[en] Beta-lactams exert their antibiotic action through their inhibition of bacterial DD-peptidases (penicillin-binding proteins). Bacteria, in general, carry several such enzymes localized on the outside of their cell membrane to catalyze the final step in cell wall (peptidoglycan) synthesis. They have been classified into two major groups, one of high molecular weight, the other of low. Members of the former group act as transpeptidases in vivo, and their inhibition by beta-lactams leads to cessation of bacterial growth. The latter group consists of DD-carboxypeptidases, and their inhibition by beta-lactams is generally not fatal to bacteria. We have previously shown that representatives of the former group are ineffective at catalyzing the hydrolysis/aminolysis of peptidoglycan-mimetic peptides in vitro [Anderson et al. (2003) Biochem. J. 373, 949-955]. The theme of these experiments is expanded in the present paper where we describe the synthesis of a series of beta-lactams (penicillins and cephalosporins) containing peptidoglycan-mimetic side chains and the kinetics of their inhibition of a panel of penicillin-binding proteins spanning the major classes (Escherichia coli PBP 2 and PBP 5, Streptococcus pneumoniae PBP 1b, PBP 2x and PBP 3, the Actinomadura R39 DD-peptidase, and the Streptomyces R61 DD-peptidase). The results of these experiments mirror and expand the previous results with peptides. Neither peptides nor beta-lactams with appropriate peptidoglycan-mimetic side chains react with the solubilized constructs of membrane-bound penicillin binding proteins (the first five enzymes above) at rates exceeding those of generic analogues. Such peptides and beta-lactams do react at greatly enhanced rates with certain soluble low molecular weight enzymes (R61 and R39 DD-peptidases). The former result is unexpected and interesting. Why do the majority of penicillin-binding proteins not recognize elements of local peptidoglycan structure? Possible answers are discussed. That this question needs to be asked casts fascinating shadows on current studies of penicillin-binding proteins for new drug design.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Josephine, Helen R.
Charlier, Paulette ; Université de Liège - ULiège > Département des sciences de la vie > Cristallographie des macromolécules biologiques
Davies, Christopher
Nicholas, Robert A.
Pratt, R. F.
Language :
English
Title :
Reactivity of penicillin-binding proteins with peptidoglycan-mimetic beta-lactams: what's wrong with these enzymes?
Publication date :
2006
Journal title :
Biochemistry
ISSN :
0006-2960
eISSN :
1520-4995
Publisher :
American Chemical Society, Washington, United States - District of Columbia
Faraci, W. S. (1992) Cytosolic enzymes in peptidoglycan biosynthesis as potential antibacterial targets, in Emerging Targets in Antibacterial and Antifungal Chemotherapy (Sutcliffe, J. and Georgopapadakou, N. H., Eds.) Chapter 8, Chapman and Hall, London.
Barbosa, M. D. F. S, Yang, G., Fang, J., Kurilla, M. G., and Pompliano, D. L. (2002) Development of a whole-cell assay for peptidoglycan biosynthesis inhibitors, Antimicrob. Agents Chemother. 46, 943-946.
Katz, A. H., and Caufield, C. E. (2003) Structure-based design approaches to cell wall biosynthesis inhibitors, Curr. Pharm. Des. 9, 857-866.
Tipper, D. J., and Strominger, J. L. (1965) Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-D-alanine, Proc. Natl. Acad. Sci. U.S.A. 54, 1133-1141.
Spratt, B. G., and Pardee, A. B. (1975) Penicillin-binding proteins and cell shape in E. coli, Nature 254, 516-517.
Popham, D. L., and Young, K. D. (2003) Role of penicillin-binding proteins in bacterial cell morphogenesis, Curr. Opin. Microbiol. 6, 594-599.
Hakenbeck, R., Konig, A., Kern, I., van der Linden, M., Keck, W., Billot-Klein, D., Legrand, R., Schoot, B., and Gutmann, L. (1998) Acquisition of five high-Mr penicillin-binding protein variants during the transfer of high-level β-lactam resistance from Streptococcus mitris to Streptococcus pneumoniae, J. Bacteriol. 180, 1831-1840.
Mouz, N., Gordon, E., Di Guilmi, A. M., Petit, I., Petillot, Y., Dupont, Y., Hakenbeck, R., Vernet, T., and Dideberg, O. (1998) Identfication of a structural determinant for resistance to β-lactam antibiotics in Gram-positive bacteria, Proc. Natl. Acad. Sci. U.S.A. 95, 13403-13406.
Macheboeuf, P., Di Guilmi, A. M., Job, V., Vernet, T., Dideberg, O., and Dessen, A. (2005) Active site restructuring regulates ligand recognition in class A penicillin-binding proteins, Proc. Natl. Acad. Sci. U.S.A. 102, 577-582.
Gordon, E., Mouz, N., Duée, E., and Dideberg, O. (2000) The crystal structure of the penicillin-binding protein 2x From Streptococcus pneumoniae and its acyl-enzyme form: implications in drug resistance, J. Mol. Biol. 299, 477-485.
Morlot, C., Pernot, L., LeGouellec, A., Di Giulmi, A. M., Vernet, T., Dideberg, O., and Dessen, A. (2005) Crystal structure of a peptidoglycan synthesis regulatory factor (PBP 3) from Streptococcus pneumoniae, J. Biol. Chem. 280, 15984-15991.
Nicholas, R. A., Krings, S., Tomberg, J., Nichola, G., and Davies, C. (2003) Crystal structures of wild-type penicillin-binding protein 5 from Escherichia coli, J. Biol. Chem. 278, 52826-52833.
Kelly, J. A., and Kuzin, A. P. (1995) The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 Å resolution, J. Mol. Biol. 254, 223-236.
Sauvage, E., Herman, R., Petrella, S., Duez, C., Bouillenne, F., Frère, J.-M., and Charlier, P. (2005) Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins, J. Biol. Chem. 280, 31249-31256.
Kishida, H., Unzai, S., Roper, D. I., Lloyd, A., Park, S.-Y., and Tame, J. R. H. (2006) Crystal structure of penicillin-binding protein 4 (dac B) from Escherichia coli, both in the native form and covalently linked to various antibiotics, Biochemistry 45, 783-792.
Lim, D., and Strynadka, N. C. J. (2002) Structural basis for the β-lactam resistance of PBP 2a from methicillin-resistant Staphylococcus aureus, Nat. Struct. Biol. 9, 870-876.
Sauvage, E., Kerff, F., Fonzé, E., Herman, R., Schoot, B., Marquette, J.-P., Taburet, Y., Prevost, D., Dumas, J., Leonard, J., Stephanie, P., Coyette, J., and Charlier, P. (2002) The 2.4 Å crystal structure of the penicillin-resistant penicillin-binding protein PBP 5fm from Enterococcus faecium in complex with benzylpenicillin, Cell. Mol. Life Sci. 59, 1223-1232.
Dessen, A., Mouz, N., Gordon, E., Hopkins, J., and Dideberg, O. (2001) Crystal structures of PBP 2x from a highly penicillin resistant Streptococcus pneumoniae clinical isolate, J. Biol. Chem. 48, 45106-45112.
Pratt, R. F. (2002) Functional evolution of the serine β-lactamase active site, J. Chem. Soc., Perkin Trans. 2, 851-861.
Frère, J. M., and Joris, B. (1985) Penicillin-sensitive enzymes in peptidoglycan biosynthesis, CRC Crit. Rev. Microbiol. 11, 299-396.
Ghuysen, J.-M and Dive, G. (1994) Biochemistry of the penicilloyl serine tranferases, in Bacterial Cell Wall (Ghuysen, J.-M., and Hakenbeck, R., Eds.) p 103, Elsevier Science B.V., Amsterdam.
Terrak, M., Ghosh, T. K., van Heijenoort, J., Van Beeumen, J., Lampilis, M., Aszodi, J., Ayala, J. A., Ghuysen, J.-M., and Nguyen-Distèche, M. (1999) The catalytic glycosyl transferase and acyl transferase modules of the cell wall peptidogycan-polymerizing penicillin-binding protein 1b of Escherichia coli, Mol. Microbiol. 34, 350-364.
Schwartz, B., Markwalder, J. A., and Wang, Y. (2001) Lipid II: total synthesis of the bacterial cell wall precurser and utilization as a substrate for glycosyl transfer and transpeptidation by penicillin binding protein (PBP) 1b of Escherichia coli, J. Am. Chem. Soc. 123, 11638-11643.
Bertsche, U., Breukink, E., Kast, J. and Vollmer, W. (2005) In vitro murein (peptidoglycan) synthesis by dimers of the bifunctional transglycosylase-transpeptidase PBP 1b of Escherichia coli, J. Biol. Chem. 280, 38096-38101.
Jamin, M., Damblon, C., Millier, S., Hakenbeck, R., and Frère, J.-M. (1993) Penicillin-binding protein 2x of Streptococcus pneumoniae: enzymic activities and interactions with β-lactams, Biochem. J. 292, 735-741.
Zhao, G., Yeh, W.-K., Carnahan, R. H., Flokowitsch, J., Meier, T. I., Alborn, W. E., Jr., Becker, G. W., and Jaskunas, S. R. (1997) Biochemical characterization of penicillin-resistant and -sensitive penicillin-binding protein 2x transpeptidase activities of Streptococcus pneumoniae and mechanistic implications in bacterial resistance to β-lactam antibiotics, J. Bacteriol. 179, 4901-4908.
Stefanova, M. E., Davies, C., Nicholas, R. A., and Gutheil, W. G. (2002) pH, inhibitor, and substrate specificity studies on Escherichia coli penicillin binding- protein 5, Biochem. Biophys. Acta 1597, 292-300.
Anderson, J. A., Adediran, S. A., Charlier, P., Nguyen-Distèche, M., Frère, J.-M., Nicholas, R. A. and Pratt, R. F. (2003) Biochem. J. 373, 949-955.
Hesek, D., Suvarov, M., Morio, K., Lee, M., Brown, S., Vakulenko, S. B. and Mobashery, S. (2004) J. Org. Chem. 69, 778-784.
Stevanova, M. E., Tomberg, J., Olesky, M., Höltje, J.-V., Gutheil, W. G., and Nicholas, R. A. (2003) Neisseria gonorrhoeae penicillin-binding protein 3 exhibits exceptionally high carboxypeptidase and β-lactam binding activities, Biochemistry 42, 14614-14625.
Reynolds, P. and Chase, H. (1981) β-Lactam-binding proteins: identification as lethal targets and probes of β-lactam accessibility, in β-Lactam Antibiotics Mode of action, new developments and future prospects (Salton, M. R. J. and Shockman, G. D., Eds.) pp 153-168, Academic Press, New York.
Livermore, D. M. (1987) Radiolabelling of penicillin-binding proteins (PBPs) in intact Pseudomonas aeruginosa cells: consequences of β-lactamase activity by PBP-5, J. Antimicrob. Chemother. 19, 733-742.
Anderson, J. W., and Pratt, R. F. (2000) Dipeptide binding to the extended active site of the Streptomyces R61 D-alanyl-D-alanine peptidase: the path to a specific substrate, Biochemistry 39, 12200-12209.
Rogers, H. J., Perkins, H. R. and Ward, J. B. (1980) Microbial cell walls and membranes, Chapter 6, Chapman and Hall, London.
McDonough, M. A., Anderson, J. W., Silvaggi, N. R., Pratt, R. F., Knox, J. R., and Kelly, J. A. (2002) Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins, J. Mol. Biol. 322, 111-122.
Lee, B. (1971) Conformation of penicillin as a transition state analog of the substrate of peptidoglycan transpeptidase, J. Mol. Biol. 61, 463-469.
Josephine, H. R., Kumar, I., and Pratt, R. F. (2004) The perfect penicillin? Inhibition of a bacterial DD-peptidase by peptidoglycan-mimetic β-lactams, J. Am. Chem. Soc. 126, 8122-8123.
Silvaggi, N., Josephine, H. R., Kuzin, A. P., Nagarajan, R., Pratt, R. F., and Kelly, J. A. (2005) Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic β-lactams: a non-covalent complex with a "perfect penicillin", J. Mol. Biol. 345, 521-533.
Waxman, D. J., and Strominger, J. L. (1983) Penicillin-binding proteins and the mechanism of action of β-lactam antibiotics, Annu. Rev. Biochem. 52, 825-869.
Rosowsky, A., Forsch, R., Uren, J., Wick, M., Kumar, A. A., and Freisheim, J. H. (1983) Methotrexate analogs. 20. Replacement of glutamate by longer-chain amino diacids: effects on dihydrofolate reductase inhibition, cytotoxicity, and in vivo antitumor activity, J. Med. Chem. 26, 1719-1724.
Brain, E. G., McMillan, I., Nayler, J. H. C., Southgate, R., and Tolliday, P. (1975) Chemistry of penicillanic acids. III. Route to 1, 2-secopenicillins, J. Chem. Soc., Perkin Trans. 1, 562-567.
Kline, T., Fromhold, M., McKennon, T. E., Cai, S., Treiberg, J., Ihle, N., Sherman, D., Schwan, W., Hickey, M. J., Warrener, P., Witte, P. R., Brody, L. L., Goltry, L., Barker, L. M., Anderson, S. U., Tanaka, S. K., Shawar, R. M., Nguyen, L. Y., Langhorne, M., Bigelow, A., Embuscado, L., and Naeemi, E. (2000) Antimicrobial effects of novel siderophores linked to beta-lactam antibiotics, Bioorg. Med. Chem. 8, 73-93.
Meroueh, S. O., Minasov, G., Lee, W., Shoichet, B. K., and Mobashery, S. (2003) Structural aspects for evolution of β-lactamases from penicillin binding proteins, J. Am. Chem. Soc. 125, 9612-9618.
Kuzmic, P. (1996) Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase, Anal. Biochem. 237, 260-273.
Xu, Y., Soto, G., Adachi, H., Van der Linden, M. P. G., Keck, W., and Pratt, R. F. (1994) Relative specificities of a series of β-lactam- reognizing enzymes towards the side chains of penicillins and acyclic thioldepsipeptides, Biochem. J. 302, 851-856.
Di Giulmi, A. M., Dessen, A., Dideberg, O., and Vernet, T. (2003) Functional characterization of penicillin-binding protein 1b from Streptococcus pneumoniae, J. Bacteriol. 185, 1650-1658.
Bentley, P. H., and Stachulski, A. V. (1983) Synthesis and biological activity of some fused β-lactam peptidoglycan analogs, J. Chem. Soc., Perkin Trans. 1, 1187-1191.
Hanessian, S., Couture, C. A., and Georgopapadakou, N. (1993) Probing the binding site of the penicillin side-chain based on the Tipper-Strominger hypothesis, Bioorg. Med. Chem. Lett. 3, 2323-2328.
Amanuma, H., and Strominger, J. L. (1980) Purification and properties of penicillin-binding proteins 5 and 6 from Escherichia coli membranes, J. Biol. Chem. 255, 11173-11180.
Nicholas, R. A., and Strominger, J. L. (1988) Relations between β-lactamases and penicillin-binding proteins: β-lactamase activity of penicillin-binding protein 5 from Escherichia coli, Rev. Infect. Dis. 10, 733-742.
Nagarajan, R., and Pratt, R. F. (2004) Synthesis and evaluation of new substrate analogues of Streptomyces R61 DD-peptidase: dissection of a specific ligand, J. Org. Chem. 69, 7472-7478.
Matsuhashi, M. (1994) Utilization of lipid-linked precursors and the formation of peptidoglycan in the process of cell growth and division: membrane enzymes involved in the final steps of peptidoglycan synthesis and the mechanism of their regulation, in Bacterial Cell Wall (Ghuysen, J.-M. and Hakenbeck, R., Eds.) Chapter 4, Elsevier Science B.V., Amsterdam.
Höltje, J.-V. (1998) Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli, Microbiol. Mol. Biol. Rev. 62, 181-203.
Goffin, C., and Ghuysen, J.-M. (2002) Biochemistry and comparative genomics of SxxK superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent, Microbiol. Mol. Biol. Rev. 66, 702-738.
Vollmer, W., von Rechenberg, M., and Höltje, J.-V. (1999) Demonstration of molecular interactions between the murein polymerase PBP1B, the lytic trans-glycosidase MltA, and the scaffolding protein MipA of Escherichia coli, J. Biol. Chem. 274, 6726-6734.
Bertsche, U., Kast, T., Wolf, B., Fraipont, C., Aarsman, M. E. G., Kannenberg, K., von Rechenberg, M., Nguyen-Distèche, M., den Blaauwen, T., Höltje, J.-V., and Vollmer, W. (2006) Interaction between two murein (peptidoglycan) synthases, PBP3 and PBP1b, in Escherichia coli, Mol. Microbiol. 61, 675-690.
Ishino, F., Park, W., Tomioka, S., Tomaki, S., Takase, I., Kunugita, K., Matzusawa, H., Asoh, S., Ohta, T., Spratt, B. G., and Matsuhashi, M. (1986) Peptidoglycan synthetic activities in membranes of Escherichia coli caused by overproduction of penicillin-binding protein 2 and rodA protein, J. Biol. Chem. 261, 7024-7031.
Matzusawa, H., Asoh, S., Kunai, K., Muraiso, K., Takasuga, A., and Ohta, T. (1989) Nucleotide sequence of the rodA gene, responsible for the rod shape of Escherichia coli: rodA and the pbpA gene, encoding penicillin-binding protein 2, constitute the rodA operon, J. Bacteriol. 171, 558-560.
Nicholas, R. A., Lamson, D. R., and Schultz, D. E. (1993) Penicillin-binding protein 1B from Escherichia coli contains a membrane association site in addition to its transmembrane anchor, J. Biol. Chem. 268, 5632-5641.
Di Giulmi, A. M., Dessen, A., Dideberg, O., and Vernet, T. (2002) Bifunctional penicillin-binding proteins: focus on the glycosyltransferase domain and its specific inhibitor moenomycin, Curr. Pharm. Biotechnol. 3, 63-75.
Korat, B., Mottl, H., and Keck, W. (1991) Penicillin-binding protein 4 of Escherichia coli: molecular cloning of the dac B gene, controlled overexpression, and alterations in murein composition, Mol. Microbiol. 5, 675-684.
Granier, B., Duez, C., Lepage, S., Englebert, S., Dusart, J., Dideberg, O., Van Beeumen, J., Frère, J.-M., and Ghuysen, J.-M. (1992) Primary and predicted secondary structures of the Actinomadura R39 extracellular DD-peptidase, a penicillin-binding protein related to the Escherichia coli PBP 4, Biochem. J. 282, 781-788.
Stubbs, M., and Bode, W. (1994) Crystal structures of thrombin and thrombin complexes as a framework for antithrombotic drug design, Perspect. Drug Discovery Des. 1, 431-452.
Breidenbach, M. A., and Brunger, A. T. (2004) Substrate recognition strategy for botulinum neurotoxin serotype A, Nature 432, 925-929.
Fuda, C., Hesek, D., Lee, M., Morio, K., Nowak, T., and Mobashery, S. (2005) Activation for catalysis of penicillin-binding protein 2a from methicillin-resistant Staphylococcus aureus by bacterial cell wall, J. Am. Chem. Soc. 127, 2056-2057.
Kumar, I., and Pratt, R. F. (2005) Transpeptidation reactions of a specific substrate catalyzed by the Streptomyces R61 DD-peptidase: The structural basis of acyl acceptor specificity, Biochemistry 44, 9961-9970.
Frère, J.-M., Nguyen-Distèche, M., Coyette, J., and Joris, B. (1992) Mode of action: interaction with the penicillin-binding proteins. In The Chemistry of β-Lactams (Page, M. I., Ed.) Chapter 5, Chapman and Hall, London.
