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Wu XR, Chen WY, Liu L, Yang KW. Discovery of hydroxamate as a promising scaffold dually inhibiting metallo- and serine-β-lactamases. Eur J Med Chem 2024; 265:116055. [PMID: 38134748 DOI: 10.1016/j.ejmech.2023.116055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
The bacterial infection mediated by β-lactamases MβLs and SβLs has grown into an emergent health threat, however, development of a molecule that dual inhibits both MβLs and SβLs is challenging. In this work, a series of hydroxamates 1a-g, 2a-e, 3a-c, 4a-c were synthesized, characterized by 1H and 13C NMR and confirmed by HRMS. Biochemical assays revealed that these molecules dually inhibited MβLs (NDM-1, IMP-1) and SβLs (KPC-2, OXA-48), with an IC50 value in the range of 0.64-41.08 and 1.01-41.91 μM (except 1a and 1d on SβLs, IC50 > 50 μM), and 1f was found to be the best inhibitor with an IC50 value in the range of 0.64-1.32 and 0.57-1.01 μM, respectively. Mechanism evaluation indicated that 1f noncompetitively and irreversibly inhibited NDM-1 and KPC-2, with Ki value of 2.5 and 0.55 μM, is a time- and dose-dependent inhibitor of both MβLs and SβLs. MIC tests shown that all hydroxamates increased the antimicrobial effect of MER on E. coli-NDM-1 and E. coli-IMP-1 (expect 1b, 1d, 1g and 2d), resulting in a 2-8-fold reduction in MICs of MER, 1e-g, 2b-d, 3a-c and 4b-c decreased 2-4-fold MICs of MER on E. coli-KPC-2, and 1c, 1f-g, 2a-c, 3b, 4a and 4c decreased 2-16-fold MICs of MER on E. coli-OXA-48. Most importantly, 1f-g, 2b-c, 3b and 4c exhibited the dual synergizing inhibition against both E. coli-MβLs and E. coli-SβLs tested, resulting in a 2-8-fold reduction in MICs of MER, and 1f was found to have the best effect on the drug-resistant bacteria tested. Also, 1f shown synergizing antimicrobial effect on five clinical isolates EC04, EC06, EC08, EC10 and EC24 that produce NDM-1, resulting in a 2-8-fold reduction in MIC of MER, but its effect on E. coli and K. pneumonia-KPC-NDM was not to be observed using the same dose of inhibitor. Mice tests shown that the monotherapy of 1f or 4a in combination with MER significantly reduced the bacterial load of E. coli-NDM-1 and E. coli-OXA-48 cells in liver and spleen, respectively. The discovery in this work offered a promising bifunctional scaffold for creating the specific molecules that dually inhibit MβLs and MβLs, in combating antibiotic-resistant bacteria.
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Affiliation(s)
- Xiao-Rong Wu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Wei-Ya Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Lu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, 710127, PR China.
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2
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Aromatic Schiff bases confer inhibitory efficacy against New Delhi metallo-β-lactamase-1 (NDM-1). Bioorg Chem 2022; 126:105910. [PMID: 35653899 DOI: 10.1016/j.bioorg.2022.105910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 12/24/2022]
Abstract
The irregular use of antibiotics has created a natural selection pressure for bacteria to adapt resistance. Bacterial resistance caused by metallo-β-lactamases (MβLs) has been the most prevalent in terms of posing a threat to human health. The New Delhi metallo-β-lactamase-1 (NDM-1) has been shown to be capable of hydrolyzing almost all β-lactams. In this work, eight aromatic Schiff bases 1-8 were prepared and identified by enzyme kinetic assays to be the potent inhibitors of NDM-1 (except 4). These molecules exhibited a more than 95 % inhibition, and an IC50 value in the range of 0.13-19 μM on the target enzyme, and 3 was found to be the most effective inhibitor (IC50 = 130 nM). Analysis of structure-activity relationship revealed that the o-hydroxy phenyl improved the inhibitory activity of Schiff bases on NDM-1. The inhibition mode assays including isothermal titration calorimetry (ITC) disclosed that both compounds 3 and 5 exhibited a reversibly mixed inhibition on NDM-1, with a Ki value of 1.9 and 10.8 μM, respectively. Antibacterial activity tests indicated that a dose of 64 μg·mL-1 Schiff bases resulted in 2-128-fold reduction in MICs of cefazolin on E. coli producing NDM-1 (except 4). Cytotoxicity assays showed that both Schiff bases 3 and 5 have low cytotoxicity on the mouse fibroblast (L929) cells at a concentration of up to 400 μM. Docking studies suggested that the hydroxyl group interacts with Gln123 and Glu152 of NDM-1, and the amino groups interact with the backbone amide groups of Glu152 and Asp223. This study provided a novel scaffold for the development of NDM-1 inhibitors.
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3
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Chigan JZ, Hu Z, Liu L, Xu YS, Ding HH, Yang KW. Quinolinyl sulfonamides and sulphonyl esters exhibit inhibitory efficacy against New Delhi metallo-β-lactamase-1 (NDM-1). Bioorg Chem 2022; 120:105654. [DOI: 10.1016/j.bioorg.2022.105654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/14/2022] [Accepted: 02/01/2022] [Indexed: 11/27/2022]
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4
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Chigan JZ, Li JQ, Ding HH, Xu YS, Liu L, Chen C, Yang KW. Hydroxamates as a potent skeleton for the development of metallo-β-lactamase inhibitors. Chem Biol Drug Des 2021; 99:362-372. [PMID: 34862744 DOI: 10.1111/cbdd.13990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/02/2021] [Accepted: 11/27/2021] [Indexed: 12/29/2022]
Abstract
Bacterial resistance caused by metallo-β-lactamases (MβLs) has become an emerging public health threat, and the development of MβLs inhibitor is an effective way to overcome the resistance. In this study, thirteen novel O-aryloxycarbonyl hydroxamates were constructed and assayed against MβLs. The obtained molecules specifically inhibited imipenemase-1 (IMP-1) and New Delhi metallo-β-lactamase-1, exhibiting an IC50 value in the range of 0.10-18.42 and 0.23-22.33 μM, respectively. The hydroxamate 5 was found to be the most potent inhibitor, with an IC50 of 0.1 and 0.23 μM using meropenem and cefazolin as substrates. ICP-MS analysis showed that 5 did not coordinate to the Zn(II) ions at the active site of IMP-1, while the rapid dilution, thermal shift and MALDI-TOF assays revealed that the hydroxamate formed a covalent bond with the enzyme. Cytotoxicity assays indicated that the hydroxamates have low toxicity in MCF-7 cells. This work provided a potent scaffold for the development of MβLs inhibitors.
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Affiliation(s)
- Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Yin-Sui Xu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Lu Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, China
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5
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Cafiero JH, Martini MC, Lozano MJ, Vacca C, Lagares A, Tomatis PE, Del Papa MF. BioF is a novel B2 metallo-β-lactamase from Pseudomonas sp. isolated from an on-farm biopurification system. Environ Microbiol 2021; 24:1247-1262. [PMID: 34725905 DOI: 10.1111/1462-2920.15822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/13/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022]
Abstract
Antimicrobial resistance represents a major global health concern and environmental bacteria are considered a source of resistance genes. Carbapenems are often used as the last antibiotic option to treat multidrug-resistant bacteria. Metallo-β-lactamases (MBLs) are able to render resistance to almost all β-lactam antibiotics, including carbapenems. Unfortunately, there are no inhibitors against MBLs for clinical use. Subclass B2 MBLs are the only enzymes working as strict carbapenemases, under-represented, encoded in chromosome genes and only functional as mono-zinc enzymes. Despite current efforts in MBLs inhibitor development, B2 carbapenemase activity is especially difficult to suppress, even in vitro. In this study we characterized BioF, a novel subclass B2 MBL identified in a new environmental Pseudomonas sp. strain isolated from an on-farm biopurification system (BPS). Although blaBioF is most likely a chromosomal gene, it is found in a genomic island and may represent a step previous to the horizontal transmission of B2 genes. The new B2 MBL is active as a mono-zinc enzyme and is a potent carbapenemase with incipient activity against some cephalosporins. BioF activity is not affected by excess zinc and is only inhibited at high metal chelator concentrations. The discovery and characterization of B2 MBL BioF as a potent carbapenemase in a BPS bacterial isolate emphasizes the importance of exploring antibiotic resistances existing in the environmental microbiota under the influence of human activities before they could emerge clinically.
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Affiliation(s)
- Juan Hilario Cafiero
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - María Carla Martini
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Mauricio Javier Lozano
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Carolina Vacca
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Antonio Lagares
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
| | - Pablo Emiliano Tomatis
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo y Esmeralda, Rosario, 2000, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, 2000, Argentina
| | - María Florencia Del Papa
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM, CCT-CONICET-La Plata), Universidad Nacional de La Plata, Calle 115 entre 49 y 50, La Plata, 1900, Argentina
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6
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A Novel Cooperative Metallo-β-Lactamase Fold Metallohydrolase from Pathogen Vibrio vulnificus Exhibits β-Lactam Antibiotic-Degrading Activities. Antimicrob Agents Chemother 2021; 65:e0032621. [PMID: 34228542 DOI: 10.1128/aac.00326-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Vibrio vulnificus is a pathogen that accounts for one of the highest mortality rates and is responsible for most reported seafood-related illnesses and deaths worldwide. Owing to the threats of pathogens with β-lactamase activity, it is important to identify and characterize β-lactamases with clinical significance. In this study, the protein sequence of the metallo-β-lactamase (MBL) fold metallohydrolase from V. vulnificus (designated Vmh) was analyzed, and its oligomeric state, β-lactamase activity, and metal binding ability were determined. BLASTp analysis indicated that the V. vulnificus Vmh protein showed no significant sequence identity with any experimentally identified Ambler class B MBLs or enzymes containing the MBL protein fold; it was also predicted to have a signal peptide of 19 amino acids at its N terminus and an MBL protein fold from amino acid residues 23 to 216. Recombinant V. vulnificus Vmh protein was overexpressed and purified. Analytical ultracentrifugation and electrospray ionization-mass spectrometry (MS) data demonstrated its monomeric state in an aqueous solution. Recombinant V. vulnificus Vmh protein showed broad degrading activities against β-lactam antibiotics, such as penicillins, cephalosporins, and imipenems, with kcat/Km values ranging from 6.23 × 102 to 1.02 × 104 M-1 s-1. The kinetic reactions of this enzyme exhibited sigmoidal behavior, suggesting the possibility of cooperativity. Zinc ions were required for the enzyme activity, which was abolished by adding the metal chelator EDTA. Inductively coupled plasma-MS indicated that this enzyme might bind two zinc ions per molecule as a cofactor.
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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8
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Li JQ, Gao H, Zhai L, Sun LY, Chen C, Chigan JZ, Ding HH, Yang KW. Dipyridyl-substituted thiosemicarbazone as a potent broad-spectrum inhibitor of metallo-β-lactamases. Bioorg Med Chem 2021; 38:116128. [PMID: 33862468 DOI: 10.1016/j.bmc.2021.116128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 11/17/2022]
Abstract
To combat the superbug infection caused by metallo-β-lactamases (MβLs), a dipyridyl-substituted thiosemicarbazone (DpC), was identified to be the broad-spectrum inhibitor of MβLs (NDM-1, VIM-2, IMP-1, ImiS, L1), with an IC50 value in the range of 0.021-1.08 µM. It reversibly and competitively inhibited NDM-1 with a Ki value of 10.2 nM. DpC showed broad-spectrum antibacterial effect on clinical isolate K. pneumonia, CRE, VRE, CRPA and MRSA, with MIC value ranged from 16 to 32 µg/mL, and exhibited synergistic antibacterial effect with meropenem on MβLs-producing bacteria, resulting in a 2-16-, 2-8-, and 8-fold reduction in MIC of meropenem against EC-MβLs, EC01-EC24, K. pneumonia, respectively. Moreover, mice experiments showed that DpC also had synergistic antibacterial action with meropenem. In this work, DpC was identified to be a potent scaffold for the development of broad-spectrum inhibitors of MβLs.
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Affiliation(s)
- Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le Zhai
- Shaanxi Key Laboratory of Phytochemistry, College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 72101, Shaanxi Province, PR China
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jia-Zhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Huan-Huan Ding
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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A Degradation Product from Hydrolysate of Imipenem with Imis Broad-Spectrum Inhibits Metallo-β-Lactamases. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.108141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Infections caused by metallo-β-lactamases (MβLs)-producing antibiotic-resistant bacteria pose a severe threat to public health. The synergistic use of current antibiotics in combination with MβL inhibitors is a promising therapeutic mode against these antibiotic-resistant bacteria. Objectives: The study aimed to probe the inhibition of MβLs and obtain the active component, P1, in the degradation product after imipenem was hydrolyzed by ImiS. Methods: The hydrolysis of two carbapenems with MβL ImiS was monitored by UV-Vis in real-time, and the degradation product from the leaving group produced after imipenem was hydrolyzed (but not for faropenem) was purified by HPLC to give one component, P1. Results: Kinetic assays revealed that P1 exhibited a broad-spectrum inhibition against VIM-2, NDM-1, ImiS, and L1, from three sub-classes of MβLs, with IC50 values of 8 - 32, 13.8 - 29.3, and 14.2 - 19.2 µM, using imipenem, cefazolin, and nitrocefin as substrates, respectively. Also, P1 showed synergistic antibacterial efficacy against drug-resistant Escherichia coli producing VIM-2, NDM-1, ImiS, and L1, in combination with antibiotics, restoring 16 to 32-fold and 32 to 128-fold efficacies of imipenem and cefazolin, respectively. Spectroscopic and Ellman's reagent analyses suggested that P1, a mercaptoethyl-form imidamide, is a mechanism-based inhibitor, while faropenem has no substrate inhibition, due to the lack of a leaving group. Conclusions: This work reveals that the hydrolysate of imipenem, a carbapenem with a good leaving group, can be used in screening for broad-spectrum inhibitors of MβLs.
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Li JQ, Chen C, Yao M, Sun LY, Gao H, Chigan J, Yang KW. Hydroxamic acid with benzenesulfonamide: An effective scaffold for the development of broad-spectrum metallo-β-lactamase inhibitors. Bioorg Chem 2020; 105:104436. [PMID: 33171408 DOI: 10.1016/j.bioorg.2020.104436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/10/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
Given that β-lactam antibiotic resistance mediated by metallo-β-lactamases (MβLs) seriously threatens human health, we designed and synthesized nineteen hydroxamic acids with benzenesulfonamide, which exhibited broad-spectrum inhibition against four tested MβLs ImiS, L1, VIM-2 and IMP-1 (except 6, 13 and 18 on IMP-1, and 18 on VIM-2), with an IC50 value in the range of 0.6-9.4, 1.3-27.4, 5.4-43.7 and 5.2-49.7 µM, respectively, and restored antibacterial activity of both cefazolin and meropenem, resulting in a 2-32-fold reduction in MIC of the antibiotics. Compound 17 shows reversible competitive inhibition on L1 with a Ki value of 2.5 µM and significantly reduced the bacterial load in the spleen and liver of mice infected by E. coli expressing L1. The docking studies suggest that 17 tightly binds to the Zn(Ⅱ) of VIM-2 and CphA by the oxygen atoms of sulfonamide group, but coordinates with the Zn(II) of L1 through the oxygen atoms of hydroxamic acid group. These studies reveal that the hydroxamic acids with benzenesulfonamide are the potent scaffolds for the development of MβL inhibitors.
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Affiliation(s)
- Jia-Qi Li
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Min Yao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jiazhu Chigan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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Metallo-β-Lactamase Inhibitors Inspired on Snapshots from the Catalytic Mechanism. Biomolecules 2020; 10:biom10060854. [PMID: 32503337 PMCID: PMC7356002 DOI: 10.3390/biom10060854] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
β-Lactam antibiotics are the most widely prescribed antibacterial drugs due to their low toxicity and broad spectrum. Their action is counteracted by different resistance mechanisms developed by bacteria. Among them, the most common strategy is the expression of β-lactamases, enzymes that hydrolyze the amide bond present in all β-lactam compounds. There are several inhibitors against serine-β-lactamases (SBLs). Metallo-β-lactamases (MBLs) are Zn(II)-dependent enzymes able to hydrolyze most β-lactam antibiotics, and no clinically useful inhibitors against them have yet been approved. Despite their large structural diversity, MBLs have a common catalytic mechanism with similar reaction species. Here, we describe a number of MBL inhibitors that mimic different species formed during the hydrolysis process: substrate, transition state, intermediate, or product. Recent advances in the development of boron-based and thiol-based inhibitors are discussed in the light of the mechanism of MBLs. We also discuss the use of chelators as a possible strategy, since Zn(II) ions are essential for substrate binding and catalysis.
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12
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Liu Y, Chen C, Sun LY, Gao H, Zhen JB, Yang KW. meta-Substituted benzenesulfonamide: a potent scaffold for the development of metallo-β-lactamase ImiS inhibitors. RSC Med Chem 2020; 11:259-267. [PMID: 33479632 PMCID: PMC7412727 DOI: 10.1039/c9md00455f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/26/2019] [Indexed: 01/25/2023] Open
Abstract
Metallo-β-lactamase (MβL) ImiS contributes to the emergence of carbapenem resistance. A potent scaffold, meta-substituted benzenesulfonamide, was constructed and assayed against MβLs. The twenty-one obtained molecules specifically inhibited ImiS (IC50 = 0.11-9.3 μM); 2g was found to be the best inhibitor (IC50 = 0.11 μM), and 1g and 2g exhibited partially mixed inhibition with K i of 8.0 and 0.55 μM. The analysis of the structure-activity relationship revealed that the meta-substitutes improved the inhibitory activity of the inhibitors. Isothermal titration calorimetry (ITC) assays showed that 2g reversibly inhibited ImiS. The benzenesulfonamides exhibited synergistic antibacterial effects against E. coli BL21 (DE3) cells with ImiS, resulting in a 2-4-fold reduction in the MIC of imipenem and meropenem. Also, mouse experiments showed that 2g had synergistic efficacy with meropenem and significantly reduced the bacterial load in the spleen and liver after a single intraperitoneal dose. Tracing the ImiS in living E. coli cells by RS at a super-resolution level (3D-SIM) showed that the target was initially associated on the surface of the cells, then there was a high density of uniform localization distributed in the cytosol of cells, and it finally accumulated in the formation of inclusion bodies at the cell poles. Docking studies suggested that the sulfonamide group acted as a zinc-binding group to coordinate with Zn(ii) and the residual amino acid within the CphA active center, tightly anchoring the inhibitor at the active site. This study provides a highly promising scaffold for the development of inhibitors of ImiS, even the B2 subclasses of MβLs.
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Affiliation(s)
- Ya Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Le-Yun Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Han Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Jian-Bin Zhen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education , College of Chemistry and Materials Science , Northwest University , Xi'an 710127 , P. R. China .
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13
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PFM-Like Enzymes Are a Novel Family of Subclass B2 Metallo-β-Lactamases from Pseudomonas synxantha Belonging to the Pseudomonas fluorescens Complex. Antimicrob Agents Chemother 2020; 64:AAC.01700-19. [PMID: 31685461 DOI: 10.1128/aac.01700-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022] Open
Abstract
A carbapenem-resistant Pseudomonas synxantha isolate recovered from chicken meat produced the novel carbapenemase PFM-1. That subclass B2 metallo-β-lactamase shared 71% amino acid identity with β-lactamase Sfh-1 from Serratia fonticola The bla PFM-1 gene was chromosomally located and likely acquired. Variants of PFM-1 sharing 90% to 92% amino acid identity were identified in bacterial species belonging to the Pseudomonas fluorescens complex, including Pseudomonas libanensis (PFM-2) and Pseudomonas fluorescens (PFM-3), highlighting that these species constitute reservoirs of PFM-like encoding genes.
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14
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Kang PW, Su JP, Sun LY, Gao H, Yang KW. 3-Bromopyruvate as a potent covalently reversible inhibitor of New Delhi metallo-β-lactamase-1 (NDM-1). Eur J Pharm Sci 2020; 142:105161. [DOI: 10.1016/j.ejps.2019.105161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/21/2019] [Accepted: 11/16/2019] [Indexed: 12/19/2022]
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15
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Ge Y, Xu LW, Liu Y, Sun LY, Gao H, Li JQ, Yang K. Dithiocarbamate as a Valuable Scaffold for the Inhibition of Metallo-β-Lactmases. Biomolecules 2019; 9:E699. [PMID: 31694268 PMCID: PMC6920875 DOI: 10.3390/biom9110699] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 01/02/2023] Open
Abstract
The 'superbug' infection caused by metallo-β-lactamases (MβLs) has grown into an emergent health threat. Given the clinical importance of MβLs, a novel scaffold, dithiocarbamate, was constructed. The obtained molecules, DC1, DC8 and DC10, inhibited MβLs NDM-1, VIM-2, IMP-1, ImiS and L1 from all three subclasses, exhibiting an IC50 < 26 μM. DC1 was found to be the best inhibitor of ImiS (IC50 < 0.22 μM). DC1-2, DC4, DC8 and DC10 restored antimicrobial effects of cefazolin and imipenem against E. coli-BL21, producing NDM-1, ImiS or L1, and DC1 showed the best inhibition of E. coli cells, expressing the three MβLs, resulting in a 2-16-fold reduction in the minimum inhibitory concentrations (MICs) of both antibiotics. Kinetics and isothermal titration calorimetry (ITC) assays showed that DC1 exhibited a reversible, and partially mixed inhibition, of NDM-1, ImiS and L1, with Ki values of 0.29, 0.14 and 5.06 µM, respectively. Docking studies suggest that the hydroxyl and carbonyl groups of DC1 form coordinate bonds with the Zn (II) ions, in the active center of NDM-1, ImiS and L1, thereby inhibiting the activity of the enzymes. Cytotoxicity assays showed that DC1, DC3, DC7 and DC9 have low toxicity in L929 mouse fibroblastic cells, at a dose of up to 250 μM. These studies revealed that the dithiocarbamate is a valuable scaffold for the development of MβLs inhibitors.
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Affiliation(s)
| | | | | | | | | | | | - Kewu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, the College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (Y.G.); (L.-W.X.); (Y.L.); (L.-Y.S.); (H.G.); (J.-Q.L.)
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16
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Halogen-Substituted Triazolethioacetamides as a Potent Skeleton for the Development of Metallo-β-Lactamase Inhibitors. Molecules 2019; 24:molecules24061174. [PMID: 30934584 PMCID: PMC6471427 DOI: 10.3390/molecules24061174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/13/2019] [Accepted: 03/23/2019] [Indexed: 11/17/2022] Open
Abstract
Metallo-β-lactamases (MβLs) are the target enzymes of β-lactam antibiotic resistance, and there are no effective inhibitors against MβLs available for clinic so far. In this study, thirteen halogen-substituted triazolethioacetamides were designed and synthesized as a potent skeleton of MβLs inhibitors. All the compounds displayed inhibitory activity against ImiS with an IC50 value range of 0.032⁻15.64 μM except 7. The chlorine substituted compounds (1, 2 and 3) inhibited NDM-1 with an IC50 value of less than 0.96 μM, and the fluorine substituted 12 and 13 inhibited VIM-2 with IC50 values of 38.9 and 2.8 μM, respectively. However, none of the triazolethioacetamides exhibited activity against L1 at inhibitor concentrations of up to 1 mM. Enzyme inhibition kinetics revealed that 9 and 13 are mixed inhibitors for ImiS with Ki values of 0.074 and 0.27μM using imipenem as the substrate. Docking studies showed that 1 and 9, which have the highest inhibitory activity against ImiS, fit the binding site of CphA as a replacement of ImiS via stable interactions between the triazole group bridging ASP120 and hydroxyl group bridging ASN233.
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17
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Xiang Y, Chen C, Wang WM, Xu LW, Yang KW, Oelschlaeger P, He Y. Rhodanine as a Potent Scaffold for the Development of Broad-Spectrum Metallo-β-lactamase Inhibitors. ACS Med Chem Lett 2018; 9:359-364. [PMID: 29670701 DOI: 10.1021/acsmedchemlett.7b00548] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/22/2018] [Indexed: 11/28/2022] Open
Abstract
A series of rhodanines was constructed, their Z-configuration was confirmed by small molecule X-ray crystal structures, and their activity against metallo-β-lactamases (MβLs) was measured. The obtained 26 molecules and a thioenolate specifically inhibited the MβL L1 with an IC50 range of 0.02-1.7 μM, and compounds 2h-m exhibited broad-spectrum inhibition of the MβLs NDM-1, VIM-2, ImiS, and L1 with IC50 values <16 μM. All inhibitors increased the antimicrobial effect of cefazolin against E. coli cells expressing L1, resulting in a 2-8-fold reduction in MIC. Docking studies suggested that the nitro (NDM-1, CphA, and L1) or carboxyl group (VIM-2) of 2l coordinates one or two Zn(II) ions, while the N-phenyl group of the inhibitor enhances its hydrophobic interaction with MβLs. These studies demonstrate that the diaryl-substituted rhodanines are good scaffolds for the design of future broad-spectrum inhibitors of MβLs.
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Affiliation(s)
- Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Cheng Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Wen-Ming Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Li-Wei Xu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, California 91766, United States
| | - Yuan He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Innovation Laboratory, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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18
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Xiang Y, Chang YN, Ge Y, Kang JS, Zhang YL, Liu XL, Oelschlaeger P, Yang KW. Azolylthioacetamides as a potent scaffold for the development of metallo-β-lactamase inhibitors. Bioorg Med Chem Lett 2017; 27:5225-5229. [PMID: 29122480 DOI: 10.1016/j.bmcl.2017.10.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/18/2017] [Accepted: 10/19/2017] [Indexed: 11/29/2022]
Abstract
In an effort to develop new inhibitors of metallo-β-lactamases (MβLs), twenty-eight azolylthioacetamides were synthesized and assayed against MβLs. The obtained benzimidazolyl and benzioxazolyl substituted 1-19 specifically inhibited the enzyme ImiS, and 10 was found to be the most potent inhibitor of ImiS with an IC50 value of 15 nM. The nitrobenzimidazolyl substituted 20-28 specifically inhibited NDM-1, with 27 being the most potent inhibitor with an IC50 value of 170 nM. Further studies with 10, 11, and 27 revealed a mixed inhibition mode with competitive and uncompetitive inhibition constants in a similar range as the IC50 values. These inhibitors resulted in a 2-4-fold decrease in imipenem MIC values using E. coli cells producing ImiS or NDM-1. While the source of uncompetitive (possibly allosteric) inhibition remains unclear, docking studies indicate that 10 and 11 may interact orthosterically with Zn2 in the active site of CphA, while 27 could bridge the two Zn(II) ions in the active site of NDM-1 via its nitro group.
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Affiliation(s)
- Yang Xiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ya-Nan Chang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Ying Ge
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Joon S Kang
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Yi-Lin Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Xiao-Long Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Innovation Laboratory of Chemical Biology, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China.
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19
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The Vibrio cholerae var regulon encodes a metallo-β-lactamase and an antibiotic efflux pump, which are regulated by VarR, a LysR-type transcription factor. PLoS One 2017; 12:e0184255. [PMID: 28898293 PMCID: PMC5595328 DOI: 10.1371/journal.pone.0184255] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/21/2017] [Indexed: 12/14/2022] Open
Abstract
The genome sequence of V. cholerae O1 Biovar Eltor strain N16961 has revealed a putative antibiotic resistance (var) regulon that is predicted to encode a transcriptional activator (VarR), which is divergently transcribed relative to the putative resistance genes for both a metallo-β-lactamase (VarG) and an antibiotic efflux-pump (VarABCDEF). We sought to test whether these genes could confer antibiotic resistance and are organised as a regulon under the control of VarR. VarG was overexpressed and purified and shown to have β-lactamase activity against penicillins, cephalosporins and carbapenems, having the highest activity against meropenem. The expression of VarABCDEF in the Escherichia coli (ΔacrAB) strain KAM3 conferred resistance to a range of drugs, but most significant resistance was to the macrolide spiramycin. A gel-shift analysis was used to determine if VarR bound to the promoter regions of the resistance genes. Consistent with the regulation of these resistance genes, VarR binds to three distinct intergenic regions, varRG, varGA and varBC located upstream and adjacent to varG, varA and varC, respectively. VarR can act as a repressor at the varRG promoter region; whilst this repression was relieved upon addition of β-lactams, these did not dissociate the VarR/varRG-DNA complex, indicating that the de-repression of varR by β-lactams is indirect. Considering that the genomic arrangement of VarR-VarG is strikingly similar to that of AmpR-AmpC system, it is possible that V. cholerae has evolved a system for resistance to the newer β-lactams that would prove more beneficial to the bacterium in light of current selective pressures.
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20
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Zhang YL, Zhang YJ, Wang WM, Yang KW. Synthesis and inhibitory activity of acetamidophosphonic acids against metallo-β-lactamases. PHOSPHORUS SULFUR 2017. [DOI: 10.1080/10426507.2016.1225741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Yi-Lin Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Lab, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China
- College of Biology Pharmacy and Food Engineering, Shangluo University, Shangluo, P. R. China
| | - Yue-Juan Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Lab, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China
| | - Wen-Ming Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Lab, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Chemical Biology Lab, College of Chemistry and Materials Science, Northwest University, Xi'an, P. R. China
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21
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Zhai L, Zhang YL, Kang JS, Oelschlaeger P, Xiao L, Nie SS, Yang KW. Triazolylthioacetamide: A Valid Scaffold for the Development of New Delhi Metallo-β-Lactmase-1 (NDM-1) Inhibitors. ACS Med Chem Lett 2016; 7:413-7. [PMID: 27096051 DOI: 10.1021/acsmedchemlett.5b00495] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/16/2016] [Indexed: 11/30/2022] Open
Abstract
The metallo-β-lactamases (MβLs) cleave the β-lactam ring of β-lactam antibiotics, conferring resistance against these drugs to bacteria. Twenty-four triazolylthioacetamides were prepared and evaluated as inhibitors of representatives of the three subclasses of MβLs. All these compounds exhibited specific inhibitory activity against NDM-1 with an IC50 value range of 0.15-1.90 μM, but no activity against CcrA, ImiS, and L1 at inhibitor concentrations of up to 10 μM. Compounds 4d and 6c are partially mixed inhibitors with K i values of 0.49 and 0.63 μM using cefazolin as the substrate. Structure-activity relationship studies reveal that replacement of hydrogen on the aromatic ring by chlorine, heteroatoms, or alkyl groups can affect bioactivity, while leaving the aromatic ring of the triazolylthiols unmodified maintains the inhibitory potency. Docking studies reveal that the typical potent inhibitors of NDM-1, 4d and 6c, form stable interactions in the active site of NDM-1, with the triazole bridging Zn1 and Zn2, and the amide interacting with Lys 211 (Lys224).
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Affiliation(s)
- Le Zhai
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
- College
of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji 721016, P. R. China
| | - Yi-Lin Zhang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Joon S. Kang
- Department
of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California 91768, United States
| | - Peter Oelschlaeger
- Department
of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, California 91766, United States
| | - Lin Xiao
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Sha-Sha Nie
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Ke-Wu Yang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry
of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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22
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SaxA-Mediated Isothiocyanate Metabolism in Phytopathogenic Pectobacteria. Appl Environ Microbiol 2016; 82:2372-2379. [PMID: 26873319 DOI: 10.1128/aem.04054-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/03/2016] [Indexed: 01/07/2023] Open
Abstract
Pectobacteria are devastating plant pathogens that infect a large variety of crops, including members of the family Brassicaceae. To infect cabbage crops, these plant pathogens need to overcome the plant's antibacterial defense mechanisms, where isothiocyanates are liberated by hydrolysis of glucosinolates. Here, we found that a Pectobacterium isolate from the gut of cabbage root fly larvae was particularly resistant to isothiocyanate and even seemed to benefit from the abundant Brassica root metabolite 2-phenylethyl isothiocyanate as a nitrogen source in an ecosystem where nitrogen is scarce. The Pectobacterium isolate harbored a naturally occurring mobile plasmid that contained a sax operon. We hypothesized that SaxA was the enzyme responsible for the breakdown of 2-phenylethyl isothiocyanate. Subsequently, we heterologously produced and purified the SaxA protein and characterized the recombinant enzyme. It hydrolyzed 2-phenylethyl isothiocyanate to yield the products carbonyl sulfide and phenylethylamine. It was also active toward another aromatic isothiocyanate but hardly toward aliphatic isothiocyanates. It belongs to the class B metal-dependent beta-lactamase fold protein family but was not, however, able to hydrolyze beta-lactam antibiotics. We discovered that several copies of the saxA gene are widespread in full and draft Pectobacterium genomes and therefore hypothesize that SaxA might be a new pathogenicity factor of the genus Pectobacterium, possibly compromising food preservation strategies using isothiocyanates.
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23
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Liu EJ, Sinclair A, Keefe AJ, Nannenga BL, Coyle BL, Baneyx F, Jiang S. EKylation: Addition of an Alternating-Charge Peptide Stabilizes Proteins. Biomacromolecules 2015; 16:3357-61. [DOI: 10.1021/acs.biomac.5b01031] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Erik J. Liu
- Department
of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
| | - Andrew Sinclair
- Department
of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
| | - Andrew J. Keefe
- Department
of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
| | - Brent L. Nannenga
- Department
of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
| | - Brandon L. Coyle
- Department
of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
| | - François Baneyx
- Department
of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
| | - Shaoyi Jiang
- Department
of Chemical Engineering, University of Washington, Box 351750, Seattle, Washington 98195, United States
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24
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Meini MR, Llarrull LI, Vila AJ. Overcoming differences: The catalytic mechanism of metallo-β-lactamases. FEBS Lett 2015; 589:3419-32. [PMID: 26297824 DOI: 10.1016/j.febslet.2015.08.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/27/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
Metallo-β-lactamases are the latest resistance mechanism of pathogenic and opportunistic bacteria against carbapenems, considered as last resort drugs. The worldwide spread of genes coding for these enzymes, together with the lack of a clinically useful inhibitor, have raised a sign of alarm. Inhibitor design has been mostly impeded by the structural diversity of these enzymes. Here we provide a critical review of mechanistic studies of the three known subclasses of metallo-β-lactamases, analyzed at the light of structural and mutagenesis investigations. We propose that these enzymes present a modular structure in their active sites that can be dissected into two halves: one providing the attacking nucleophile, and the second one stabilizing a negatively charged reaction intermediate. These are common mechanistic elements in all metallo-β-lactamases. Nucleophile activation does not necessarily requires a Zn(II) ion, but a Zn(II) center is essential for stabilization of the anionic intermediate. Design of a common inhibitor could be therefore approached based in these convergent mechanistic features despite the structural differences.
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Affiliation(s)
- María-Rocío Meini
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 200 Rosario, Argentina
| | - Leticia I Llarrull
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 200 Rosario, Argentina; Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 2000 Rosario, Argentina.
| | - Alejandro J Vila
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 570, 200 Rosario, Argentina; Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, 2000 Rosario, Argentina.
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25
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Liu XL, Shi Y, Kang JS, Oelschlaeger P, Yang KW. Amino Acid Thioester Derivatives: A Highly Promising Scaffold for the Development of Metallo-β-lactamase L1 Inhibitors. ACS Med Chem Lett 2015; 6:660-4. [PMID: 26101570 DOI: 10.1021/acsmedchemlett.5b00098] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/23/2015] [Indexed: 11/29/2022] Open
Abstract
In light of the biomedical significance of metallo-β-lactamases (MβLs), ten new mercaptoacetic acid thioester amino acid derivatives were synthesized and characterized. Biological activity assays indicated that all these synthesized compounds are very potent inhibitors of L1, exhibiting an IC50 value range of 0.018-2.9 μM and a K i value range of 0.11-0.95 μM using cefazolin as substrate. Partial thioesters also showed effective inhibitory activities against NDM-1 and ImiS with an IC50 value range of 12-96 and 3.6-65 μM, respectively. Also, all these thioesters increased susceptibility of E. coli cells expressing L1 to cefazolin, indicated by a 2-4-fold reduction in MIC of the antibiotic. Docking studies revealed potential binding modes of the two most potent L1 inhibitors to the active site in which the carboxylate group interacts with both Zn(II) ions and Ser221. This work introduces a highly promising scaffold for the development of metallo-β-lactamase L1 inhibitors.
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Affiliation(s)
- Xiao-Long Liu
- Key Laboratory of Synthetic and Natural Functional Molecule
Chemistry of Ministry of Education, College of Chemistry and Materials
Science, Northwest University, Xi’an 710127, P. R. China
| | - Ying Shi
- Key Laboratory of Synthetic and Natural Functional Molecule
Chemistry of Ministry of Education, College of Chemistry and Materials
Science, Northwest University, Xi’an 710127, P. R. China
| | - Joon S. Kang
- Department of Biological Sciences, California State Polytechnic University, Pomona, 3801 West Temple Avenue, Pomona, California 91768, United States
| | - Peter Oelschlaeger
- Department
of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, California 91766, United States
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule
Chemistry of Ministry of Education, College of Chemistry and Materials
Science, Northwest University, Xi’an 710127, P. R. China
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Yang SK, Kang JS, Oelschlaeger P, Yang KW. Azolylthioacetamide: A Highly Promising Scaffold for the Development of Metallo-β-lactamase Inhibitors. ACS Med Chem Lett 2015; 6:455-60. [PMID: 25893049 DOI: 10.1021/ml500534c] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 02/12/2015] [Indexed: 11/28/2022] Open
Abstract
A new scaffold, azolylthioacetamide, was constructed and assayed against metallo-β-lactamases (MβLs). The obtained molecules specifically inhibited MβL ImiS, and 1c was found to be the most potent inhibitor, with a K i = 1.2 μM using imipenem as substrate. Structure-activity relationships reveal that the aromatic carboxyl improves inhibitory activity of the inhibitors, but the aliphatic carboxyl does not. Compounds 1c-d and 1h-i showed the best antibacterial activities against E. coli BL21(DE3) cells producing CcrA or ImiS, resulting in 32- and 8-fold reduction in MIC values, respectively; 1c and 1f-j resulted in a reduction in MIC against P. aeruginosa. Docking studies revealed that 1a, 1c, and 1d fit tightly into the substrate binding site of CphA as a proxy for ImiS with the aromatic carboxylate forming interactions with Lys224, the Zn(II) ion, the backbone of Asn233, and hydrophobic portions of the inhibitors aligning with hydrophobic patches of the protein surface.
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Affiliation(s)
- Shao-Kang Yang
- Key Laboratory of Synthetic and Natural Functional Molecule
Chemistry of Ministry of Education, College of Chemistry and Materials
Science, Northwest University, Xi’an 710127, P. R. China
| | - Joon S. Kang
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California 91768, United States
| | - Peter Oelschlaeger
- Department
of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona, California 91766, United States
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule
Chemistry of Ministry of Education, College of Chemistry and Materials
Science, Northwest University, Xi’an 710127, P. R. China
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Aitha M, Moritz L, Sahu ID, Sanyurah O, Roche Z, McCarrick R, Lorigan GA, Bennett B, Crowder MW. Conformational dynamics of metallo-β-lactamase CcrA during catalysis investigated by using DEER spectroscopy. J Biol Inorg Chem 2015; 20:585-94. [PMID: 25827593 PMCID: PMC4733638 DOI: 10.1007/s00775-015-1244-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
Previous crystallographic and mutagenesis studies have implicated the role of a position-conserved hairpin loop in the metallo-β-lactamases in substrate binding and catalysis. In an effort to probe the motion of that loop during catalysis, rapid-freeze-quench double electron-electron resonance (RFQ-DEER) spectroscopy was used to interrogate metallo-β-lactamase CcrA, which had a spin label at position 49 on the loop and spin labels (at positions 82, 126, or 233) 20-35 Å away from residue 49, during catalysis. At 10 ms after mixing, the DEER spectra show distance increases of 7, 10, and 13 Å between the spin label at position 49 and the spin labels at positions 82, 126, and 233, respectively. In contrast to previous hypotheses, these data suggest that the loop moves nearly 10 Å away from the metal center during catalysis and that the loop does not clamp down on the substrate during catalysis. This study demonstrates that loop motion during catalysis can be interrogated on the millisecond time scale.
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Affiliation(s)
- Mahesh Aitha
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Lindsay Moritz
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Indra D. Sahu
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Omar Sanyurah
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Zahilyn Roche
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Robert McCarrick
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Gary A. Lorigan
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
| | - Brian Bennett
- Physics Department, Marquette University, 540 N. 15th Street, Milwaukee, Wisconsin 53233, USA, and Department of Biophysics, Medical College of Wisconsin, 8701 W. Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, 650 East High Street, Oxford, Ohio 45056, USA
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28
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Yang X, Zhou YJ, He P, Guo YH, Liu CJ, Yang KW. Activation free energy of Zn(II), Co(II) binding to metallo-β-lactamase ImiS. CHINESE CHEM LETT 2014. [DOI: 10.1016/j.cclet.2014.06.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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29
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Phelan EK, Miraula M, Selleck C, Ollis DL, Schenk G, Mitić N. Metallo-β-Lactamases: A Major Threat to Human Health. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajmb.2014.43011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Miraula M, Brunton CS, Schenk G, Mitić N. Identification and preliminary characterization of novel B3-type metallo-β-lactamases. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajmb.2013.34026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Feng L, Yang KW, Zhou LS, Xiao JM, Yang X, Zhai L, Zhang YL, Crowder MW. N-Heterocyclic dicarboxylic acids: Broad-spectrum inhibitors of metallo-β-lactamases with co-antibacterial effect against antibiotic-resistant bacteria. Bioorg Med Chem Lett 2012; 22:5185-9. [DOI: 10.1016/j.bmcl.2012.06.074] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 06/20/2012] [Accepted: 06/25/2012] [Indexed: 11/29/2022]
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32
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Gao HZ, Yang KW, Wu XL, Liu JY, Feng L, Xiao JM, Zhou LS, Jia C, Shi Z. Novel Conjugation of Norvancomycin–Fluorescein for Photodynamic Inactivation of Bacillus subtilis. Bioconjug Chem 2011; 22:2217-21. [DOI: 10.1021/bc200382d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hui-Zhou Gao
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Xiang-Long Wu
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Jia-Yun Liu
- Clinical Laboratory, Xijing Hospital, The Fourth Military Medical University
of Chinese PLA, Xi’an 710032, P. R. China
| | - Lei Feng
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Jian-Min Xiao
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Li-Sheng Zhou
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Chao Jia
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
| | - Zhen Shi
- Key Laboratory of Synthetic
and Natural Functional Molecule Chemistry of Ministry of Education;
College of Chemistry and Materials Science, Northwest University, Xi’an 710069, P. R. China
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Biochemical characterization of Sfh-I, a subclass B2 metallo-beta-lactamase from Serratia fonticola UTAD54. Antimicrob Agents Chemother 2011; 55:5392-5. [PMID: 21876065 DOI: 10.1128/aac.00429-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The subclass B2 metallo-β-lactamase (MBL) Sfh-I from Serratia fonticola UTAD54 was cloned and overexpressed in Escherichia coli. The recombinant protein binds one equivalent of zinc, as shown by mass spectrometry, and preferentially hydrolyzes carbapenem substrates. However, compared to other B2 MBLs, Sfh-I also shows limited hydrolytic activity against some additional substrates and is not inhibited by a second equivalent of zinc. These data confirm Sfh-I to be a subclass B2 metallo-β-lactamase with some distinctive properties.
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Fonseca F, Bromley EHC, Saavedra MJ, Correia A, Spencer J. Crystal structure of Serratia fonticola Sfh-I: activation of the nucleophile in mono-zinc metallo-β-lactamases. J Mol Biol 2011; 411:951-9. [PMID: 21762699 DOI: 10.1016/j.jmb.2011.06.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/20/2011] [Accepted: 06/24/2011] [Indexed: 02/02/2023]
Abstract
Metallo-β-lactamases (MBLs) or class B β-lactamases are zinc-dependent enzymes capable of inactivating almost all classes of β-lactam antibiotics. To date, no MBL inhibitors are available for clinical use. Of the three MBL subclasses, B2 enzymes, unlike those from subclasses B1 and B3, are fully active with one zinc ion bound and possess a narrow spectrum of activity, hydrolyzing carbapenem substrates almost exclusively. These remain the least studied MBLs. Sfh-I, originally identified from the aquatic bacterium Serratia fonticola UTAD54, is a divergent member of this group. Previous B2 MBL structures, available only for the CphA enzyme from Aeromonas hydrophila, all contain small molecules bound in their active sites. In consequence, the mechanism by which these enzymes activate the water nucleophile required for β-lactam hydrolysis remains to be unambiguously established. Here we report crystal structures of Sfh-I as a complex with glycerol and in the unliganded form, revealing for the first time the disposition of water molecules in the B2 MBL active site. Our data indicate that the hydrolytic water molecule is activated by His118 rather than by Asp120 and/or zinc. Consistent with this proposal, we show that the environment of His118 in B2 MBLs is distinct from that of the B1 and B3 enzymes, where this residue acts as a zinc ligand, and offer a structure-based mechanism for β-lactam hydrolysis by these enzymes.
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Affiliation(s)
- Fátima Fonseca
- Center for Environmental and Marine Studies and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal.
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35
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The mechanisms of catalysis by metallo beta-lactamases. Bioinorg Chem Appl 2010:576297. [PMID: 18551183 PMCID: PMC2422870 DOI: 10.1155/2008/576297] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 01/29/2008] [Accepted: 02/26/2008] [Indexed: 01/03/2023] Open
Abstract
Class B β-lactamases or metallo-β-lactamases (MBLs) require zinc ions to catalyse the hydrolysis of β-lactam antibiotics such as penicillins, cephalosporins, carbapenems, and cephamycins. There are no clinically useful inhibitors against MBLs which are responsible for the resistance of some bacteria to antibiotics. There are two metal-ion binding sites that have different zinc ligands but the exact roles of the metal-ion remain controversial, and distinguishing between their relative importance is complex. The metal-ion can act as a Lewis acid by co-ordination to the β-lactam carbonyl oxygen to facilitate nucleophilic attack and stabilise the negative charge developed on this oxygen in the tetrahedral intermediate anion. The metal-ion also lowers the pKa of the directly co-ordinated water molecule so that the metal-bound hydroxide ion is a better nucleophile than water and is used to attack the β-lactam carbonyl carbon. An intrinsic property of binuclear metallo hydrolytic enzymes that depend on a metal-bound water both as the attacking nucleophile and as a ligand for the second metal-ion is that this water molecule, which is consumed during hydrolysis of the substrate, has to be replaced to maintain the catalytic cycle. With MBL this is reflected in some unusual kinetic profiles.
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36
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The N-terminal domain of y-box binding protein-1 induces cell cycle arrest in g2/m phase by binding to cyclin d1. Int J Cell Biol 2010; 2009:243532. [PMID: 20414334 PMCID: PMC2855077 DOI: 10.1155/2009/243532] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 12/31/2009] [Indexed: 12/11/2022] Open
Abstract
Y-box binding protein YB-1 is a multifunctional protein involved in cell proliferation, regulation of transcription and translation. Our previous study indicated that disruption of one allele of Chk-YB-1b gene in DT-40 cells resulted in major defects in the cell cycle. The abnormalities seen in heterozygous mutants could be attributed to a dominant negative effect exerted by the disrupted YB-1 allele product. To test this hypothesis the N-terminal sequence of the YB-1 was fused with the third helix of antennapedia and the green fluorescent protein. These purified fusion proteins were introduced into rat hepatoma cells and their effect on cell proliferation was studied. Results indicate that the N-terminal 77 amino acid domain of the YB-1 protein induced the cells to arrest in G2/M phase of the cell cycle and undergo apoptosis. Additional deletion analysis indicated that as few as 26 amino acids of the N-terminus of YB-1 can cause these phenotypic changes. We further demonstrated that this N-terminal 77 amino acid domain of YB-1 sequesters cyclin D1 in the cytoplasm of cells at G2/M phase of cell cycle. We conclude that the N-terminal domain of YB-1 plays a major role in cell cycle progression through G2/M phase of cell cycle.
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37
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Salsbury FR, Crowder MW, Kingsmore SF, Huntley JJA. Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. J Mol Model 2008; 15:133-45. [PMID: 19039608 DOI: 10.1007/s00894-008-0410-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 07/19/2008] [Indexed: 11/28/2022]
Abstract
The beta-lactam-based antibiotics are among the most prescribed and effective antibacterial agents. Widespread use of these antibiotics, however, has created tremendous pressure for the emergence of resistance mechanisms in bacteria. The most common cause of antibiotic resistance is bacterial production of actamases that efficiently degrade antibiotics. The metallo-beta-lactamases are of particular clinical concern due to their transference between bacterial strains. We used molecular dynamics (MD) simulations to further study the conformational changes that occur due to binding of an inhibitor to the dicanzinc metallo-beta-lactamase from Bacteroides fragilis. Our studies confirm previous findings that the major flap is a major source of plasticity within the active site, therefore its dynamic response should be considered in drug development. However, our results also suggest the need for care in using MD simulations in evaluating loop mobility, both due to relaxation times and to the need to accurately model the zinc active site. Our study also reveals two new robust responses to ligand binding. First, there are specific localized changes in the zinc active site--a local loop flip--due to ligand intercalation that may be critical to the function of this enzyme. Second, inhibitor binding perturbs the dynamics throughout the protein, without otherwise perturbing the enzyme structure. These dynamic perturbations radiate outward from the active site and their existence suggests that long-range communication and dynamics may be important in the activity of this enzyme.
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Affiliation(s)
- Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston Salem, NC 27109, USA.
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Hu Z, Periyannan GR, Crowder MW. Folding strategy to prepare Co(II)-substituted metallo-beta-lactamase L1. Anal Biochem 2008; 378:177-83. [PMID: 18445468 PMCID: PMC2587373 DOI: 10.1016/j.ab.2008.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 04/01/2008] [Accepted: 04/03/2008] [Indexed: 11/24/2022]
Abstract
In an effort to overcome previous problems with the preparation of Co(II)-substituted metallo-beta-lactamase L1, two strategies were undertaken. Attempts to prepare Co(II)-substituted L1 using biological incorporation resulted in an enzyme that contained only 1 Eq of cobalt and exhibited no catalytic activity. Co(II)-substituted L1 could be prepared by refolding metal-free L1 in the presence of Co(II), and the resulting enzyme contained 1.8 Eq of cobalt, yielded a UV-Vis spectrum consistent with 5-coordinate Co(II), and exhibited a k(cat) of 63 s(-1) and K(m) of 20 microM when using nitrocefin as the substrate. Pre-steady-state fluorescence and UV-Vis studies demonstrated that refolded, Co(II)-substituted L1 uses the same kinetic mechanism as Zn(II)-containing L1, in which a reaction intermediate is formed when using nitrocefin as substrate. The described refolding strategy can be used to prepare other Co(II)-substituted Zn(II)-metalloenzymes, particularly those that contain a solvent-exposable disulfide, which often causes oxidation of Co(II) to Co(III).
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Affiliation(s)
- Zhenxin Hu
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
| | - Gopal R. Periyannan
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, OH 45056
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Sharma N, Hu Z, Crowder MW, Bennett B. Conformational changes in the metallo-beta-lactamase ImiS during the catalytic reaction: an EPR spectrokinetic study of Co(II)-spin label interactions. J Am Chem Soc 2008; 130:8215-22. [PMID: 18528987 DOI: 10.1021/ja0774562] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metallo-beta-lactamases are responsible for conferring antibiotic resistance on certain pathogenic bacteria. In consequence, the search for inhibitors that may be useful in combating antibiotic resistance has fueled much study of the active sites of these enzymes. There exists circumstantial evidence that the binding of substrates and inhibitors to metallo-beta-lactamases may involve binding to the organic part of the molecule, in addition to or prior to binding to one or more active site metal ions. It has also been postulated that a conformational change may accompany this putative binding. In the present study, electron paramagnetic resonance spectrokinetic study of a spin-labeled variant of the class B2 metallo-beta-lactamase ImiS identified movement of a component residue on a conserved alpha-helix in a catalytically competent time upon formation of a transient reaction intermediate with the substrate imipenem. In a significant subpopulation of ImiS, this conformational change was not associated with substrate binding to the active site metal ion but, rather, represents a distinct step in the reaction with ImiS. This observation has implications regarding the determinants of substrate specificity in metallo-beta-lactamases and the design of potentially clinically useful inhibitors.
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Affiliation(s)
- Narayan Sharma
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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40
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Llarrull LI, Tioni MF, Kowalski J, Bennett B, Vila AJ. Evidence for a dinuclear active site in the metallo-beta-lactamase BcII with substoichiometric Co(II). A new model for metal uptake. J Biol Chem 2007; 282:30586-95. [PMID: 17715135 DOI: 10.1074/jbc.m704613200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Metallo-beta-lactamases are zinc-dependent enzymes that constitute one of the main resistance mechanisms to beta-lactam antibiotics. Metallo-beta-lactamases have been characterized both in mono- and dimetallic forms. Despite many studies, the role of each metal binding site in substrate binding and catalysis is still unclear. This is mostly due to the difficulties in assessing the metal content and site occupancy in solution. For this reason, Co(II) has been utilized as a useful probe of the active site structure. We have employed UV-visible, EPR, and NMR spectroscopy to study Co(II) binding to the metallo-beta-lactamase BcII from Bacillus cereus. The spectroscopic features were attributed to the two canonical metal binding sites, the 3H (His(116), His(118), and His(196)) and DCH (Asp(120), Cys(221), and His(263)) sites. These data clearly reveal the coexistence of mononuclear and dinuclear Co(II)-loaded forms at Co(II)/enzyme ratios as low as 0.6. This picture is consistent with the macroscopic dissociation constants here determined from competition binding experiments. A spectral feature previously assigned to the DCH site in the dinuclear species corresponds to a third, weakly bound Co(II) site. The present work emphasizes the importance of using different spectroscopic techniques to follow the metal content and localization during metallo-beta-lactamase turnover.
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Affiliation(s)
- Leticia I Llarrull
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina
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41
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Badarau A, Damblon C, Page M. The activity of the dinuclear cobalt-beta-lactamase from Bacillus cereus in catalysing the hydrolysis of beta-lactams. Biochem J 2007; 401:197-203. [PMID: 16961465 PMCID: PMC1698674 DOI: 10.1042/bj20061002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Metallo-beta-lactamases are native zinc enzymes that catalyse the hydrolysis of beta-lactam antibiotics, but are also able to function with cobalt(II) and require one or two metal-ions for catalytic activity. The hydrolysis of cefoxitin, cephaloridine and benzylpenicillin catalysed by CoBcII (cobalt-substituted beta-lactamase from Bacillus cereus) has been studied at different pHs and metal-ion concentrations. An enzyme group of pK(a) 6.52+/-0.1 is found to be required in its deprotonated form for metal-ion binding and catalysis. The species that results from the loss of one cobalt ion from the enzyme has no significant catalytic activity and is thought to be the mononuclear CoBcII. It appears that dinuclear CoBcII is the active form of the enzyme necessary for turnover, while the mononuclear CoBcII is only involved in substrate binding. The cobalt-substituted enzyme is a more efficient catalyst than the native enzyme for the hydrolysis of some beta-lactam antibiotics suggesting that the role of the metal-ion is predominantly to provide the nucleophilic hydroxide, rather than to act as a Lewis acid to polarize the carbonyl group and stabilize the oxyanion tetrahedral intermediate.
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Affiliation(s)
- Adriana Badarau
- *Department of Chemical and Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, U.K
| | - Christian Damblon
- †Biological NMR Centre, Department of Biochemistry, Henry Wellcome Building, Lancaster Road, University of Leicester, Leicester LE1 9HN, U.K
| | - Michael I. Page
- *Department of Chemical and Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, U.K
- To whom correspondence should be addressed (email )
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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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Costello A, Periyannan G, Yang KW, Crowder MW, Tierney DL. Site-selective binding of Zn(II) to metallo-beta-lactamase L1 from Stenotrophomonas maltophilia. J Biol Inorg Chem 2006; 11:351-8. [PMID: 16489411 DOI: 10.1007/s00775-006-0083-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 01/20/2006] [Indexed: 11/27/2022]
Abstract
Extended X-ray absorption fine structure studies of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia containing 1 and 2 equiv of Zn(II) and containing 2 equiv of Zn(II) plus hydrolyzed nitrocefin are presented. The data indicate that the first, catalytically dominant metal ion is bound by L1 at the consensus Zn1 site. The data further suggest that binding of the first metal helps preorganize the ligands for binding of the second metal ion. The di-Zn enzyme displays a well-defined metal-metal interaction at 3.42 A. Reaction with the beta-lactam antibiotic nitrocefin results in a product-bound species, in which the ring-opened lactam rotates in the active site to present the S1 sulfur atom of nitrocefin to one of the metal ions for coordination. The product bridges the two metal ions, with a concomitant lengthening of the Zn-Zn interaction to 3.62 A.
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Affiliation(s)
- Alison Costello
- Department of Chemistry, University of New Mexico, 87131, Albuquerque, NM, USA
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