Beta-Lactamases and DD-Peptidases: Active Site Chemistry

Summary

Principal Investigator: REX PRATT
Abstract: Project Summary Bacterial resistance to l3-lactam antibiotics continues to become more prevalent and more clinically important. A large part of the resistance can be understood and investigated experimentally in terms of the chemistry of the interactions of R-lactam antibiotics with the active sites of two groups of bacterial enzymes, the Illactamases on one hand, which catalyze the hydrolysis of the antibiotics, and the D-alanyl-D-alanine transpeptidase/carboxypeptidases on the other, which catalyze the synthesis and maintenance of the peptide cross-links of bacterial cell walls, and which are inhibited by 13-lactam antibiotics. There is now good reason to believe that all of these l-lactam binding sites have much in common. An understanding of the structure and function of these sites and of the relationship between them is fundamental to future antibiotics design - both 1-lactam and otherwise. The object of the proposed research is to explore further the chemical functionality and the substrate binding properties of a series of these active sites, using a number of modified substrates, novel inhibitors and potential effedtors. Particular focus will be on the development of novel inhibitors of the (1lactamases and the extension of these inhibitors to DD-peptidases. The specificity of the DD-peptidases for peptidoglycan structural motifs will be examined closely. Crystal structures will be used in conjunction with molecular modeling to interpret the results obtained and apply them to further inhibitor design. In silico and in vitro screening methods will also be used with the OD-peptidases to obtain new lead compounds. These studies will lead to new insight into the chemistry of R-lactamase and transpeptidase active sites, and thus to new directions in antibiotic design. E Gyp 0-. ... G'O --a tail ... 'Fn "-'a'- .N. >.t (Nn Nn. om' m' "L" O-- Oil 0.0)-7-.o 9,' -_p >'7 ='L
Funding Period: ----------------1982 - ---------------2011-
more information: NIH RePORT

Top Publications

  1. pmc Deacylation transition states of a bacterial DD-peptidase
    S A Adediran
    Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
    Biochemistry 45:13074-82. 2006
  2. pmc Crystal structures of covalent complexes of β-lactam antibiotics with Escherichia coli penicillin-binding protein 5: toward an understanding of antibiotic specificity
    George Nicola
    Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
    Biochemistry 49:8094-104. 2010
  3. pmc Kinetics and stereochemistry of hydrolysis of an N-(phenylacetyl)-α-hydroxyglycine ester catalyzed by serine β-lactamases and DD-peptidases
    Ryan B Pelto
    Department of Chemistry, Wesleyan University, Lawn Ave, Middletown, CT 06459, USA
    Org Biomol Chem 10:7356-62. 2012
  4. pmc Kinetics and mechanism of inhibition of a serine beta-lactamase by O-aryloxycarbonyl hydroxamates
    Ryan B Pelto
    Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
    Biochemistry 47:12037-46. 2008
  5. pmc Reactions of peptidoglycan-mimetic beta-lactams with penicillin-binding proteins in vivo and in membranes
    Ish Kumar
    ACS Chem Biol 2:620-4. 2007
  6. pmc Inhibition of chymotrypsin by a complex of ortho-vanadate and benzohydroxamic acid: structure of the inert complex and its mechanistic interpretation
    Aaron Moulin
    Rosenstiel Basic Medical Sciences Research Center, Program in Biochemistry, and Program in Biophysics, Brandeis University, Waltham, Massachusetts 02454, USA
    Biochemistry 46:5982-90. 2007
  7. pmc Approaches to the simultaneous inactivation of metallo- and serine-beta-lactamases
    Sudhakar Reddy Ganta
    Department of Chemistry, Southern Methodist University, Dallas TX 75275 0314, United States
    Bioorg Med Chem Lett 19:1618-22. 2009
  8. pmc Intramolecular cooperativity in the reaction of diacyl phosphates with serine beta-lactamases
    Sudipta Majumdar
    Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, USA
    Biochemistry 48:8293-8. 2009
  9. pmc Structural basis of the inhibition of class A beta-lactamases and penicillin-binding proteins by 6-beta-iodopenicillanate
    Eric Sauvage
    Centre d Ingénierie des Protéines and Centre de Recherches du Cyclotron, Universite de Liege, B 4000 Sart Tilman, Belgium
    J Am Chem Soc 131:15262-9. 2009
  10. pmc Serendipitous discovery of α-hydroxyalkyl esters as β-lactamase substrates
    Ryan B Pelto
    Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
    Biochemistry 49:10496-506. 2010

Scientific Experts

  • E Sauvage
  • R F Pratt
  • Ryan B Pelto
  • George Nicola
  • Sudhakar Reddy Ganta
  • Sudipta Majumdar
  • Aaron Moulin
  • Ish Kumar
  • S A Adediran
  • Joshua Tomberg
  • Robert A Nicholas
  • Christopher Davies
  • James Spencer
  • Orjan Samuelsen
  • John D Buynak
  • Sundar Ram Reddy Pagadala
  • Senthil Perumal
  • Jason H Bell
  • Dagmar Ringe
  • Helen R Josephine
  • I Kumar

Detail Information

Publications11

  1. pmc Deacylation transition states of a bacterial DD-peptidase
    S A Adediran
    Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
    Biochemistry 45:13074-82. 2006
    ..The structural and mechanistic bases of these observations are discussed; they should inform transition state analogue design...
  2. pmc Crystal structures of covalent complexes of β-lactam antibiotics with Escherichia coli penicillin-binding protein 5: toward an understanding of antibiotic specificity
    George Nicola
    Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
    Biochemistry 49:8094-104. 2010
    ..Because the ring nitrogen occupies a similar position in all three complexes, this supports the hypothesis that deacylation is blocked by the continued presence of the leaving group after opening of the β-lactam ring...
  3. pmc Kinetics and stereochemistry of hydrolysis of an N-(phenylacetyl)-α-hydroxyglycine ester catalyzed by serine β-lactamases and DD-peptidases
    Ryan B Pelto
    Department of Chemistry, Wesleyan University, Lawn Ave, Middletown, CT 06459, USA
    Org Biomol Chem 10:7356-62. 2012
    ..Both α-hydroxy and α-amido substituents on a glycine ester substrate can therefore enhance its productive interaction with the β-lactamase active site, although their effects are not additive; this may also be true for inhibitors...
  4. pmc Kinetics and mechanism of inhibition of a serine beta-lactamase by O-aryloxycarbonyl hydroxamates
    Ryan B Pelto
    Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA
    Biochemistry 47:12037-46. 2008
    ..Such an alternative mode of reaction may lead to the design of novel inhibitors...
  5. pmc Reactions of peptidoglycan-mimetic beta-lactams with penicillin-binding proteins in vivo and in membranes
    Ish Kumar
    ACS Chem Biol 2:620-4. 2007
    ..This suggests that in vivo, as in vitro, these enzymes do not specifically recognize elements of peptidoglycan structure local to the reaction center. Substrate recognition must thus involve extended structure...
  6. pmc Inhibition of chymotrypsin by a complex of ortho-vanadate and benzohydroxamic acid: structure of the inert complex and its mechanistic interpretation
    Aaron Moulin
    Rosenstiel Basic Medical Sciences Research Center, Program in Biochemistry, and Program in Biophysics, Brandeis University, Waltham, Massachusetts 02454, USA
    Biochemistry 46:5982-90. 2007
    ..The entire complex can be seen as a reasonable mimic of a phosphyl transfer transition state where the leaving group is extended into the S1 site...
  7. pmc Approaches to the simultaneous inactivation of metallo- and serine-beta-lactamases
    Sudhakar Reddy Ganta
    Department of Chemistry, Southern Methodist University, Dallas TX 75275 0314, United States
    Bioorg Med Chem Lett 19:1618-22. 2009
    ..The substitution of the amide N-H bond by N-OH may represent a useful strategy for the inhibition of other serine hydrolases...
  8. pmc Intramolecular cooperativity in the reaction of diacyl phosphates with serine beta-lactamases
    Sudipta Majumdar
    Department of Chemistry, Wesleyan University, Lawn Avenue, Middletown, Connecticut 06459, USA
    Biochemistry 48:8293-8. 2009
    ..Such cooperativity brings fresh opportunities and challenges to the search for novel beta-lactamase inhibitors...
  9. pmc Structural basis of the inhibition of class A beta-lactamases and penicillin-binding proteins by 6-beta-iodopenicillanate
    Eric Sauvage
    Centre d Ingénierie des Protéines and Centre de Recherches du Cyclotron, Universite de Liege, B 4000 Sart Tilman, Belgium
    J Am Chem Soc 131:15262-9. 2009
    ..The BS3 structure reveals a new mode of carboxylate interaction with a class A beta-lactamase active site that should be of interest in future inhibitor design...
  10. pmc Serendipitous discovery of α-hydroxyalkyl esters as β-lactamase substrates
    Ryan B Pelto
    Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
    Biochemistry 49:10496-506. 2010
    ..Molecular modeling was employed to explore how the α-hydroxy group might interact with the class C β-lactamase active site. Incorporation of the α-hydroxyalkyl moiety into novel inhibitors will be of considerable interest...