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The inactivation of bacterial DD-peptidase by β-sultams

Llinas, Antonio, Ahmed, Naveed, Cordaro, Massimiliano, Laws, Andrew P., Frere, Jean-Marie, Delmarcelle, Michael, Silvaggi, Nicholas R., Kelly, Judith A. and Page, Michael I. (2005) The inactivation of bacterial DD-peptidase by β-sultams. Biochemistry, 44 (21). pp. 7738-7746. ISSN 1520-4995

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N-Acyl--sultams are time-dependent, irreversible active site-directed inhibitors of Streptomyces R61 DD-peptidase. The rate of inactivation is first order with respect to -sultam concentration, and the second-order rate constants show a dependence on pH similar to that for the hydrolysis of a substrate. Inactivation is due to the formation of a stable 1:1 enzyme-inhibitor complex as a result of the active site serine being sulfonylated by the -sultam as shown by ESI-MS analysis and by X-ray crystallography. A striking feature of the sulfonyl enzyme is that the inhibitor is not bound to the oxyanion hole but interacts extensively with the "roof" of the active site where the Arg 285 is located

Item Type: Article
Additional Information: Copyright © 2005 American Chemical Society
Subjects: Q Science > Q Science (General)
Q Science > QD Chemistry
Schools: School of Applied Sciences
School of Applied Sciences > Biomolecular Sciences Research Centre
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References: 1. Spratt, B. G. (1975) Distinct penicillin binding proteins involved in the division elongation and shape of Escherichia coli K12, Proc. Natl. Acad. Sci. U.S.A. 72, 2999-3003. 2. Koch, A. L. (2000) Penicillin binding proteins, â-lactams, and lactamases: offensives attacks, and defensive countermeasures, Crit. ReV. Microbiol. 26, 205-220. 3. Ghuysen, J. M. (1991) Serine beta-lactamases and penicillinbinding proteins, Annu. ReV. Microbiol. 45, 37-67. 4. 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. 5. Tipper, D. J., and Strominger, J. L. (1965) Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl-alanine, Proc. Natl. Acad. Sci. U.S.A. 54, 1133- 1141. 6. Kelly, J. A., Dideberg, O., Charlier, P., Wery, J.-P., Libert, M., Moews, P. C., Knox J. R., Duez, C., Fraipont, C., Joris, B., Dusart, J., Fre`re, J.-M., and Ghuysen, J.-M. (1986) On the origin of bacterial resistance to penicillin: comparison of a â-lactamase and a penicillin target, Science 231, 1429-1431. 7. Massova, I., and Mobashery, S. (1999) Structural and mechanistic aspects of evolution of beta-lactamases and penicillin-binding proteins, Curr. Pharm. Des. 5, 929-937. 8. 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. 9. Fre`re, J.-M., and Joris, B. (1985) Penicillin-sensitive enzymes in peptidoglycan biosynthesis, CRC Crit. ReV. Microbiol. 11, 299- 396. 10. Kelly, J. A., Knox, J. R., Moews, P. C., Hite, G. J., Bartolone, J. B., Zhao, H., Joris B., Fre`re, J.-M., and Ghuysen, J.-M. (1985) 2.8Å Structure of penicillin-sensitive D-alanylcarboxypeptidasetranspeptidase from Streptomyces R61 and complexes with â-lactams, J. Biol. Chem. 260, 6449-6458. 11. Jamin, M., Adam, M., Damblon, C., Christiaens, L., and Fre`re, J.-M. (1991) Accumulation of acyl-enzyme in DD-peptidasecatalysed reactions with analogues of peptide substrates, Biochem. J. 280, 499-506. 12. Kiener, P. A., and Waley, S. G. (1978) Reversible inhibitors of penicillinases, Biochem. J. 169, 197-204; Beesley, T., Gascoyne, N., Knott-Hunziker, V., Petursson, S., Waley, S. G., Jaurin, B., and Grunstrom, T. (1983) The inhibition of class C beta-lactamases by boronic acids, Biochem. J. 209, 229-233; Crompton, I. E., Cuthbert, B. K., Lowe, G., and Waley, S. G. (1988) Beta-lactamase inhibitors. The inhibition of serine beta-lactamases by specific boronic acids, Biochem. J. 251, 453-459; Ness, S., Martin, R., Kindler, A. M., Paetzel, M., Gold, M., Jensen, S. E., Jones, J. B., and Strynadka, N. C. (2000) Structure-based design guides the improved efficacy of deacylation transition state analogue inhibitors of TEM-1 beta-Lactamase, Biochemistry 39, 5312-5321; Powers, R. A., Blazquez, J., Weston, G. S., Morosini, M. I., Baquero, F., and Shoichet, B. K. (1999) The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase, Protein Sci. 8, 2330-2337. 13. Pratt, R. F. (1989) Inhibition of a class C â-lactamase by a specific phosphonate monoester, Science 246, 917-919; Rahil, J., and Pratt, R. F. (1991) Phosphonate monoester inhibitors of class A beta-lactamases, Biochem. J. 275, 793-795; Rahil, J., and Pratt, R. F. (1992) Mechanism of inhibition of the class C beta-lactamase of Enterobacter cloacae P99 by phosphonate monoesters, Biochemistry 31, 5869-5878; Rahil, J., and Pratt, R. F. (1993) Structure-activity relationships in the inhibition of serine betalactamases by phosphonic acid derivatives, Biochem. J. 296, 389- 393; Lobkovsky, E., Billings, E. M., Moews, P. C., Rahil, J., Pratt, R. F., and Knox, J. R. (1994) Crystallographic structure of a phosphonate derivative of the Enterobacter cloacae P99 cephalosporinase: mechanistic interpretation of a beta-lactamase transition- state analog, Biochemistry 33, 6762-6772; Rahil, J., and Pratt, R. F. (1994) Characterization of covalently bound enzyme inhibitors as transition-state analogs by protein stability measurements: phosphonate monoester inhibitors of a beta-lactamase, Biochemistry 33, 116-125; Kaur, K., Lan, M. J., and Pratt, R. F. (2001) Mechanism of inhibition of the class C beta-lactamase of Enterobacter cloacae P99 by cyclic acyl phosph(on)ates: rescue by return, J. Am. Chem. Soc. 123, 10436-10443; Kaur, K., Adediran, S. A., Lan, M. J.,and Pratt, R. F. (2003) Inhibition of beta-lactamases by monocyclic acyl phosph(on)ates, Biochemistry 42, 1529-1536; Nagarajan, R., and Pratt, R. F. (2004) Thermodynamic evaluation of a covalently bonded transition state analogue inhibitor: inhibition of â-lactamases by phosphonates, Biochemistry 43, 9664-9673. 14. Baxter, N. J., Laws, A. P., Rigoreau, L., and Page, M. I. (1996) The hydrolytic reactivity of â-sultams, J. Chem. Soc., Perkin Trans. 2, 2245-2246. 15. Beardsell, M., Hinchliffe, P. S., Wood, J. M., Wilmouth, R. C., Schofield, C. J., and Page, M. I. (2001) â-SultamssA novel class of serine protease inhibitors, Chem. Commun., 497-498. 16. Hinchliffe, P. S., Wood, J. M., Davis, A. M., Austin, R. P., Beckett, R. P., and Page, M. I. (2003) Structure-reactivity relationships in the inactivation of elastase by â-sultams, Org. Biomol. Chem. 1, 67-80. 17. Lee, W., McDonough, M. A., Kotra, L., Li, Z. H., Silvaggi, N. R., Takeda, Y., Kelly, J. A., and Mobashery, S. (2001) A 1.2Å snapshot of the final step of bacterial cell wall biosynthesis, Proc. Natl. Acad. Sci. U.S.A. 98, 1427-1431. 18. Silvaggi, N. R., Anderson, J. W., Brinsmade, S. R., Pratt, R. F., and Kelly, J. A. (2003) Crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analog of a tetrahedral transition state, Biochemistry 42, 1199-1208. 19. Silvaggi, N. R., Kaur, K., Adediran, S. A., Pratt, R. F., and Kelly J. A. (2004) Toward better antibiotics: crystallographic studies of a novel class of DD-peptidase/beta-lactamase inhibitors, Biochemistry 43, 7046-7053. 20. Kuzin, A. P., Liu, H., Kelly, J. A., and Knox, J. R. (1995) Binding of cephalothin and cefotaxime to D-ala-D-ala peptidase reveals a functional basis of a natural mutation in a low-affinity penicillinbinding protein and in extended-spectrum â-lactamases, Biochemistry 34, 9532-9540. 21. Fre`re, J.-M., Leyh-Bouille, M., Ghuysen, J.-M., Nieto, M., and Perkins, H. R. (1976) Extracellular DD-carboxypeptidasestranspeptidases from Streptomyces, Methods Enzymol. 45, 610- 636. 22. Champseix, A., Chanet-Ray, J., Ettienne, A., Le Berre, A., Masson, J., Napierale, C., and Vessiere, R. (1985) Synthe`ses de â-sultames (thiaze´tidines-1,2 dioxyde-1,1), Bull. Soc. Chim. Fr. 3, 463-472. 23. Dean, J. A., Ed. (1973) Lange’s Handbook of Chemistry, 11 ed., pp 5-7, McGraw-Hill, New York. 24. Kelly, J. A., Knox, J. R., Zhao, H., Fre`re, J.-M., and Ghuysen, J.-M. (1989) Crystallographic mapping of â-lactams bound to a D-alanyl-D-alanine peptidase target enzyme, J. Mol. Biol. 209, 281-295. 25. Otwinowski, Z., and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. 276, 307-326. 26. Bru¨nger, A. T., Adams, P. D., Clove, G. M., Delano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D54, 905-921. 27. Sheldrick, G. M., and Schneider, T. R. (1997) SHELXL: highresolution refinement, Methods Enzymol. 277, 319-343. 28. McRee, D. E. (1999) XtalView/XfitsA versatile program for manipulating atomic coordinates and electron density, J. Struct. Biol. 125, 156-165. 29. Moews, P. C., Knox, J. R., Dideberg, O., Charlier, P., and Fre`re, J.-M. (1990) The structure of the â-lactamase of Bacillus licheniformis 749/C at 2.0Å resolution, Proteins: Struct., Funct., Genet. 7, 156-171. 30. Massova, I., and Mobashery, S. (1998) Kinship and diversification of bacterial penicillin-binding proteins and â-lactamases, Antimicrob. Agents Chemother. 42, 1-17. 31. Varetto, L., Fre`re, J.-M., Nguyen-Disteche, M., Ghuysen, J.-M., and Houssier, C. (1987) The pH dependence of the active-site serine DD-peptidase of Streptomyces R61, Eur. J. Biochem. 162, 525-531. 32. Fisher, J. F., Meroueh, S. O., and Mobashery, S. (2005) Bacterial resistance to â-lactam antibiotics: compelling opportunism, compelling opportunity, Chem. ReV. 105, 395-424. 33. 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. Inactivation of Peptidase by â-Sultams Biochemistry, Vol. 44, No. 21, 2005 7745 34. Fahrney, D. E., and Gold, A. M. (1963) Sulfonyl fluorides as inhibitors of esterases. I. Rates of reaction with acetylcholinesterase, R-chymotrypsin and trypsin, J. Am. Chem. Soc. 85, 997- 1000; Turini, P., Kurooka, S., Steer, M., Corbascio, A. M., and Singer, T. P. (1967) The action of phenylmethysulfonyl fluoride on human acetylcholinesterase, chymotrypsin and trypsin, J. Pharm. Exp. Ther. 167, 98-104; Lawrence, J. B. (1972) Urea denaturation of active-site spin-labeled R-chymotrypsin, Biochemistry 11, 2921-2924; Lawrence, J. B., and Shan, S. W. (1974) Spin-labeled sulfonyl fluorides as active site probes of protease structure. I. Comparison of the active site environments in R-chymotrypsin and trypsin, J. Biol. Chem. 249, 1668-1677; Hideaki, T., Hiroyasu, N., and Lawrence, J. B. (1984) Synthesis and evaluation of 19-F labelled sulfonyl fluorides as probes of protease structure: R-chymotrypsin, Biochem. J. 96, 349-355. 35. Gold, A. M., and Fahrney, D. (1964) Sulfonyl fluorides as inhibitors of esterases. II. Formation and Reactions of phenylmethanesulfonyl alpha-chymotrypsin, Biochemistry 3, 783-791. 36. Page, M. I., and Williams, A. (1997) in Organic and Bio-organic Mechanisms, pp 52-80, Longmans, Harlow. 37. Baxter, N. J., Laws, A., Rigoreau, L. J. M., and Page, M. I. (2000) Reactivity and mechanism in the hydrolysis of â-sultams, J. Am. Chem. Soc. 122, 3375-3385. 38. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950; Fenn, T. D., Ringe, D., and Petsko, G. A. (2003) J. Appl. Crystallogr. 36, 944-947. BI050110O
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Date Deposited: 08 Feb 2008 10:57
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