51
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Affiliation(s)
- David D Boehr
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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52
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Wang C, Guo H. Inhibitor Binding by Metallo-β-lactamase IMP-1 from Pseudomonas aeruginosa: Quantum Mechanical/Molecular Mechanical Simulations. J Phys Chem B 2007; 111:9986-92. [PMID: 17663582 DOI: 10.1021/jp073864g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics of the IMP-1 enzyme complexed with three prototypical inhibitors are investigated using a quantum mechanical/molecular mechanical (QM/MM) method based on the self-consistent-charge density-functional tight-binding model. The binding patterns of the inhibitors observed in X-ray diffraction experiments are well reproduced in 600 ps molecular dynamics simulations at room temperature. These inhibitors anchor themselves in the enzyme active site by direct coordination with the two zinc ions, displacing the hydroxide nucleophile that bridges the two zinc ions. In addition, they also interact with several active-site residues and those in two mobile loops. The excellent agreement with experimental structural data validates the QM/MM treatment used in our simulations.
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Affiliation(s)
- Canhui Wang
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA
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53
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Oelschlaeger P, Pleiss J. Hydroxyl Groups in the ββ Sandwich of Metallo-β-lactamases Favor Enzyme Activity: Tyr218 and Ser262 Pull Down the Lid. J Mol Biol 2007; 366:316-29. [PMID: 17157873 DOI: 10.1016/j.jmb.2006.11.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Revised: 11/01/2006] [Accepted: 11/07/2006] [Indexed: 10/23/2022]
Abstract
Metallo-beta-lactamases (MBLs) efficiently hydrolyze and thereby inactivate various beta-lactam antibiotics in clinical use. Their potential to evolve into more efficient enzymes threatens public health. Recently, we have identified the designed F218Y mutant of IMP-1 as an enzyme with superior catalytic efficiency compared to the wild-type. Thus, it may be found in clinical isolates in the future. In an effort to elucidate the molecular mechanisms involved in enhanced activity, we carried out molecular dynamics simulations of ten MBL variants in complex with a cefotaxime intermediate. The stability of these near-transition state enzyme-substrate intermediate complexes was modeled and compared to the experimental catalytic efficiencies k(cat)/K(M). For each of the ten complexes ten independent simulations were performed. In each simulation the temperature was gradually increased and determined upon breakdown of the complex. Rankings based on the experimental catalytic efficiencies and the data from computer simulations were in good agreement. From trajectory analysis of stable simulations, the combination of Tyr218 and Ser262 was found to lead to an altered hydrogen bonding network, which translates into a closing down movement of a beta-hairpin loop covering the active site. These observations may explain the significantly decreased K(M) and increased k(cat)/K(M) values of this variant toward all substrates recently tested in experiment. Previously, we have discovered that mutations G262S (yielding IMP-1) and G262A in IMP-6 stabilize the Zn(II) ligand His263 and thus the enzyme-substrate intermediate complex through a domino effect, which enhances conversion of drugs like ceftazidime, penicillins, and imipenem. Together, the domino effect and the altered beta-hairpin loop conformation explain how IMP-6 can evolve through mutations G262S and F218Y into an enzyme with up to one order of magnitude increased catalytic efficiencies toward these important antibiotics. Furthermore, the previously proposed binding of a third zinc ion close to the active site of IMP-6 mutant S121G was corroborated by our simulations.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Chemistry, SGM 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA.
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54
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Sharma NP, Hajdin C, Chandrasekar S, Bennett B, Yang KW, Crowder MW. Mechanistic studies on the mononuclear ZnII-containing metallo-beta-lactamase ImiS from Aeromonas sobria. Biochemistry 2006; 45:10729-38. [PMID: 16939225 PMCID: PMC2597473 DOI: 10.1021/bi060893t] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In an effort to understand the reaction mechanism of a B2 metallo-beta-lactamase, steady-state and pre-steady-state kinetic and rapid freeze quench electron paramagnetic resonance (EPR) studies were conducted on ImiS and its reaction with imipenem and meropenem. pH dependence studies revealed no inflection points in the pH range of 5.0-8.5, while proton inventories demonstrated at least 1 rate-limiting proton transfer. Site-directed mutagenesis studies revealed that Lys224 plays a catalytic role in ImiS, while the side chain of Asn233 does not play a role in binding or catalysis. Stopped-flow fluorescence studies on ImiS, which monitor changes in tryptophan fluorescence on the enzyme, and its reaction with imipenem and meropenem revealed biphasic fluorescence time courses with a rate of fluorescence loss of 160 s(-)(1) and a slower rate of fluorescence regain of 98 s(-)(1). Stopped-flow UV-vis studies, which monitor the concentration of substrate, revealed a rapid loss in absorbance during catalysis with a rate of 97 s(-)(1). These results suggest that the rate-limiting step in the reaction catalyzed by ImiS is C-N bond cleavage. Rapid freeze quench EPR studies on Co(II)-substituted ImiS demonstrated the appearance of a rhombic signal after 10 ms that is assigned to a reaction intermediate that has a five-coordinate metal center. A distinct product (EP) complex was also observed and began to appear in 18-19 ms. When these results are taken together, they allow for a reaction mechanism to be offered for the B2 metallo-beta-lactamases and demonstrate that the mono- and dinuclear Zn(II)-containing enzymes share a common rate-limiting step, which is C-N bond cleavage.
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Affiliation(s)
- Narayan P. Sharma
- Department of Chemistry and Biochemistry, 112 Hughes Hall, Miami University, Oxford, OH 45056
| | - Christine Hajdin
- Department of Chemistry and Biochemistry, 112 Hughes Hall, Miami University, Oxford, OH 45056
| | - Sowmya Chandrasekar
- Department of Chemistry and Biochemistry, 112 Hughes Hall, Miami University, Oxford, OH 45056
| | - Brian Bennett
- National Biomedical EPR Center, Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509
| | - Ke-Wu Yang
- Department of Chemistry and Biochemistry, 112 Hughes Hall, Miami University, Oxford, OH 45056
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, 112 Hughes Hall, Miami University, Oxford, OH 45056
- To whom correspondence should be addressed: M. W. Crowder, e-mail: , phone: (513) 529-7274, fax: (513) 529-5715
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55
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Park HS, Nam SH, Lee JK, Yoon CN, Mannervik B, Benkovic SJ, Kim HS. Design and evolution of new catalytic activity with an existing protein scaffold. Science 2006; 311:535-8. [PMID: 16439663 DOI: 10.1126/science.1118953] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The design of enzymes with new functions and properties has long been a goal in protein engineering. Here, we report a strategy to change the catalytic activity of an existing protein scaffold. This was achieved by simultaneous incorporation and adjustment of functional elements through insertion, deletion, and substitution of several active site loops, followed by point mutations to fine-tune the activity. Using this approach, we were able to introduce beta-lactamase activity into the alphabeta/betaalpha metallohydrolase scaffold of glyoxalase II. The resulting enzyme, evMBL8 (evolved metallo beta-lactamase 8), completely lost its original activity and, instead, catalyzed the hydrolysis of cefotaxime with a (kcat/Km)app of 1.8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100.
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Affiliation(s)
- Hee-Sung Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Kusung-Dong, Yusung-Gu, Daejon 305-701, Korea
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56
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Murphy TA, Catto LE, Halford SE, Hadfield AT, Minor W, Walsh TR, Spencer J. Crystal structure of Pseudomonas aeruginosa SPM-1 provides insights into variable zinc affinity of metallo-beta-lactamases. J Mol Biol 2006; 357:890-903. [PMID: 16460758 DOI: 10.1016/j.jmb.2006.01.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 12/28/2005] [Accepted: 01/03/2006] [Indexed: 10/25/2022]
Abstract
Metallo-beta-lactamases (mbetals) confer broad-spectrum resistance to beta-lactam antibiotics upon host bacteria and escape the action of existing beta-lactamase inhibitors. SPM-1 is a recently discovered mbetal that is distinguished from related enzymes by possession of a substantial central insertion and by sequence variation at positions that maintain active site structure. Biochemical data show SPM-1 to contain two Zn2+ sites of differing affinities, a phenomenon that is well documented amongst mbetals but for which a structural explanation has proved elusive. Here, we report the crystal structure of SPM-1 to 1.9 A resolution. The structure reveals SPM-1 to lack a mobile loop implicated in substrate binding by related mbetals and to accommodate the central insertion in an extended helical interdomain region. Deleting this had marginal effect upon binding and hydrolysis of a range of beta-lactams. These data suggest that the interactions of SPM-1 with substrates differ from those employed by other mbetals. SPM-1 as crystallised contains a single Zn2+. Both the active site hydrogen-bonding network and main-chain geometry at Asp120, a key component of the binding site for the second zinc ion, differ significantly from previous mbetal structures. We propose that variable interactions made by the Asp120 carbonyl group modulate affinity for a second Zn2+ equivalent in mbetals of the B1 subfamily. We further predict that SPM-1 possesses the capacity to evolve variants of enhanced catalytic activity by point mutations altering geometry and hydrogen bonding in the vicinity of the second Zn2+ site.
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Affiliation(s)
- Tanya A Murphy
- Department of Cellular and Molecular Medicine, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, UK
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57
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Weston J. Mode of action of bi- and trinuclear zinc hydrolases and their synthetic analogues. Chem Rev 2005; 105:2151-74. [PMID: 15941211 DOI: 10.1021/cr020057z] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jennie Weston
- Institut für Organische und Makromolekulare Chemie, Friedrich-Schiller-Universität, Jena, Germany.
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58
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Antony J, Piquemal JP, Gresh N. Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry. J Comput Chem 2005; 26:1131-47. [PMID: 15937993 DOI: 10.1002/jcc.20245] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Using the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D- and L-thiomandelate to a 104-residue model of the metallo-beta-lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a continuum reaction field procedure indicated the D-isomer to be more stably bound than the L-one, conform to the experimental result. The most stably bound complex has the S(-) ligand bridging monodentately the two Zn(II) cations and one carboxylate O(-) H-bonded to the Asn193 side chain. We have validated the SIBFA energy results by performing additional SIBFA as well as quantum chemical (QC) calculations on small (88 atoms) model complexes extracted from the 104-residue complexes, which include the residues involved in inhibitor binding. Computations were done in parallel using uncorrelated (HF) as well as correlated (DFT, LMP2, MP2) computations, and the comparisons extended to corresponding captopril complexes (Antony et al., J Comput Chem 2002, 23, 1281). The magnitudes of the SIBFA intermolecular interaction energies were found to correctly reproduce their QC counterparts and their trends for a total of twenty complexes.
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Affiliation(s)
- Jens Antony
- Freie Universität Berlin, FB Mathematik und Informatik, Institut für Mathematik II, AG Biocomputing, Arnimallee 2-6, D-14195 Berlin, Germany
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59
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Oelschlaeger P, Mayo SL, Pleiss J. Impact of remote mutations on metallo-beta-lactamase substrate specificity: implications for the evolution of antibiotic resistance. Protein Sci 2005; 14:765-74. [PMID: 15722450 PMCID: PMC2279297 DOI: 10.1110/ps.041093405] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Metallo-beta-lactamases have raised concerns due to their ability to hydrolyze a broad spectrum of beta-lactam antibiotics. The G262S point mutation distinguishing the metallo-beta-lactamase IMP-1 from IMP-6 has no effect on the hydrolysis of the drugs cephalothin and cefotaxime, but significantly improves catalytic efficiency toward cephaloridine, ceftazidime, benzylpenicillin, ampicillin, and imipenem. This change in specificity occurs even though residue 262 is remote from the active site. We investigated the substrate specificities of five other point mutants resulting from single-nucleotide substitutions at positions near residue 262: G262A, G262V, S121G, F218Y, and F218I. The results suggest two types of substrates: type I (nitrocefin, cephalothin, and cefotaxime), which are converted equally well by IMP-6, IMP-1, and G262A, but even more efficiently by the other mutants, and type II (ceftazidime, benzylpenicillin, ampicillin, and imipenem), which are hydrolyzed much less efficiently by all the mutants. G262V, S121G, F218Y, and F218I improve conversion of type I substrates, whereas G262A and IMP-1 improve conversion of type II substrates, indicating two distinct evolutionary adaptations from IMP-6. Substrate structure may explain the catalytic efficiencies observed. Type I substrates have R2 electron donors, which may stabilize the substrate intermediate in the binding pocket. In contrast, the absence of these stabilizing interactions with type II substrates may result in poor conversion. This observation may assist future drug design. As the G262A and F218Y mutants confer effective resistance to Escherichia coli BL21(DE3) cells (high minimal inhibitory concentrations), they are likely to evolve naturally.
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Affiliation(s)
- Peter Oelschlaeger
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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60
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Walsh TR, Toleman MA, Poirel L, Nordmann P. Metallo-beta-lactamases: the quiet before the storm? Clin Microbiol Rev 2005; 18:306-25. [PMID: 15831827 PMCID: PMC1082798 DOI: 10.1128/cmr.18.2.306-325.2005] [Citation(s) in RCA: 997] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ascendancy of metallo-beta-lactamases within the clinical sector, while not ubiquitous, has nonetheless been dramatic; some reports indicate that nearly 30% of imipenem-resistant Pseudomonas aeruginosa strains possess a metallo-beta-lactamase. Acquisition of a metallo-beta-lactamase gene will invariably mediate broad-spectrum beta-lactam resistance in P. aeruginosa, but the level of in vitro resistance in Acinetobacter spp. and Enterobacteriaceae is less dependable. Their clinical significance is further embellished by their ability to hydrolyze all beta-lactams and by the fact that there is currently no clinical inhibitor, nor is there likely to be for the foreseeable future. The genes encoding metallo-beta-lactamases are often procured by class 1 (sometimes class 3) integrons, which, in turn, are embedded in transposons, resulting in a highly transmissible genetic apparatus. Moreover, other gene cassettes within the integrons often confer resistance to aminoglycosides, precluding their use as an alternative treatment. Thus far, the metallo-beta-lactamases encoded on transferable genes include IMP, VIM, SPM, and GIM and have been reported from 28 countries. Their rapid dissemination is worrisome and necessitates the implementation of not just surveillance studies but also metallo-beta-lactamase inhibitor studies securing the longevity of important anti-infectives.
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Affiliation(s)
- Timothy R Walsh
- Department of Pathology and Microbiology, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom.
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61
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Materon IC, Beharry Z, Huang W, Perez C, Palzkill T. Analysis of the context dependent sequence requirements of active site residues in the metallo-beta-lactamase IMP-1. J Mol Biol 2005; 344:653-63. [PMID: 15533435 DOI: 10.1016/j.jmb.2004.09.074] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2004] [Revised: 09/23/2004] [Accepted: 09/24/2004] [Indexed: 11/27/2022]
Abstract
The metallo-beta-lactamase IMP-1 catalyzes the hydrolysis of a broad range of beta-lactam antibiotics to provide bacterial resistance to these compounds. In this study, 29 amino acid residue positions in and near the active-site pocket of the IMP-1 enzyme were randomized individually by site-directed mutagenesis of the corresponding codons in the bla(IMP-1) gene. The 29 random libraries were used to identify positions that are critical for the catalytic and substrate-specific properties of the IMP-1 enzyme. Mutants from each of the random libraries were selected for the ability to confer to Escherichia coli resistance to ampicillin, cefotaxime, imipenem or cephaloridine. The DNA sequence of several functional mutants was determined for each of the substrates. Comparison of the sequences of mutants obtained from the different antibiotic selections indicates the sequence requirements for each position in the context of each substrate. The zinc-chelating residues in the active site were found to be essential for hydrolysis of all antibiotics tested. Several positions, however, displayed context-dependent sequence requirements, in that they were essential for one substrate(s) but not others. The most striking examples included Lys69, Asp84, Lys224, Pro225, Gly232, Asn233, Asp236 and Ser262. In addition, comparison of the results for all 29 positions indicates that hydrolysis of imipenem, cephaloridine and ampicillin has stringent sequence requirements, while the requirements for hydrolysis of cefotaxime are more relaxed. This suggests that more information is required to specify active-site pockets that carry out imipenem, cephaloridine or ampicillin hydrolysis than one that catalyzes cefotaxime hydrolysis.
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Affiliation(s)
- Isabel C Materon
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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62
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Jin W, Arakawa Y, Yasuzawa H, Taki T, Hashiguchi R, Mitsutani K, Shoga A, Yamaguchi Y, Kurosaki H, Shibata N, Ohta M, Goto M. Comparative study of the inhibition of metallo-beta-lactamases (IMP-1 and VIM-2) by thiol compounds that contain a hydrophobic group. Biol Pharm Bull 2005; 27:851-6. [PMID: 15187432 DOI: 10.1248/bpb.27.851] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For the purpose of screening of inhibitors that are effective for wide range of metallo-beta-lactamases, the inhibitory effect of two series of compounds, 2-omega-phenylalkyl-3-mercaptopropionic acid (PhenylCnSH (n=1-4)) and N-[(7-chloro-quinolin-4-ylamino)-alkyl]-3-mercapto-propionamide (QuinolineCnSH (n=2-6)), where n denotes the alkyl chain length, on metallo-beta-lactamases IMP-1 and VIM-2 was examined. These inhibitors contain a thiol group and a hydrophobic group linked by variable-length methylene chain. PhenylCnSH (n=1-4) was found to be a potent inhibitor of both IMP-1 and VIM-2. PhenylC4SH was the potent inhibitor of both IMP-1 (IC(50)=1.2 microM) and VIM-2 (IC(50)=1.1 microM) among this study. When the number of methylene units was varied, QuinolineC4SH showed the maximum inhibitory activity against IMP-1 and VIM-2 (IC(50)=2.5 microM and IC(50)=2.4 microM). The relationship between the inhibitory effect of the alkyl chain length was different for both series of inhibitors, suggesting that IMP-1 has a tighter binding site than VIM-2. QuinolineCnSH did not serve as a fluorescence reagent for metallo-beta-lactamases.
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Affiliation(s)
- Wanchun Jin
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Oe Honmachi, Japan
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63
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Olsen L, Rasmussen T, Hemmingsen L, Ryde U. Binding of Benzylpenicillin to Metallo-β-lactamase: A QM/MM Study. J Phys Chem B 2004. [DOI: 10.1021/jp0482215] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lars Olsen
- Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark, Department of Theoretical Chemistry, University of Lund, Chemical Center, P.O.B. 124 S-221 00 Lund, Sweden, and Department of Physics, The Quantum Protein Centre, The Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - T. Rasmussen
- Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark, Department of Theoretical Chemistry, University of Lund, Chemical Center, P.O.B. 124 S-221 00 Lund, Sweden, and Department of Physics, The Quantum Protein Centre, The Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - L. Hemmingsen
- Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark, Department of Theoretical Chemistry, University of Lund, Chemical Center, P.O.B. 124 S-221 00 Lund, Sweden, and Department of Physics, The Quantum Protein Centre, The Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - U. Ryde
- Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark, Department of Theoretical Chemistry, University of Lund, Chemical Center, P.O.B. 124 S-221 00 Lund, Sweden, and Department of Physics, The Quantum Protein Centre, The Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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64
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Mercuri PS, García-Sáez I, De Vriendt K, Thamm I, Devreese B, Van Beeumen J, Dideberg O, Rossolini GM, Frère JM, Galleni M. Probing the Specificity of the Subclass B3 FEZ-1 Metallo-β-lactamase by Site-directed Mutagenesis. J Biol Chem 2004; 279:33630-8. [PMID: 15159411 DOI: 10.1074/jbc.m403671200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The subclass B3 FEZ-1 beta-lactamase produced by Fluoribacter (Legionella) gormanii is a Zn(II)-containing enzyme that hydrolyzes the beta-lactam bond in penicillins, cephalosporins, and carbapenems. FEZ-1 has been extensively studied using kinetic, computational modeling and x-ray crystallography. In an effort to probe residues potentially involved in substrate binding and zinc binding, five site-directed mutants of FEZ-1 (H121A, Y156A, S221A, N225A, and Y228A) were prepared and characterized using metal analyses and steady state kinetics. The activity of H121A is dependent on zinc ion concentration. The H121A monozinc form is less active than the dizinc form, which exhibits an activity similar to that of the wild type enzyme. Tyr156 is not essential for binding and hydrolysis of the substrate. Substitution of residues Ser221 and Asn225 modifies the substrate profile by selectively decreasing the activity against carbapenems. The Y228A mutant is inhibited by the product formed upon hydrolysis of cephalosporins. A covalent bond between the side chain of Cys200 and the hydrolyzed cephalosporins leads to the formation of an inactive and stable complex.
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Affiliation(s)
- Paola Sandra Mercuri
- Centre d'Ingénierie des Protéines, B6 Sart Tilman, Université de Liège, B-4000 Liège, Belgium
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65
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Dal Peraro M, Vila AJ, Carloni P. Substrate binding to mononuclear metallo-β-lactamase from Bacillus cereus. Proteins 2003; 54:412-23. [PMID: 14747990 DOI: 10.1002/prot.10554] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Structure and dynamics of substrate binding (cefotaxime) to the catalytic pocket of the mononuclear zinc-beta-lactamase from Bacillus cereus are investigated by molecular dynamics simulations. The calculations, which are based on the hydrogen-bond pattern recently proposed by Dal Peraro et al. (J Biol Inorg Chem 2002; 7:704-712), are carried out for both the free and the complexed enzyme. In the resting state, active site pattern and temperature B-factors are in agreement with crystallographic data. In the complexed form, cefotaxime is accommodated into a stable orientation in the catalytic pocket within the nanosecond timescale, interacting with the enzyme zinc-bound hydroxide and the surrounding loops. The beta-lactam ring remains stable and very close to the hydroxide nucleophile agent, giving a stable representation of the productive enzyme-substrate complex.
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Affiliation(s)
- Matteo Dal Peraro
- International School for Advanced Studies, SISSA and INFM-DEMOCRITOS, Trieste, Italy
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66
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Abstract
Proteins are in constant motion between different conformational states with similar energies. This has often been ignored in drug design. However, protein flexibility is fundamental to understanding the ways in which drugs exert biological effects, their binding-site location, binding orientation, binding kinetics, metabolism and transport. Protein flexibility allows increased affinity to be achieved between a drug and its target. This is crucial, because the lipophilicity and number of polar interactions allowed for an oral drug is limited by absorption, distribution, metabolism and toxicology considerations.
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Affiliation(s)
- Simon J Teague
- AstraZeneca R&D Charnwood, Bakewell Road, Loughborough, Leicester LE11 5RH, UK.
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67
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Huntley JJ, Fast W, Benkovic SJ, Wright PE, Dyson HJ. Role of a solvent-exposed tryptophan in the recognition and binding of antibiotic substrates for a metallo-beta-lactamase. Protein Sci 2003; 12:1368-75. [PMID: 12824483 PMCID: PMC2323931 DOI: 10.1110/ps.0305303] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2003] [Revised: 03/31/2003] [Accepted: 04/03/2003] [Indexed: 10/27/2022]
Abstract
Numerous X-ray crystal structures of the metallo-beta-lactamase from Bacteroides fragilis and related organisms show a beta-hairpin loop immediately adjacent to the active-site zinc atom(s). Both crystallographic and NMR information show that the end of this beta-hairpin loop, which contains a solvent exposed tryptophan residue, Trp49, is highly flexible in the absence of substrates or other ligands, giving rise in some of the X-ray structures to a lack of observable electron density in this region. We report an investigation of the role of this mobile, solvent-exposed tryptophan using site-directed mutagenesis, steady state kinetics measurements and characterization by NMR. Trp49 appears to have a role both in substrate binding and in promotion of catalysis. Substitution of this residue with a number of different side chains indicates that the binding interaction depends on the bulky hydrophobic and aromatic nature of the indole ring, which can provide relatively non-specific interactions with a variety of antibiotic substrates. In this way, the tryptophan at this position provides a large degree of the breadth of substrate specificity for the metallo-beta-lactamase. Previous studies established that the antibiotic binding site was sufficiently plastic that the derivatization of existing antibiotics is unlikely to result in the successful treatment of bacterial infections incorporating this resistance element. Rather, a more productive approach may be to design therapeutics directed towards this solvent-exposed tryptophan residue.
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Affiliation(s)
- James J.A. Huntley
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Walter Fast
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Stephen J. Benkovic
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Peter E. Wright
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - H. Jane Dyson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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68
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García-Saez I, Hopkins J, Papamicael C, Franceschini N, Amicosante G, Rossolini GM, Galleni M, Frère JM, Dideberg O. The 1.5-A structure of Chryseobacterium meningosepticum zinc beta-lactamase in complex with the inhibitor, D-captopril. J Biol Chem 2003; 278:23868-73. [PMID: 12684522 DOI: 10.1074/jbc.m301062200] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of the class-B beta-lactamase, BlaB, from the pathogenic bacterium, Chryseobacterium meningosepticum, in complex with the inhibitor, d-captopril, has been solved at 1.5-A resolution. The enzyme has the typical alphabeta/betaalpha metallo-beta-lactamase fold and the characteristic two metal binding sites of members of the subclass B1, in which two Zn2+ ions were identified. d-Captopril, a diastereoisomer of the commercial drug, captopril, acts as an inhibitor by displacing the catalytic hydroxyl ion required for antibiotic hydrolysis and intercalating its sulfhydryl group between the two Zn2+ ions. Interestingly, d-captopril is located on one side of the active site cleft. The x-ray structure of the complex of the closely related enzyme, IMP-1, with a mercaptocarboxylate inhibitor, which also contains a sulfhydryl group bound to the two Zn2+ ions, shows the ligand to be located on the opposite side of the active site cleft. A molecule generated by fusion of these two inhibitors would cover the entire cleft, suggesting an interesting approach to the design of highly specific inhibitors.
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Affiliation(s)
- Isabel García-Saez
- Laboratoire de Cristallographie Macromoléculaire, Institut de Biologie Structurale Jean-Pierre Ebel (CNRS-Commissariat à l'Energie Atomique, Saclay, France
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69
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Goto M, Yasuzawa H, Higashi T, Yamaguchi Y, Kawanami A, Mifune S, Mori H, Nakayama H, Harada K, Arakawa Y. Dependence of hydrolysis of beta-lactams with a zinc(II)-beta-lactamase produced from Serratia marcescens (IMP-1) on pH and concentration of zinc(II) ion: dissociation of Zn(II) from IMP-1 in acidic medium. Biol Pharm Bull 2003; 26:589-94. [PMID: 12736495 DOI: 10.1248/bpb.26.589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The pH dependence for the hydrolysis of beta-lactam antibiotics by a metallo-beta-lactamase (IMP-1) produced from Serratia marcescens was investigated varying the concentration of Zn(II). The activity of IMP-1 for imipenem was decreased at pH less than pH 5.3 without external addition of Zn(II) ions but was recovered with addition of Zn(II). Varying the concentration of external Zn(II), the molar activity of the enzyme, k(obs), that was defined by the velocity of hydrolysis of imipenem/concentration of IMP-1 was expressed by k(obs)=v(init)/[E](T)=k(max)[Zn]/(K(d)+[Zn]) in which K(d) stands for the dissociation constant between Zn(II) and IMP-1. The dissociation constants, K(d), vary with pH; K(d)=840 x 10(-6) M at pH 4.3 and K(d)=0.19 x 10(-6) M at pH 6.0. The plot of -log K(d) against pH showed a straight line having a slope of 4.0 below pH 5.0, showing the existence of four functional groups which may be protonated upon dissociation of Zn(II) ion(s). The k(cat), K(m), and k(cat)/K(m) of hydrolysis of imipenem and cephalothin in the presence of sufficient concentration of Zn(NO(3))(2) for saturation of IMP-1 with Zn(II) showed similar dependency to each other on pH between pH 6.0 and 9.0.
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Affiliation(s)
- Masafumi Goto
- Laboratory of Pharmaceutical Physical Chemistry, Faculty of Pharmaceutical Sciences, Kumamoto University, Honmachi, Japan.
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70
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Moali C, Anne C, Lamotte-Brasseur J, Groslambert S, Devreese B, Van Beeumen J, Galleni M, Frère JM. Analysis of the importance of the metallo-beta-lactamase active site loop in substrate binding and catalysis. CHEMISTRY & BIOLOGY 2003; 10:319-29. [PMID: 12725860 DOI: 10.1016/s1074-5521(03)00070-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the mobile loop comprising residues 60-66 in metallo-beta-lactamases has been studied by site-directed mutagenesis, determination of kinetic parameters for six substrates and two inhibitors, pre-steady-state characterization of the interaction with chromogenic nitrocefin, and molecular modeling. The W64A mutation was performed in IMP-1 and BcII (after replacement of the BcII 60-66 peptide by that of IMP-1) and always resulted in increased K(i) and K(m) and decreased k(cat)/K(m) values, an effect reinforced by complete deletion of the loop. k(cat) values were, by contrast, much more diversely affected, indicating that the loop does not systematically favor the best relative positioning of substrate and enzyme catalytic groups. The hydrophobic nature of the ligand is also crucial to strong interactions with the loop, since imipenem was almost insensitive to loop modifications.
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Affiliation(s)
- Catherine Moali
- Centre d'Ingénierie des Protéines, Université de Liège, Sart-Tilman, B-4000 Liege, Belgium
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71
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Kato N, Yamazoe K, Han CG, Ohtsubo E. New insertion sequence elements in the upstream region of cfiA in imipenem-resistant Bacteroides fragilis strains. Antimicrob Agents Chemother 2003; 47:979-85. [PMID: 12604530 PMCID: PMC149317 DOI: 10.1128/aac.47.3.979-985.2003] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The 747-bp cfiA gene, which encodes a metallo-beta-lactamase, and the regions flanking cfiA in six imipenem-resistant and four imipenem-susceptible Bacteroides fragilis strains isolated in Japan were analyzed by PCR and DNA sequencing. The nucleotide sequences of the cfiA genes (designated cfiA(1) to cfiA(10)) of all 10 strains tested varied from that of the standard cfiA gene from B. fragilis TAL2480. However, putative proteins encoded by the cfiA variants contained conserved amino acid residues important for zinc binding and hairpin loop formation, suggesting that cfiA variants have the capability of producing metallo-beta-lactamases with full catalytic activities. PCR assay indicated that six metallo-beta-lactamase-producing, imipenem-resistant strains had an insertion mutation in the region immediately upstream of cfiA. Nucleotide sequencing of the PCR-amplified fragments along with the upstream region of cfiA revealed that there were five new kinds of insertion sequence (IS) elements (designated IS612, IS613, IS614, IS615, and IS616, with a size range of 1,594 to 1,691 bp), of which only IS616 was found to be almost identical to IS1188, one of the IS elements previously identified in the upstream region of cfiA. These elements had target site duplications of 4 or 5 bp in length, terminal inverted repeats (14, 15, or 17 bp in size), and a large open reading frame encoding a putative transposase which is required for the transcription of IS elements. Each element was inserted such that the transcriptional direction of the transposase was opposite to that of cfiA. A computer-aided homology search revealed that, based on the homology of their putative transposases, the sizes of their terminal inverted repeat sequences, and their target site duplications, IS612, IS613, IS614, and IS615 belong to the IS4 family, which includes IS942, previously found in some drug-resistant B. fragilis strains, but that IS616 belongs to the IS1380 family. All the IS elements appear to have putative promoter motif sequences (the -7 region's TAnnTTTG motif and the -33 region's TTG or TG) in their end regions, suggesting that the IS elements provide a promoter for the transcription of cfiA upon insertion. These data provide additional proof that various IS elements may exist to provide a promoter to express the cfiA gene.
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Affiliation(s)
- Naoki Kato
- Institute of Anaerobic Bacteriology, Gifu University School of Medicine, Japan.
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72
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Krauss M, Gresh N, Antony J. Binding and Hydrolysis of Ampicillin in the Active Site of a Zinc Lactamase. J Phys Chem B 2003. [DOI: 10.1021/jp027097r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Krauss
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland, Laboratoire de Pharmacochimie Moleculaire, U 266 INSERM, FRE 2463 CNRS, Universite Rene-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, and Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
| | - N. Gresh
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland, Laboratoire de Pharmacochimie Moleculaire, U 266 INSERM, FRE 2463 CNRS, Universite Rene-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, and Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
| | - J. Antony
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland, Laboratoire de Pharmacochimie Moleculaire, U 266 INSERM, FRE 2463 CNRS, Universite Rene-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, and Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
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73
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Suárez D, Díaz N, Merz KM. Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem. J Comput Chem 2002; 23:1587-600. [PMID: 12395427 DOI: 10.1002/jcc.10157] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Herein, we present results from MD simulations of the Michaelis complex formed between the dizinc beta-lactamase from B. fragilis and imipenem. We considered two catalytically important configurations, which differ in the presence or absence of a hydroxide bridge connecting the two zinc ions in the active site. The structural and dynamical effects induced by substrate binding, the specific roles of the conserved residues and the zinc-bound water molecules, the near attack conformers of the Michaelis complex, and so forth, are discussed in detail. The relative stability of the two configurations was estimated from QM linear scaling calculations on the enzyme-substrate complex combined with Poisson-Boltzmann electrostatic calculations and normal mode calculations. Importantly, we find that the two configurations have similar energies, indicating that these two structures could readily be interchanged, thereby facilitating catalysis. The configuration with the hydroxide bound to the two zinc ions is predicted to be the resting form of the enzyme, while the configuration without the bridge is the reactive form that was found to place the hydroxide in position to attack the carbonyl of the beta-lactam ring. Thus, we propose that the enzyme initiates catalysis by converting from the hydroxide bridge form into the configuration that lacks the hydroxide bridge. This interconversion increases the nucleophilicity of the hydroxide ion and exposes it to the beta-lactam carbonyl, which ultimately facilitates nucleophilic attack. The implications of the observed modes of binding, the possible influence of mutating the Lys184 and Asn193 residues on substrate binding, and the reaction mechanism are also discussed in detail.
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Affiliation(s)
- Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006 Oviedo, Asturias, Spain
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74
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Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R. Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2002; 23:1281-96. [PMID: 12210153 DOI: 10.1002/jcc.10111] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.
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Affiliation(s)
- Jens Antony
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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75
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Carenbauer AL, Garrity JD, Periyannan G, Yates RB, Crowder MW. Probing substrate binding to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia by using site-directed mutagenesis. BMC BIOCHEMISTRY 2002; 3:4. [PMID: 11876827 PMCID: PMC77373 DOI: 10.1186/1471-2091-3-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2001] [Accepted: 02/13/2002] [Indexed: 11/23/2022]
Abstract
BACKGROUND The metallo-beta-lactamases are Zn(II)-containing enzymes that hydrolyze the beta-lactam bond in penicillins, cephalosporins, and carbapenems and are involved in bacterial antibiotic resistance. There are at least 20 distinct organisms that produce a metallo-beta-lactamase, and these enzymes have been extensively studied using X-ray crystallographic, computational, kinetic, and inhibition studies; however, much is still unknown about how substrates bind and the catalytic mechanism. In an effort to probe substrate binding to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia, nine site-directed mutants of L1 were prepared and characterized using metal analyses, CD spectroscopy, and pre-steady state and steady state kinetics. RESULTS Site-directed mutations were generated of amino acids previously predicted to be important in substrate binding. Steady-state kinetic studies using the mutant enzymes and 9 different substrates demonstrated varying Km and kcat values for the different enzymes and substrates and that no direct correlation between Km and the effect of the mutation on substrate binding could be drawn. Stopped-flow fluorescence studies using nitrocefin as the substrate showed that only the S224D and Y228A mutants exhibited weaker nitrocefin binding. CONCLUSIONS The data presented herein indicate that Ser224, Ile164, Phe158, Tyr228, and Asn233 are not essential for tight binding of substrate to metallo-beta-lactamase L1. The results in this work also show that Km values are not reliable for showing substrate binding, and there is no correlation between substrate binding and the amount of reaction intermediate formed during the reaction. This work represents the first experimental testing of one of the computational models of the metallo-beta-lactamases.
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Affiliation(s)
- Anne L Carenbauer
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - James D Garrity
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Gopal Periyannan
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Robert B Yates
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
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76
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Materon IC, Palzkill T. Identification of residues critical for metallo-beta-lactamase function by codon randomization and selection. Protein Sci 2001; 10:2556-65. [PMID: 11714924 PMCID: PMC2374027 DOI: 10.1110/ps.40884] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
IMP-1 beta-lactamase is a zinc metallo-enzyme encoded by the transferable bla(IMP-1) gene, which confers resistance to virtually all beta-lactam antibiotics including carbapenems. To understand how IMP-1 recognizes and hydrolyzes beta-lactam antibiotics it is important to determine which amino acid residues are critical for catalysis and which residues control substrate specificity. We randomized 27 individual codons in the bla(IMP-1) gene to create libraries that contain all possible amino acid substitutions at residue positions in and near the active site of IMP-1. Mutants from the random libraries were selected for the ability to confer ampicillin resistance to Escherichia coli. Of the positions randomized, >50% do not tolerate amino acid substitutions, suggesting they are essential for IMP-1 function. The remaining positions tolerate amino acid substitutions and may influence the substrate specificity of the enzyme. Interestingly, kinetic studies for one of the functional mutants, Asn233Ala, indicate that an alanine substitution at this position significantly increases catalytic efficiency as compared with the wild-type enzyme.
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Affiliation(s)
- I C Materon
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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77
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Mollard C, Moali C, Papamicael C, Damblon C, Vessilier S, Amicosante G, Schofield CJ, Galleni M, Frere JM, Roberts GC. Thiomandelic acid, a broad spectrum inhibitor of zinc beta-lactamases: kinetic and spectroscopic studies. J Biol Chem 2001; 276:45015-23. [PMID: 11564740 DOI: 10.1074/jbc.m107054200] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Resistance to beta-lactam antibiotics mediated by metallo-beta-lactamases is an increasingly worrying clinical problem. Candidate inhibitors include mercaptocarboxylic acids, and we report studies of a simple such compound, thiomandelic acid. A series of 35 analogues were synthesized and examined as metallo-beta-lactamase inhibitors. The K(i) values (Bacillus cereus enzyme) are 0.09 microm for R-thiomandelic acid and 1.28 microm for the S-isomer. Structure-activity relationships show that the thiol is essential for activity and the carboxylate increases potency; the affinity is greatest when these groups are close together. Thioesters of thiomandelic acid are substrates for the enzyme, liberating thiomandelic acid, suggesting a starting point for the design of "pro-drugs." Importantly, thiomandelic acid is a broad spectrum inhibitor of metallo-beta-lactamases, with a submicromolar K(i) value for all nine enzymes tested, except the Aeromonas hydrophila enzyme; such a wide spectrum of activity is unprecedented. The binding of thiomandelic acid to the B. cereus enzyme was studied by NMR; the results are consistent with the idea that the inhibitor thiol binds to both zinc ions, while its carboxylate binds to Arg(91). Amide chemical shift perturbations for residues 30-40 (the beta(3)-beta(4) loop) suggest that this small inhibitor induces a movement of this loop of the kind seen for other larger inhibitors.
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Affiliation(s)
- C Mollard
- Biological NMR Centre, Department of Biochemistry, University of Leicester, P.O. Box 138, University Rd., Leicester LE1 9HN, United Kingdom
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78
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Spencer J, Clarke AR, Walsh TR. Novel mechanism of hydrolysis of therapeutic beta-lactams by Stenotrophomonas maltophilia L1 metallo-beta-lactamase. J Biol Chem 2001; 276:33638-44. [PMID: 11443136 DOI: 10.1074/jbc.m105550200] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Stopped-flow tryptophan fluorescence under single turnover and pseudo-first-order conditions has been used to investigate the kinetic mechanism of beta-lactam hydrolysis by the Stenotrophomonas maltophilia L1 metallo-beta-lactamase. For the cephalosporin substrates nitrocefin and cefaclor and the carbapenem meropenem, a substantial quench of fluorescence is observed on association of substrate with enzyme. We have assigned this to a rearrangement event subsequent to formation of an initial collision complex. For the colorimetric compound nitrocefin, decay of this dark inter- mediate represents the overall rate-determining step for the reaction and is equivalent to decay of a previously observed state in which the beta-lactam amide bond has already been cleaved. For both cefaclor and meropenem, the rate-determining step for hydrolysis is loss of a second, less quenched state, in which, however, the beta-lactam amide bond remains intact. We suggest, therefore, that the mechanism of hydrolysis of nitrocefin by binuclear metallo-beta-lactamases may be atypical and that cleavage of the beta-lactam amide bond is the rate-determining step for breakdown of the majority of beta-lactam substrates by the L1 enzyme.
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Affiliation(s)
- J Spencer
- Department of Pathology and Microbiology, University of Bristol School of Medical Sciences, University Walk, Bristol BS8 1TD, United Kingdom.
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79
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Salsbury FR, Crowley MF, Brooks CL. Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding. Proteins 2001; 44:448-59. [PMID: 11484222 DOI: 10.1002/prot.1110] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structure and dynamics of an inhibitor-bound complex of the metallo-beta-lactamase from Bacteroides fragilis are studied by using molecular dynamics. A search of the conformational space was performed to obtain three distinct models of the complex, which were then subjected to solvated molecular dynamics. A solvated molecular dynamics study of the apo protein was performed to serve as a baseline for comparison with the bound simulations. We find loop conformation changes due to binding as well as a decrease in flexibility of the protein as a whole and especially in the major loop of the beta-lactamase. We report the structural and dynamical features of the inhibitor-bound and apo models, as well as experimentally measurable quantities, which should be capable of distinguishing the two binding modes we have determined.
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Affiliation(s)
- F R Salsbury
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
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80
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Toney JH, Hammond GG, Fitzgerald PM, Sharma N, Balkovec JM, Rouen GP, Olson SH, Hammond ML, Greenlee ML, Gao YD. Succinic acids as potent inhibitors of plasmid-borne IMP-1 metallo-beta-lactamase. J Biol Chem 2001; 276:31913-8. [PMID: 11390410 DOI: 10.1074/jbc.m104742200] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
IMP-1 metallo-beta-lactamase (class B) is a plasmid-borne zinc metalloenzyme that efficiently hydrolyzes beta-lactam antibiotics, including carbapenems, rendering them ineffective. Because IMP-1 has been found in several clinically important carbapenem-resistant pathogens, there is a need for inhibitors of this enzyme that could protect broad spectrum antibiotics such as imipenem from hydrolysis and thus extend their utility. We have identified a series of 2,3-(S,S)-disubstituted succinic acids that are potent inhibitors of IMP-1. Determination of high resolution crystal structures and molecular modeling of succinic acid inhibitor complexes with IMP-1 has allowed an understanding of the potency, stereochemistry, and structure-activity relationships of these inhibitors.
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Affiliation(s)
- J H Toney
- Department of Biochemistry, Merck Research Laboratories, Rahway, New Jersey 07065-0900, USA.
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81
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Mercuri PS, Bouillenne F, Boschi L, Lamotte-Brasseur J, Amicosante G, Devreese B, van Beeumen J, Frère JM, Rossolini GM, Galleni M. Biochemical characterization of the FEZ-1 metallo-beta-lactamase of Legionella gormanii ATCC 33297T produced in Escherichia coli. Antimicrob Agents Chemother 2001; 45:1254-62. [PMID: 11257043 PMCID: PMC90452 DOI: 10.1128/aac.45.4.1254-1262.2001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bla(FEZ-1) gene coding for the metallo-beta-lactamase of Legionella (Fluoribacter) gormanii ATCC 33297T was overexpressed via a T7 expression system in Escherichia coli BL21(DE3)(pLysS). The product was purified to homogeneity in two steps with a yield of 53%. The FEZ-1 metallo-beta-lactamase exhibited a broad-spectrum activity profile, with a preference for cephalosporins such as cephalothin, cefuroxime, and cefotaxime. Monobactams were not hydrolyzed. The beta-lactamase was inhibited by metal chelators. FEZ-1 is a monomeric enzyme with a molecular mass of 29,440 Da which possesses two zinc-binding sites. Its zinc content did not vary in the pH range of 5 to 9, but the presence of zinc ions modified the catalytic efficiency of the enzyme. A model of the FEZ-1 three-dimensional structure was built.
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Affiliation(s)
- P S Mercuri
- Centre d'Ingénierie des Protéines, Université de Liège, B-4000 Liège, Belgium
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82
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Abstract
The use of beta-lactamase inhibitors in combination with a beta-lactamase-susceptible antibiotic is a useful strategy to rescue otherwise good antibiotics from failure. However, recent years have seen a rise in the numbers of beta-lactamases that are insensitive to the available beta-lactamase inhibitors. This review summarizes of the mechanisms of action of the principal types of inhibitors and the ways in which beta-lactamase are thought to develop resistance towards them. Ten general classes of inhibitors are reviewed, especially those of therapeutic importance (clavulanic acid, penam sulfones and carbapenems). Copyright 2000 Harcourt Publishers Ltd.
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Affiliation(s)
- Malcolm G. P. Page
- Pharma Division, Preclinical Research, F. Hoffmann-La Roche Ltd, Basel, CH-4070, Switzerland
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