1
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Yamaguchi Y, Kato K, Ichimaru Y, Jin W, Sakai M, Abe M, Wachino JI, Arakawa Y, Miyagi Y, Imai M, Fukuishi N, Yamagata Y, Otsuka M, Fujita M, Kurosaki H. Crystal Structures of Metallo-β-Lactamase (IMP-1) and Its D120E Mutant in Complexes with Citrate and the Inhibitory Effect of the Benzyl Group in Citrate Monobenzyl Ester. J Med Chem 2021; 64:10019-10026. [PMID: 34242022 DOI: 10.1021/acs.jmedchem.1c00308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The emergence and rapid spread of carbapenem-resistant pathogens producing metallo-β-lactamases such as IMP-1 and NDM-1 have been of great concern in the global clinical setting. The X-ray crystal structures of IMP-1 from Serratia marcescens and its single mutant, D120E, in complexes with citrate were determined at resolutions of 2.00 and 1.85 Å, respectively. Two crystal structures indicate that a single mutation at position 120 caused a structural change around Zn1, where the geometry changes from a tetrahedron in the native IMP-1 to a square pyramid in D120E. Based on these two complex structures, the authors synthesized citrate monobenzyl ester 1 to evaluate the structural requirement for the inhibitory activity against IMP-1 and compared the inhibitory activities with nonsubstituted citrate. The introduction of a benzyl group into citrate enhanced the inhibitory activity in comparison to citrate (IC50 > 5 mM).
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Affiliation(s)
- Yoshihiro Yamaguchi
- Environmental Safety Center, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto 860-8555, Japan
| | - Koichi Kato
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan.,Faculty of Pharmacy, Meijo University, 150 Yagotoyama, Tempaku-ku, Nagoya, Aichi 468-8503, Japan
| | - Yoshimi Ichimaru
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Wanchun Jin
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Misa Sakai
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Miki Abe
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yukina Miyagi
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Masanori Imai
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Nobuyuki Fukuishi
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan.,Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hiromasa Kurosaki
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya, Aichi 463-8521, Japan
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2
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Chen JZ, Fowler DM, Tokuriki N. Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase. eLife 2020; 9:56707. [PMID: 32510322 PMCID: PMC7308095 DOI: 10.7554/elife.56707] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022] Open
Abstract
Metallo-β-lactamases (MBLs) degrade a broad spectrum of β-lactam antibiotics, and are a major disseminating source for multidrug resistant bacteria. Despite many biochemical studies in diverse MBLs, molecular understanding of the roles of residues in the enzyme’s stability and function, and especially substrate specificity, is lacking. Here, we employ deep mutational scanning (DMS) to generate comprehensive single amino acid variant data on a major clinical MBL, VIM-2, by measuring the effect of thousands of VIM-2 mutants on the degradation of three representative classes of β-lactams (ampicillin, cefotaxime, and meropenem) and at two different temperatures (25°C and 37°C). We revealed residues responsible for expression and translocation, and mutations that increase resistance and/or alter substrate specificity. The distribution of specificity-altering mutations unveiled distinct molecular recognition of the three substrates. Moreover, these function-altering mutations are frequently observed among naturally occurring variants, suggesting that the enzymes have continuously evolved to become more potent resistance genes.
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Affiliation(s)
- John Z Chen
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, United States.,Department of Bioengineering, University of Washington, Seattle, United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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3
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Spyrakis F, Celenza G, Marcoccia F, Santucci M, Cross S, Bellio P, Cendron L, Perilli M, Tondi D. Structure-Based Virtual Screening for the Discovery of Novel Inhibitors of New Delhi Metallo-β-lactamase-1. ACS Med Chem Lett 2018; 9:45-50. [PMID: 29348810 DOI: 10.1021/acsmedchemlett.7b00428] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/25/2017] [Indexed: 11/29/2022] Open
Abstract
Bacterial resistance has become a worldwide concern after the emergence of metallo-β-lactamases (MBLs). They represent one of the major mechanisms of bacterial resistance against beta-lactam antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 NDM-1, the most prevalent type, is extremely efficient in inactivating nearly all-available antibiotics including last resort carbapenems. No inhibitors for NDM-1 are currently available in therapy, making the spread of NDM-1 producing bacterial strains a serious menace. With this perspective, we performed a structure-based in silico screening of a commercially available library using FLAPdock and identified several, non-β-lactam derivatives as promising candidates active against NDM-1. The binding affinities of the highest scoring hits were measured in vitro revealing, for some of them, low micromolar affinity toward NDM-1. For the best inhibitors, efficacy against resistant bacterial strains overexpressing NDM-1 was validated, confirming their favorable synergistic effect in combination with the carbapenem Meropenem.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41100 Modena, Italy
| | - Giuseppe Celenza
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Francesca Marcoccia
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Matteo Santucci
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41100 Modena, Italy
| | - Simon Cross
- Dipartimento
di Chimica, Biologia e Biotechnologia, Università degli Studi di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Pierangelo Bellio
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Laura Cendron
- Dipartimento
di Biologia, Università degli Studi di Padova, Viale G. Colombo
3, 35131 Padova, Italy
| | - Mariagrazia Perilli
- Dipartimento
di Scienze cliniche applicate e biotecnologiche, Università dell’Aquila, Via Vetoio 1, 67100 L’Aquila, Italy
| | - Donatella Tondi
- Dipartimento
di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 103, 41100 Modena, Italy
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4
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Tehrani KHME, Martin NI. Thiol-Containing Metallo-β-Lactamase Inhibitors Resensitize Resistant Gram-Negative Bacteria to Meropenem. ACS Infect Dis 2017; 3:711-717. [PMID: 28820574 PMCID: PMC5644712 DOI: 10.1021/acsinfecdis.7b00094] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The prevalence of infections caused by metallo-β-lactamase (MBL) expressing Gram-negative bacteria has grown at an alarming rate in recent years. Despite the fact that MBLs can deactivate virtually all β-lactam antibiotics, there are as of yet no approved drugs available that inhibit their activity. We here examine the ability of previously reported thiol-based MBL inhibitors to synergize with meropenem and cefoperazone against a panel of Gram-negative carbapenem-resistant isolates expressing different β-lactamases. Among the compounds tested, thiomandelic acid 3 and 2-mercapto-3-phenylpropionic acid 4 were found to efficiently potentiate the activity of meropenem, especially against an imipenemase (IMP) producing strain of K. pneumoniae. In light of the zinc-dependent hydrolytic mechanism employed by MBLs, biophysical studies using isothermal titration calorimetry were also performed, revealing a correlation between the synergistic activity of thiols 3 and 4 and their zinc-binding ability with measured Kd values of 9.8 and 20.0 μM, respectively.
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Affiliation(s)
- Kamaleddin Haj Mohammad Ebrahim Tehrani
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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5
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Structural Insights into TMB-1 and the Role of Residues 119 and 228 in Substrate and Inhibitor Binding. Antimicrob Agents Chemother 2017; 61:AAC.02602-16. [PMID: 28559248 DOI: 10.1128/aac.02602-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/18/2017] [Indexed: 12/13/2022] Open
Abstract
Metallo-β-lactamases (MBLs) threaten the effectiveness of β-lactam antibiotics, including carbapenems, and are a concern for global public health. β-Lactam/β-lactamase inhibitor combinations active against class A and class D carbapenemases are used, but no clinically useful MBL inhibitor is currently available. Tripoli metallo-β-lactamase-1 (TMB-1) and TMB-2 are members of MBL subclass B1a, where TMB-2 is an S228P variant of TMB-1. The role of S228P was studied by comparisons of TMB-1 and TMB-2, and E119 was investigated through the construction of site-directed mutants of TMB-1, E119Q, E119S, and E119A (E119Q/S/A). All TMB variants were characterized through enzyme kinetic studies. Thermostability and crystallization analyses of TMB-1 were performed. Thiol-based inhibitors were investigated by determining the 50% inhibitory concentrations (IC50) and binding using surface plasmon resonance (SPR) for analysis of TMB-1. Thermostability measurements found TMB-1 to be stabilized by high NaCl concentrations. Steady-state enzyme kinetics analyses found substitutions of E119, in particular, substitutions associated with the penicillins, to affect hydrolysis to some extent. TMB-2 with S228P showed slightly reduced catalytic efficiency compared to TMB-1. The IC50 levels of the new thiol-based inhibitors were 0.66 μM (inhibitor 2a) and 0.62 μM (inhibitor 2b), and the equilibrium dissociation constant (KD ) of inhibitor 2a was 1.6 μM; thus, both were more potent inhibitors than l-captopril (IC50 = 47 μM; KD = 25 μM). The crystal structure of TMB-1 was resolved to 1.75 Å. Modeling of inhibitor 2b in the TMB-1 active site suggested that the presence of the W64 residue results in T-shaped π-π stacking and R224 cation-π interactions with the phenyl ring of the inhibitor. In sum, the results suggest that residues 119 and 228 affect the catalytic efficiency of TMB-1 and that inhibitors 2a and 2b are more potent inhibitors for TMB-1 than l-captopril.
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6
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Metallo-β-lactamase inhibitors by bioisosteric replacement: Preparation, activity and binding. Eur J Med Chem 2017; 135:159-173. [DOI: 10.1016/j.ejmech.2017.04.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/24/2017] [Accepted: 04/11/2017] [Indexed: 01/28/2023]
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7
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Christopeit T, Leiros HKS. Fragment-based discovery of inhibitor scaffolds targeting the metallo-β-lactamases NDM-1 and VIM-2. Bioorg Med Chem Lett 2016; 26:1973-7. [DOI: 10.1016/j.bmcl.2016.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/11/2022]
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8
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Christopeit T, Carlsen TJO, Helland R, Leiros HKS. Discovery of Novel Inhibitor Scaffolds against the Metallo-β-lactamase VIM-2 by Surface Plasmon Resonance (SPR) Based Fragment Screening. J Med Chem 2015; 58:8671-82. [DOI: 10.1021/acs.jmedchem.5b01289] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tony Christopeit
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Trine Josefine O. Carlsen
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ronny Helland
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hanna-Kirsti S. Leiros
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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9
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Majewski MW, Watson KD, Cho S, Miller PA, Franzblau SG, Miller MJ. Syntheses and Biological Evaluations of Highly Functionalized Hydroxamate Containing and N-Methylthio Monobactams as Anti-Tuberculosis and β-Lactamase Inhibitory Agents. MEDCHEMCOMM 2015; 7:141-147. [PMID: 26918106 DOI: 10.1039/c5md00340g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Both the resurgence of tuberculosis (TB) and antibiotic resistance continue to threaten modern healthcare and new means of combating pathogenic bacterial infections are needed. The syntheses of monobactams possessing hydroxamate and N-methylthio functionality are described, as well as their anti-TB, in vitro β-lactamase inhibitory, and general antimicrobial evaluations. A number of compounds exhibited significant anti-TB and β-lactamase inhibitory activity, with MIC values in the range of 25 to < 0.19 μM against Mycobacteria tuberculosis (M.tb), and Ki values in the range of 25-0.03 μM against purified NDM-1 and VIM-1 lystate metallo β-lactamases. This work suggests that these scaffolds may serve as promising leads in developing new antibiotics and/or β-lactamase inhibitors.
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Affiliation(s)
- Mark W Majewski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Kyle D Watson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, MIC 964, Rm. 412, University of Illinois at Chicago, IL, 60612, USA
| | - Patricia A Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Scott G Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, MIC 964, Rm. 412, University of Illinois at Chicago, IL, 60612, USA
| | - Marvin J Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
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10
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Xiao J, Fang M, Shi Y, Chen H, Shen B, Chen J, Lao X, Xu H, Zheng H. Identification and Validation Novel of VIM-2 Metallo-β-lactamase Tripeptide Inhibitors. Mol Inform 2015; 34:559-67. [DOI: 10.1002/minf.201400178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 03/16/2015] [Indexed: 11/07/2022]
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11
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Faridoon, Ul Islam N. An Update on the Status of Potent Inhibitors of Metallo-β-Lactamases. Sci Pharm 2013; 81:309-27. [PMID: 23833706 PMCID: PMC3700068 DOI: 10.3797/scipharm.1302-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/28/2013] [Indexed: 11/22/2022] Open
Abstract
The production of metallo-β-lactamases is the most important strategy by which pathogenic bacteria become resistant to currently known β-lactam antibiotics. The emergence of these enzymes is particularly concerning for the future treatment of bacterial infections. There are no clinically available drugs capable of inhibiting any of the metallo-β-lactamases, so there is an urgent need to find such inhibitors. In this review, an up-to-date status of the inhibitors investigated for the inhibition of metallo-β-lactamases has been given so that this rich source of structural information of presently known metallo-β-lactamases could be helpful in generating a broad-spectrum potent inhibitor of metallo-β-lactamases.
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Affiliation(s)
- Faridoon
- Chemistry Department, Islamia College University, Peshawar-25120, Pakistan
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12
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Kim Y, Tesar C, Mire J, Jedrzejczak R, Binkowski A, Babnigg G, Sacchettini J, Joachimiak A. Structure of apo- and monometalated forms of NDM-1--a highly potent carbapenem-hydrolyzing metallo-β-lactamase. PLoS One 2011; 6:e24621. [PMID: 21931780 PMCID: PMC3169612 DOI: 10.1371/journal.pone.0024621] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 08/14/2011] [Indexed: 11/19/2022] Open
Abstract
The New Delhi Metallo-β-lactamase (NDM-1) gene makes multiple pathogenic microorganisms resistant to all known β-lactam antibiotics. The rapid emergence of NDM-1 has been linked to mobile plasmids that move between different strains resulting in world-wide dissemination. Biochemical studies revealed that NDM-1 is capable of efficiently hydrolyzing a wide range of β-lactams, including many carbapenems considered as "last resort" antibiotics. The crystal structures of metal-free apo- and monozinc forms of NDM-1 presented here revealed an enlarged and flexible active site of class B1 metallo-β-lactamase. This site is capable of accommodating many β-lactam substrates by having many of the catalytic residues on flexible loops, which explains the observed extended spectrum activity of this zinc dependent β-lactamase. Indeed, five loops contribute "keg" residues in the active site including side chains involved in metal binding. Loop 1 in particular, shows conformational flexibility, apparently related to the acceptance and positioning of substrates for cleavage by a zinc-activated water molecule.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, United States of America
| | | | - Joseph Mire
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Andrew Binkowski
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - James Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, United States of America
- The University of Chicago, Department of Molecular Genetics & Cell Biology, Chicago, Illinois, United States of America
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13
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Karsten Baumgart AM, Molinari MA, de Oliveira Silveira AC. Prevalence of carbapenem resistant Pseudomonas aeruginosa and Acinetobacter baumannii in highcomplexity hospital. Braz J Infect Dis 2010. [DOI: 10.1016/s1413-8670(10)70089-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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14
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Weide T, Saldanha SA, Minond D, Spicer TP, Fotsing JR, Spaargaren M, Frère JM, Bebrone C, Sharpless KB, Hodder PS, Fokin VV. NH-1,2,3-Triazole-based Inhibitors of the VIM-2 Metallo-β-Lactamase: Synthesis and Structure-Activity Studies. ACS Med Chem Lett 2010; 1:150-154. [PMID: 20625539 DOI: 10.1021/ml900022q] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Metallo-ß-lactamases (MBL) are an emerging cause of bacterial resistance to antibiotic treatment. The VIM-2 ß-lactamase is the most commonly encountered MBL in clinical isolates worldwide. Described here are potent and selective small molecule inhibitors of VIM-2 containing the arylsulfonyl-NH-1,2,3-triazole chemotype that potentiate the efficacy of the ß-lactam, imipenem, in E. coli.
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Affiliation(s)
- Timo Weide
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - S. Adrian Saldanha
- Lead Identification, Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458
| | - Dmitriy Minond
- Lead Identification, Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458
| | - Timothy P. Spicer
- Lead Identification, Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458
| | - Joseph R. Fotsing
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Michael Spaargaren
- Lead Identification, Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458
| | - Jean-Marie Frère
- Centre for Protein Engineering, University of Liège, Allée du 6 Août B6, Sart-Tilman 4000 Liège, Belgium
| | - Carine Bebrone
- Centre for Protein Engineering, University of Liège, Allée du 6 Août B6, Sart-Tilman 4000 Liège, Belgium
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Peter S. Hodder
- Lead Identification, Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458
| | - Valery V. Fokin
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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15
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Oelschlaeger P, Ai N, Duprez KT, Welsh WJ, Toney JH. Evolving carbapenemases: can medicinal chemists advance one step ahead of the coming storm? J Med Chem 2010; 53:3013-27. [PMID: 20121112 DOI: 10.1021/jm9012938] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Oelschlaeger
- Chemistry Department and Center for Macromolecular Modeling and Materials Design, California State Polytechnic University, Pomona, California, USA.
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16
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Minond D, Saldanha SA, Subramaniam P, Spaargaren M, Spicer T, Fotsing JR, Weide T, Fokin VV, Sharpless KB, Galleni M, Bebrone C, Lassaux P, Hodder P. Inhibitors of VIM-2 by screening pharmacologically active and click-chemistry compound libraries. Bioorg Med Chem 2009; 17:5027-37. [PMID: 19553129 DOI: 10.1016/j.bmc.2009.05.070] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 05/22/2009] [Accepted: 05/27/2009] [Indexed: 12/27/2022]
Abstract
VIM-2 is an Ambler class B metallo-beta-lactamase (MBL) capable of hydrolyzing a broad-spectrum of beta-lactam antibiotics. Although the discovery and development of MBL inhibitors continue to be an area of active research, an array of potent, small molecule inhibitors is yet to be fully characterized for VIM-2. In the presented research, a compound library screening approach was used to identify and characterize VIM-2 inhibitors from a library of pharmacologically active compounds as well as a focused 'click' chemistry library. The four most potent VIM-2 inhibitors resulting from a VIM-2 screen were characterized by kinetic studies in order to determine K(i) and mechanism of enzyme inhibition. As a result, two previously described pharmacologic agents, mitoxantrone (1,4-dihydroxy-5,8-bis([2-([2-hydroxyethyl]amino)ethyl]amino)-9,10-anthracenedione) and 4-chloromercuribenzoic acid (pCMB) were found to be active, the former as a non-competitive inhibitor (K(i)=K(i)(')=1.5+/-0.2microM) and the latter as a slowly reversible or irreversible inhibitor. Additionally, two novel sulfonyl-triazole analogs from the click library were identified as potent, competitive VIM-2 inhibitors: N-((4-((but-3-ynyloxy)methyl)-1H-1,2,3-triazol-5-yl)methyl)-4-iodobenzenesulfonamide (1, K(i)=0.41+/-0.03microM) and 4-iodo-N-((4-(methoxymethyl)-1H-1,2,3-triazol-5-yl)methyl)benzenesulfonamide (2, K(i)=1.4+/-0.10microM). Mitoxantrone and pCMB were also found to potentiate imipenem efficacy in MIC and synergy assays employing Escherichia coli. Taken together, all four compounds represent useful chemical probes to further investigate mechanisms of VIM-2 inhibition in biochemical and microbiology-based assays.
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Affiliation(s)
- Dmitriy Minond
- Lead Identification, Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #1A1, Jupiter, 33458 FL, USA
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17
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Natarajan JK, Alumasa JN, Yearick K, Ekoue-Kovi KA, Casabianca LB, de Dios AC, Wolf C, Roepe PD. 4-N-, 4-S-, and 4-O-chloroquine analogues: influence of side chain length and quinolyl nitrogen pKa on activity vs chloroquine resistant malaria. J Med Chem 2008; 51:3466-79. [PMID: 18512900 DOI: 10.1021/jm701478a] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Using predictions from heme-quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure-function principles. We vary side chain length for both monoethyl and diethyl 4-N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4-O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4-N, 4-S, and 4-O derivatives vs mu-oxo dimeric heme, measure binding constants for monomeric vs dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs CQR malaria.
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Affiliation(s)
- Jayakumar K Natarajan
- Department of Chemistry, Center for Infectious Disease, Georgetown University, 37th and O Streets, Washington, DC 20057, USA
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18
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Yamaguchi Y, Jin W, Matsunaga K, Ikemizu S, Yamagata Y, Wachino JI, Shibata N, Arakawa Y, Kurosaki H. Crystallographic investigation of the inhibition mode of a VIM-2 metallo-beta-lactamase from Pseudomonas aeruginosa by a mercaptocarboxylate inhibitor. J Med Chem 2007; 50:6647-53. [PMID: 18052313 DOI: 10.1021/jm701031n] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The VIM-2 metallo-beta-lactamase enzyme from Pseudomonas aeruginosa catalyzes the hydrolysis of most beta-lactam antibiotics including carbapenems, and there are currently no potent inhibitors of such enzymes. We found rac-2-omega-phenylpropyl-3-mercaptopropionic acid, phenylC3SH, to be a potent inhibitor of VIM-2. The structure of the VIM-2-phenylC3SH complex was determined by X-ray crystallography to 2.3 A. The structure revealed that the thiol group of phenylC3SH bridged to the two zinc(II) ions and the phenyl group interacted with Tyr67(47) on loop1 near the active site, by pi-pi stacking interactions. The methylene group interacted with Phe61(42) located at the bottom of loop1 through CH-pi interactions. Dynamic movements were observed in Arg228(185) and Asn233(190) on loop2, compared with the native structure (PDB code: 1KO3 ). These results suggest that the above-mentioned four residues play important roles in the binding and recognition of inhibitors or substrates and in stabilizing a loop in the VIM-2 enzyme.
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Affiliation(s)
- Yoshihiro Yamaguchi
- Environmental Safety Center, Kumamoto University, Department of Structure-Function Physical Chemistry, Graduate School of Pharmaceutical Sciences, Japan.
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Horsfall LE, Garau G, Liénard BMR, Dideberg O, Schofield CJ, Frère JM, Galleni M. Competitive inhibitors of the CphA metallo-beta-lactamase from Aeromonas hydrophila. Antimicrob Agents Chemother 2007; 51:2136-42. [PMID: 17307979 PMCID: PMC1891371 DOI: 10.1128/aac.00866-06] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Various inhibitors of metallo-beta-lactamases have been reported; however, none are effective for all subgroups. Those that have been found to inhibit the enzymes of subclass B2 (catalytically active with one zinc) either contain a thiol (and show less inhibition towards this subgroup than towards the dizinc members of B1 and B3) or are inactivators behaving as substrates for the dizinc family members. The present work reveals that certain pyridine carboxylates are competitive inhibitors of CphA, a subclass B2 enzyme. X-ray crystallographic analyses demonstrate that pyridine-2,4-dicarboxylic acid chelates the zinc ion in a bidentate manner within the active site. Salts of these compounds are already available and undergoing biomedical testing for various nonrelated purposes. Pyridine carboxylates appear to be useful templates for the development of more-complex, selective, nontoxic inhibitors of subclass B2 metallo-beta-lactamases.
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Affiliation(s)
- L E Horsfall
- Centre d'Ingéniérie des Protéines, Université de Liège, Allée de 6 Aout B6, Sart-Tilman, Liège, Belgium
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Walsh TR, Toleman MA, Poirel L, Nordmann P. Metallo-beta-lactamases: the quiet before the storm? Clin Microbiol Rev 2005; 18:306-25. [PMID: 15831827 PMCID: PMC1082798 DOI: 10.1128/cmr.18.2.306-325.2005] [Citation(s) in RCA: 992] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ascendancy of metallo-beta-lactamases within the clinical sector, while not ubiquitous, has nonetheless been dramatic; some reports indicate that nearly 30% of imipenem-resistant Pseudomonas aeruginosa strains possess a metallo-beta-lactamase. Acquisition of a metallo-beta-lactamase gene will invariably mediate broad-spectrum beta-lactam resistance in P. aeruginosa, but the level of in vitro resistance in Acinetobacter spp. and Enterobacteriaceae is less dependable. Their clinical significance is further embellished by their ability to hydrolyze all beta-lactams and by the fact that there is currently no clinical inhibitor, nor is there likely to be for the foreseeable future. The genes encoding metallo-beta-lactamases are often procured by class 1 (sometimes class 3) integrons, which, in turn, are embedded in transposons, resulting in a highly transmissible genetic apparatus. Moreover, other gene cassettes within the integrons often confer resistance to aminoglycosides, precluding their use as an alternative treatment. Thus far, the metallo-beta-lactamases encoded on transferable genes include IMP, VIM, SPM, and GIM and have been reported from 28 countries. Their rapid dissemination is worrisome and necessitates the implementation of not just surveillance studies but also metallo-beta-lactamase inhibitor studies securing the longevity of important anti-infectives.
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Affiliation(s)
- Timothy R Walsh
- Department of Pathology and Microbiology, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom.
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