Biochemistry
Article
(3) Wyrembak, P. M., Babaoglu, K., Pelto, R. B., Shoichet, B. K., and
Pratt, R. F. (2007) O-Aryloxycarbonyl hydroxamates: New β-
lactamase inhibitors that cross-link the active site. J. Am. Chem. Soc.
129, 9548−9549.
β-lactamase of Enterobacter cloacae GC1, a natural mutant with a
tandem tripeptide insertion. Biochemistry 38, 10256−10261.
(22) Curley, K., and Pratt, R. F. (1997) Effectiveness of tetrahedral
adducts as transition-state analogs and inhibitors of the class C β-
lactamase of Enterobacter cloacae P99. J. Am. Chem. Soc. 119, 1529−
1538.
(23) Bernstein, N. J., and Pratt, R. (1999) On the importance of a
methyl group in β-lactamase evolution: Free energy profiles and
molecular modeling. Biochemistry 38, 10499−10510.
(24) 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.
(25) Pratt, R. F. (1992) On the definition and classification of
mechanism-based enzyme inhibitors. Bioorg. Med. Chem. Lett. 2, 1323−
1326.
(26) Pazhanisamy, S., Govardhan, C. P., and Pratt, R. F. (1989) β-
Lactamase-catalyzed aminolysis of depsipeptides; amine specificity and
steady state kinetics. Biochemistry 28, 6863−6870.
(27) Crichlow, G. V., Nukaga, M., Doppalapudi, V. R., Buynak, J. D.,
and Knox, J. R. (2001) Inhibition of class C β-lactamases; structure of
a reaction intermediate with a cefem sulfone. Biochemistry 40, 6233−
6239.
(28) Tilvawala, R. (2014) Design of hydroxamic acid-based inhibitors
for serine β-lactamases. PhD thesis, Wesleyan University, Ch 3.
(29) Woon, E. C. Y., Zervosen, A., Sauvage, E., Simmons, K. J., Zivec,
M., Inglis, S. R., Fishwick, C. W. G., Gobec, S., Charlier, P., Luxen, A.,
and Schofield, C. J. (2011) Structure guided development of potent
reversibly binding penicillin binding protein inhibitors. ACS Med.
Chem. Lett. 2, 219−223.
(30) Powers, R. A., Caselli, E., Focia, P. J., Prati, F., and Shoichet, B.
K. (2001) Structures of ceftazidime and its transition-state analogue in
complex with AmpC β-lactamase: Implications for resistance
mutations and inhibitor design. Biochemistry 40, 9207−9214.
(31) Nukaga, M., Kumar, S., Nukaga, K., Pratt, R. F., and Knox, J. R.
(2004) Hydrolysis of third generation cephalosporins by class C β-
lactamases. Structure of a transition state analog of cefotaxime in wild-
type and extended spectrum enzymes. J. Biol. Chem. 279, 9344−9352.
(32) Tondi, D., Morandi, M., Bonnet, R., Costi, M. P., and Shoichet,
B. K. (2005) Structure-based optimization of a non-β-lactam lead
results in inhibitors that do not up-regulate β-lactamase expression in
cell culture. J. Am. Chem. Soc. 127, 4632−4639.
(4) Pelto, R. B., and Pratt, R. F. (2008) Kinetics and mechanisms of
inhibition of serine β-lactamases by O-aryloxycarbonyl hydroxamates.
Biochemistry 47, 12037−12046.
(5) Ghuysen, J.-M. (1991) Serine β-lactamases and penicillin-binding
proteins. Annu. Rev. Microbiol. 45, 37−67.
(6) Sauvage, E., Kerff, F., Terrak, M., Ayala, J. A., and Charlier, P.
(2008) The penicillin-binding proteins: Structure and role in
peptidoglycan biosynthesis. FEMS Microbiol. Rev. 32, 234−258.
(7) Pratt, R. F. (2002) Functional evolution of the serine β-lactamase
active site. J. Chem. Soc. Perkin Trans. 2, 851−861.
(8) Crompton, I. E., Cuthbert, B. K., Lowe, G., and Waley, S. G.
(1988) β-Lactamase inhibitors. The inhibition of serine β-lactamases
by specific boronic acids. Biochem. J. 251, 453−459.
(9) Zervosen, A., Bouillez, A., Herman, A., Amoroso, A., Joris, B.,
Sauvage, E., Charlier, P., and Luxen, A. (2012) Synthesis and
evaluation of boronic acids as inhibitors of penicillin binding proteins
of classes A, B and C. Bioorg. Med. Chem. 20, 3915−3924.
(10) 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.
(11) 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.
(12) Anderson, J. W., Adediran, S. A., Charlier, P., Nguyen-Distec
̀
he,
M., Frere, J.-M., Nicholas, R. A., and Pratt, R. F. (2003) On the
̀
substrate specificity of bacterial DD-peptidases: Evidence from two
series of peptidoglycan-mimetic peptides. Biochem. J. 373, 949−955.
(13) Josephine, H. R., Charlier, P., Davies, C., Nicholas, R. A., and
Pratt, R. F. (2006) Reactivity of penicillin-binding proteins with
peptidoglycan-mimetic β-lactams: What’s wrong with these enzymes?
Biochemistry 45, 15873−15883.
(14) Dzhekieva, L., Rocaboy, M., Kerff, F., Charlier, P., Sauvage, E.,
and Pratt, R. F. (2010) Crystal structure of a complex between the
Actinomadura R39 DD-peptidase and a peptidoglycan-mimetic
boronate inhibitor: Interpretation of a transition state analogue in
terms of catalytic mechanism. Biochemistry 49, 6411−6419.
(15) Kuzmic, P. (1996) Program DYNAFIT for the analysis of
enzyme kinetic data: Application to HIV proteinase. Anal. Biochem.
237, 260−272.
(16) Tilvawala, R., and Pratt, R. F. (2013) Covalent inhibition of
serine β-lactamases by novel hydroxamic and acid derivatives.
Biochemistry 52, 3712−3720.
(17) Adediran, S. A., Cabaret, D., Flavell, R. R., Sammons, J. A.,
Wakselman, M., and Pratt, R. F. (2006) Synthesis and β-lactamase
reactivity of α-substituted phenaceturates. Bioorg. Med. Chem. 14,
7023−7033.
(33) Eidam, D., Romagnoli, C., Dalmasso, G., Barelier, S., Caselli, E.,
Bonnet, R., Shoichet, B. K., and Prati, F. (2012) Fragment-guided
design of subnanomolar β-lactamase inhibitors active in vivo. Proc.
Natl. Acad. Sci. U. S. A. 109, 17448−17453.
(34) Caselli, E., Powers, R. A., Blasczcak, L. C., Wu, C. Y. E., Prati, F.,
and Shoichet, B. K. (2001) Energetic, structural, and antimicrobial
analyses of β-lactam side chain recognition by β-lactamases. Chem.
Biol. 8, 17−32.
(35) Xu, Y., Soto, G., Hirsch, K. R., and Pratt, R. F. (1996) Kinetics
and mechanism of hydrolysis of depsipeptides by the β-lactamase of
Enterobacter cloacae P99. Biochemistry 35, 3595−3603.
(18) 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: mecha-
nistic interpretation of a β-lactamase transition state analog.
Biochemistry 33, 6762−6772.
(19) Kumar, S., Adediran, S. A., Nukaga, M., and Pratt, R. F. (2004)
Kinetics of turnover of cefotaxime by the Enterobacter cloacae P99 and
GC1 β-lactamases: Two free enzyme forms of the P99 β-lactamase
detected by a combination of pre- and post-steady state kinetics.
Biochemistry 43, 2664−2672.
(20) Beadle, B. M., Trehan, I., Focia, P. J., and Shoichet, B. K. (2002)
Structural milestones in the reaction pathway of an amide hydrolase:
substrate, acyl, and product complexes of cephalothin with Amp C β-
lactamase. Structure 10, 413−424.
(21) Crichlow, G. V., Kuzin, A. P., Nukaga, M., Mayama, K., Sawai,
T., and Knox, J. R. (1999) Structure of the extended-spectrum class C
7384
Biochemistry 2015, 54, 7375−7384