread (having been detecte...

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“…Previously, structures and models of tricyclic and bicyclic penem inhibitors have suggested that formation of the 7-membered thiazepine ring leads to an SHV-1 acyl enzyme complex in which there is a favorable interaction between the C6 aromatic side chain and the Y105 residue in SHV (29,32,44). Models of the acyl enzyme complex of penem-2 with both WT SHV and the Y105 variants were prepared (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Only in the meropenem-bound SHV is residue Y105 rotated by approximately 90 degrees toward the entrance of the active site (33). Limited crystal structure data and molecular models of penem inhibitors have indicated that the Y105 in SHV provided van der Waals interactions that stabilized the acyl enzyme complex (29,44).…”

Section: Discussionmentioning

confidence: 99%

Substitutions at Position 105 in SHV Family β-Lactamases Decrease Catalytic Efficiency and Cause Inhibitor Resistance

Conklin

Taracila

et al. 2012

Antimicrob Agents Chemother

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Ambler position 105 in class A ␤-lactamases is implicated in resistance to clavulanic acid, although no clinical isolates with mutations at this site have been reported. We hypothesized that Y105 is important in resistance to clavulanic acid because changes in positioning of the inhibitor for ring oxygen protonation could occur. In addition, resistance to bicyclic 6-methylidene penems, which are interesting structural probes that inhibit all classes of serine ␤-lactamases with nanomolar affinity, might emerge with substitutions at position 105, especially with nonaromatic substitutions. All 19 variants of SHV-1 with variations at position 105 were prepared. Antimicrobial susceptibility testing showed that Escherichia coli DH10B expressing Y105 variants retained activity against ampicillin, except for the Y105L variant, which was susceptible to all ␤-lactams, similar to the case for the host control strain. Several variants had elevated MICs to ampicillin-clavulanate. However, all the variants remained susceptible to piperacillin in combination with a penem inhibitor (MIC, <2/4 mg/liter). The Y105E, -F, -M, and -R variants demonstrated reduced catalytic efficiency toward ampicillin compared to the wild-type (WT) enzyme, which was caused by increased K m . Clavulanic acid and penem K i values were also increased for some of the variants, especially Y105E. Mutagenesis at position 105 in SHV yields mutants resistant to clavulanate with reduced catalytic efficiency for ampicillin and nitrocefin, similar to the case for the class A carbapenemase KPC-2. Our modeling analyses suggest that resistance is due to oxyanion hole distortion. Susceptibility to a penem inhibitor is retained although affinity is decreased, especially for the Y105E variant. Residue 105 is important to consider when designing new inhibitors.

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Structure-Activity Relationship of 6-Methylidene Penems Bearing 6,5 Bicyclic Heterocycles as Broad-Spectrum β-Lactamase Inhibitors: Evidence for 1,4-Thiazepine Intermediates with C7 R Stereochemistry by Computational Methods

Cited by 38 publications

References 32 publications

Three Decades of β-Lactamase Inhibitors

Three Decades of β-Lactamase Inhibitors

Inhibitor Resistance in the KPC-2 β-Lactamase, a Preeminent Property of This Class A β-Lactamase

Substitutions at Position 105 in SHV Family β-Lactamases Decrease Catalytic Efficiency and Cause Inhibitor Resistance

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