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Qin J, Wang Z, Xu H, Li Y, Zhou J, Yaxier N, Wang C, Fu P. IncX3 plasmid-mediated spread of blaNDM gene in Enterobacteriaceae among children in China. J Glob Antimicrob Resist 2024; 37:199-207. [PMID: 38641225 DOI: 10.1016/j.jgar.2024.03.021] [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: 11/02/2023] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/21/2024] Open
Abstract
OBJECTIVES The blaNDM gene was prevalent among children and became the predominant cause of severe infection in infants and children. This study aimed to investigate the epidemiology and molecular characteristics of blaNDM in Enterobacteriaceae among children in China. METHODS Carbapenem-resistant Enterobacteriaceae (CRE) were collected in the Children's Hospital of Fudan University from January 2016 to December 2022. Five carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48) were screened by PCR method. Multilocus sequence typing (MLST) was conducted for phylogenetic analyses. blaNDM-carrying plasmids were typed by PCR-based Incompatibility (Inc) typing method. Moreover, plasmid comparison was performed with 213 publicly available IncX3 plasmids. RESULTS A total of 330 CRE strains were enrolled, 96.4% of which carried carbapenemase genes. blaNDM gene accounted for 64.8% (214 strains) and included four variants, including blaNDM-1 (59.8%), blaNDM-5 (39.3%), blaNDM-7 (0.5%), and blaNDM-9 (0.5%). There were no predominant MLST lineages of blaNDM carrying strains. IncX3 was the major plasmid carrying blaNDM-1 (68.0%) and blaNDM-5 (72.6%) and was dominant in blaNDM-Klebsiella penumoniae (79.8%), blaNDM-Escherichia coli (58.2%), and blaNDM-Enterobacter cloacae (61.0%), respectively. Most (79.0%) clinical IncX3 plasmids in the world carried blaNDM, and the prevalence of blaNDM in IncX3 plasmids was more common in China (95.8%) than other countries (58.1%, P <0.01). CONCLUSION blaNDM is highly prevalent in CRE among children in China. The spread of blaNDM was mainly mediated by IncX3 plasmids. Surveillance and infection control on the spread of blaNDM among children are important.
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Affiliation(s)
- Jie Qin
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Zixuan Wang
- Department of Infectious Diseases, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Huihui Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Yijia Li
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Jinlan Zhou
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Nijiati Yaxier
- Orthopedics Department, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China
| | - Chuanqing Wang
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China.
| | - Pan Fu
- Lab of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Centre, Shanghai, China.
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Dong X, Liu W, Dong Y, Wang K, Li K, Bian L. Metallo-β-lactamase SMB-1 evolves into a more efficient hydrolase under the selective pressure of meropenem. J Inorg Biochem 2023; 247:112323. [PMID: 37478781 DOI: 10.1016/j.jinorgbio.2023.112323] [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: 04/18/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
Metallo-β-lactamases (MβLs) are the primary mechanism of resistance to carbapenem antibiotics. To elucidate how MβLs have evolved with the introduction and use of antibiotics, the mutation and evolution of SMB-1 from Serratia marcescens were investigated in microbial evolution plates containing discontinuous meropenem (MEM) concentration gradients. The results revealed 2-point mutations, A242G and S257R; 1 double-site mutation, C240G/E258G; and 3 frameshift mutations, M5, M12, and M13, which are all missense mutations situated at the C-terminus. Compared with that of the wild-type (WT), the minimum inhibitory concentrations (MICs) of MEM for A242G, C240G/E258G, M5, M12, and M13 increased at least 120-fold, and that of S257R increased 8-fold. The catalytic efficiency kcat/Km increased by 365% and 647%, respectively. Concerning the structural changes, the structure at the active site changed from an ordered structure to an unordered conformation. Simultaneously, the flexibility of loop 1 was enhanced. These changes increased the volume of the active site cavity; thus, this was more conducive to exposing the Zn2+ site, facilitating substrate binding and conversion to products. In A242G, structural changes in Gly-242 can be transmitted to the active region via a network of interactions between the side chains of Gly-242 and the amino acid side chains near the active pocket. Together, these results pointed to the process of persistent drug tolerance and resistance, the SMB-1 enzyme evolved into a more exquisite structure with increased flexibility and stability, and stronger hydrolysis activity via genetic mutations and structural changes.
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Affiliation(s)
- Xiaoting Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Wenli Liu
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Yuxuan Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kun Wang
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kewei Li
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Liujiao Bian
- College of Life Science, Northwest University, Xi'an 710069, China.
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3
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González LJ, Bahr G, González MM, Bonomo RA, Vila AJ. In-cell kinetic stability is an essential trait in metallo-β-lactamase evolution. Nat Chem Biol 2023; 19:1116-1126. [PMID: 37188957 DOI: 10.1038/s41589-023-01319-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/21/2023] [Indexed: 05/17/2023]
Abstract
Protein stability is an essential property for biological function. In contrast to the vast knowledge on protein stability in vitro, little is known about the factors governing in-cell stability. Here we show that the metallo-β-lactamase (MBL) New Delhi MBL-1 (NDM-1) is a kinetically unstable protein on metal restriction that has evolved by acquiring different biochemical traits that optimize its in-cell stability. The nonmetalated (apo) NDM-1 is degraded by the periplasmic protease Prc that recognizes its partially unstructured C-terminal domain. Zn(II) binding renders the protein refractory to degradation by quenching the flexibility of this region. Membrane anchoring makes apo-NDM-1 less accessible to Prc and protects it from DegP, a cellular protease degrading misfolded, nonmetalated NDM-1 precursors. NDM variants accumulate substitutions at the C terminus that quench its flexibility, enhancing their kinetic stability and bypassing proteolysis. These observations link MBL-mediated resistance with the essential periplasmic metabolism, highlighting the importance of the cellular protein homeostasis.
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Affiliation(s)
- Lisandro J González
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariano M González
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.
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Imkamp F, Kolesnik-Goldmann N, Bodendoerfer E, Zbinden R, Mancini S. Detection of Extended-Spectrum β-Lactamases (ESBLs) and AmpC in Class A and Class B Carbapenemase-Producing Enterobacterales. Microbiol Spectr 2022; 10:e0213722. [PMID: 36287018 PMCID: PMC9769508 DOI: 10.1128/spectrum.02137-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/30/2022] [Indexed: 01/06/2023] Open
Abstract
In carbapenemase-producing Enterobacterales (CPE) additional β-lactam resistance mechanisms such as extended-spectrum-β-lactamases (ESBL) and/or AmpC-β-lactamases are generally difficult to detect by phenotypical methods. Recently, a modified version of the CLSI ESBL confirmatory combination disc diffusion (CDD) test, which involves the addition of boronic acid and EDTA on discs containing ESBL and AmpC substrates ± inhibitors, has been proposed for the detection of ESBL in class A and class B CPE. Here, the performance of the modified CDD test was evaluated using 121 genotypically characterized class A and class B CPE. Also, the effectiveness of the NG-Test CTX-M-MULTI lateral flow immunoassay was evaluated for ESBL detection. For class A CPE (n = 47), the modified CDD method exhibited an equal specificity (95.7%) and a higher sensitivity (100%) compared to the standard method (91.7%). The CTX-M-MULTI test detected ESBL in all CTX-M-type ESBL producers (n = 23), whereas it was negative for all CTX-M-type ESBL-negative isolates (n = 24). For class B CPE (n = 71), the modified method significantly improved both sensitivity (95%) and specificity (100%) in detecting ESBL compared to the standard method (17.5% sensitivity and 83.9% specificity). In comparison, the CTX-M-MULTI led to identification of ESBL in all CTX-M-ESBL-producers (n = 39) and no false-positive signal was generated with the CTX-M-type-ESBL-negative isolates (n = 30). Furthermore, the modified CDD improved the robustness of the method for AmpC detection (inconclusive results were produced in 53/57 and 10/57 cases with the standard and modified method, respectively), although the sensitivity of the test was poor (23.5%). Here, we propose a practical and cost-effective approach combining the modified CDD and the CTX-M-MULTI test for detection of ESBL and/or AmpC in class A and B CPE. IMPORTANCE Antimicrobial resistance is a growing public health threat of broad concern worldwide. Timely detection of antibiotic resistance mechanisms can help to monitor and to curb the spread of resistant bacteria within the hospital setting as well as in the environment. In this work we report an accurate and affordable method to phenotypically identify difficult-to-detect resistance determinants in highly resistant (carbapenemase-producing) bacteria. This method may be implemented in any diagnostic microbiology lab and may reduce the underreporting of relevant resistance mechanisms.
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Affiliation(s)
- Frank Imkamp
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
| | | | - Elias Bodendoerfer
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
| | - Stefano Mancini
- Institute of Medical Microbiology, University Zurich, Zurich, Switzerland
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5
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Fung YH, Kong WP, Leung ASL, Du R, So PK, Wong WL, Leung YC, Chen YW, Wong KY. NDM-1 Zn1-binding residue His116 plays critical roles in antibiotic hydrolysis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140833. [PMID: 35944887 DOI: 10.1016/j.bbapap.2022.140833] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/28/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Bacteria expressing NDM-1 have been labeled as superbugs because it confers upon them resistance to a broad range of β-lactam antibiotics. The enzyme has a di‑zinc active centre, with the Zn2 site extensively studied. The roles of active-site Zn1 ligand residues are, however, still not fully understood. We carried out structure-function studies using the mutants, H116A, H116N, and H116Q. Zinc content analysis showed that Zn1 binding was weakened by 40 to 60% in the H116 mutants. The enzymatic-activity studies showed that the lower hydrolysis rates were mainly caused by their weaker substrate binding. The catalytic efficiency (kcat/Km) of the mutants followed the order: WT > > H116Q (decreased by 4-20 fold) > H116A (decreased by 20-700 fold) ≥ H116N (decreased by 6-800 fold). The maximum effect was observed on H116N against penicillin G, whereas ampicillin was not hydrolyzed at all. The fold-increase of Km values, which informs the weakening of substrate binding, were: H116A by 5-45 fold; H116N by 6-100 fold; H116Q by 2-10 fold. Molecular dynamics simulations suggested that the Zn1 site mutations affected the positions of Zn2 and the bridging hydroxide, by 0.8 to 1.2 Å, with the largest changes of ~1.5 Å observed on Zn2 ligand C221. A native hydrogen bond between H118 and D236 was disrupted in the H116N and H116Q mutants, which led to increased flexibility of loop 10. Consequently, residue N233 was no longer maintained at an optimal position for substrate binding. H116 connected loop 7 across Zn1 to loop 10, thereby contributed to the overall integrity. This work revealed that the H116-Zn1 interaction plays a critical role in defining the substrate-binding site. From these results, it can be inferred that inhibition strategies targeting the zinc ions may be a new direction for drug development.
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Affiliation(s)
- Yik-Hong Fung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wai-Po Kong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Alan Siu Lun Leung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Ruolan Du
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Pu-Kin So
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Wing-Leung Wong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yun-Chung Leung
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yu Wai Chen
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- The State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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6
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López C, Delmonti J, Bonomo RA, Vila AJ. Deciphering the evolution of metallo-β-lactamases: a journey from the test tube to the bacterial periplasm. J Biol Chem 2022; 298:101665. [PMID: 35120928 DOI: 10.1016/j.jbc.2022.101665] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the evolution of metallo-β-lactamases (MBLs) is fundamental to deciphering the mechanistic basis of resistance to carbapenems in pathogenic and opportunistic bacteria. Presently, these MBL producing pathogens are linked to high rates of morbidity and mortality worldwide. However, the study of the biochemical and biophysical features of MBLs in vitro provides an incomplete picture of their evolutionary potential, since this limited and artificial environment disregards the physiological context where evolution and selection take place. Herein, we describe recent efforts aimed to address the evolutionary traits acquired by different clinical variants of MBLs in conditions mimicking their native environment (the bacterial periplasm) and considering whether they are soluble or membrane-bound proteins. This includes addressing the metal content of MBLs within the cell under zinc starvation conditions, and the context provided by different bacterial hosts that result in particular resistance phenotypes. Our analysis highlights recent progress bridging the gap between in vitro and in-cell studies.
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Affiliation(s)
- Carolina López
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Juliana Delmonti
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA; Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina.
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Enzyme Inhibitors: The Best Strategy to Tackle Superbug NDM-1 and Its Variants. Int J Mol Sci 2021; 23:ijms23010197. [PMID: 35008622 PMCID: PMC8745225 DOI: 10.3390/ijms23010197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 01/06/2023] Open
Abstract
Multidrug bacterial resistance endangers clinically effective antimicrobial therapy and continues to cause major public health problems, which have been upgraded to unprecedented levels in recent years, worldwide. β-Lactam antibiotics have become an important weapon to fight against pathogen infections due to their broad spectrum. Unfortunately, the emergence of antibiotic resistance genes (ARGs) has severely astricted the application of β-lactam antibiotics. Of these, New Delhi metallo-β-lactamase-1 (NDM-1) represents the most disturbing development due to its substrate promiscuity, the appearance of variants, and transferability. Given the clinical correlation of β-lactam antibiotics and NDM-1-mediated resistance, the discovery, and development of combination drugs, including NDM-1 inhibitors, for NDM-1 bacterial infections, seems particularly attractive and urgent. This review summarizes the research related to the development and optimization of effective NDM-1 inhibitors. The detailed generalization of crystal structure, enzyme activity center and catalytic mechanism, variants and global distribution, mechanism of action of existing inhibitors, and the development of scaffolds provides a reference for finding potential clinically effective NDM-1 inhibitors against drug-resistant bacteria.
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Yan YH, Li W, Chen W, Li C, Zhu KR, Deng J, Dai QQ, Yang LL, Wang Z, Li GB. Structure-guided optimization of 1H-imidazole-2-carboxylic acid derivatives affording potent VIM-Type metallo-β-lactamase inhibitors. Eur J Med Chem 2021; 228:113965. [PMID: 34763944 DOI: 10.1016/j.ejmech.2021.113965] [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: 09/14/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023]
Abstract
Production of metallo-β-lactamases (MBLs) in bacterial pathogens is an important cause of resistance to the 'last-resort' carbapenem antibiotics. Development of effective MBL inhibitors to reverse carbapenem resistance in Gram-negative bacteria is still needed. We herein report X-ray structure-guided optimization of 1H-imidazole-2-carboxylic acid (ICA) derivatives by considering how to engage with the active-site flexible loops and improve penetration into Gram-negative bacteria. Structure-activity relationship studies revealed the importance of appropriate substituents at ICA 1-position to achieve potent inhibition to class B1 MBLs, particularly the Verona Integron-encoded MBLs (VIMs), mainly by involving ingenious interactions with the flexible active site loops as observed by crystallographic analyses. Of the tested ICA inhibitors, 55 displayed potent synergistic antibacterial activity with meropenem against engineered Escherichia coli strains and even intractable clinically isolated Pseudomonas aeruginosa producing VIM-2 MBL. The morphologic and internal structural changes of bacterial cells after treatment further demonstrated that 55 crossed the outer membrane and reversed the activity of meropenem. Moreover, 55 showed good pharmacokinetic and safety profile in vivo, which could be a potential candidate for combating VIM-mediated Gram-negative carbapenem resistance.
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Affiliation(s)
- Yu-Hang Yan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Wenfang Li
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wei Chen
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, China
| | - Chao Li
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, China
| | - Kai-Rong Zhu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Ji Deng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Qing-Qing Dai
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Sichuan, 610039, China
| | - Zhenling Wang
- State Key Laboratory of Biotherapy and Cancer Center, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Sichuan, 610041, China.
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Identification of a Novel blaNDM Variant, blaNDM-33, in an Escherichia coli Isolate from Hospital Wastewater in China. mSphere 2021; 6:e0077621. [PMID: 34643418 PMCID: PMC8513677 DOI: 10.1128/msphere.00776-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since the discovery of NDM-1 and the worldwide reporting of different variants have raised alarms concerning global health, the problem of carbapenem-resistant Enterobacterales (CRE) has become increasingly serious. Therefore, research on the hydrolytic activity and molecular structure of NDM variants is beneficial to the development of antibacterial drugs. NDM has been evolving into variants that possess different hydrolysis activities toward β-lactam antibiotics. Here, we characterized a novel blaNDM variant, named blaNDM-33, identified from a multidrug-resistant Escherichia coli strain from hospital sewage. NDM-33 differed from NDM-5 with a single-amino-acid substitution (A72T). blaNDM-5 was located in the Tn125-related blaNDM-33 region from an IncX3-type plasmid, pHD6415-NDM, that can be transferred horizontally. The genetic construct of blaNDM-33 showed higher MICs of carbapenems than a blaNDM-5 construct. Enzyme kinetics showed that NDM-33 had higher enzymatic activity for meropenem and cefazolin than NDM-5. The emergence of this novel NDM variant could pose a threat to public health because of its transferability and enhanced carbapenem activity. IMPORTANCE Our study described a novel NDM-33 variant from an E. coli strain isolated from hospital sewage, where it was associated with human disease and antibiotic exposure. Importantly, hospital sewage was increasingly considered to be related to CRE hosts. Pathogens were transmitted from reservoirs through direct and indirect contact, ingestion, and inhalation of contaminated water or aerosols. In addition, under the selective pressure of antibiotics, NDM variants will become the main strain in the hospital water system and evolve into high virulence and high resistance. The monitoring of NDM mutants is of great significance for preventing and controlling the evolution of superbugs.
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10
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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: 103] [Impact Index Per Article: 34.3] [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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11
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Kazi MI, Perry BW, Card DC, Schargel RD, Ali HB, Obuekwe VC, Sapkota M, Kang KN, Pellegrino MW, Greenberg DE, Castoe TA, Boll JM. Discovery and characterization of New Delhi metallo-β-lactamase-1 inhibitor peptides that potentiate meropenem-dependent killing of carbapenemase-producing Enterobacteriaceae. J Antimicrob Chemother 2021; 75:2843-2851. [PMID: 32591801 DOI: 10.1093/jac/dkaa242] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/20/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Metallo-β-lactamases (MBLs) are an emerging class of antimicrobial resistance enzymes that degrade β-lactam antibiotics, including last-resort carbapenems. Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are increasingly prevalent, but treatment options are limited. While several serine-dependent β-lactamase inhibitors are formulated with commonly prescribed β-lactams, no MBL inhibitors are currently approved for combinatorial therapies. New compounds that target MBLs to restore carbapenem activity against CPE are therefore urgently needed. Herein we identified and characterized novel synthetic peptide inhibitors that bound to and inhibited NDM-1, which is an emerging β-lactam resistance mechanism in CPE. METHODS We leveraged Surface Localized Antimicrobial displaY (SLAY) to identify and characterize peptides that inhibit NDM-1, which is a primary carbapenem resistance mechanism in CPE. Lead inhibitor sequences were chemically synthesized and MBCs and MICs were calculated in the presence/absence of carbapenems. Kinetic analysis with recombinant NDM-1 and select peptides tested direct binding and supported NDM-1 inhibitor mechanisms of action. Inhibitors were also tested for cytotoxicity. RESULTS We identified approximately 1700 sequences that potentiated carbapenem-dependent killing against NDM-1 Escherichia coli. Several also enhanced meropenem-dependent killing of other CPE. Biochemical characterization of a subset indicated the peptides penetrated the bacterial periplasm and directly bound NDM-1 to inhibit enzymatic activity. Additionally, each demonstrated minimal haemolysis and cytotoxicity against mammalian cell lines. CONCLUSIONS Our approach advances a molecular platform for antimicrobial discovery, which complements the growing need for alternative antimicrobials. We also discovered lead NDM-1 inhibitors, which serve as a starting point for further chemical optimization.
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Affiliation(s)
- Misha I Kazi
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Richard D Schargel
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Hana B Ali
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Victor C Obuekwe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Madhab Sapkota
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Katie N Kang
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - David E Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Joseph M Boll
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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12
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Shin WS, Nguyen ME, Bergstrom A, Jennings IR, Crowder MW, Muthyala R, Sham YY. Fragment-based screening and hit-based substructure search: Rapid discovery of 8-hydroxyquinoline-7-carboxylic acid as a low-cytotoxic, nanomolar metallo β-lactamase inhibitor. Chem Biol Drug Des 2021; 98:481-492. [PMID: 34148302 DOI: 10.1111/cbdd.13912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/25/2021] [Accepted: 06/06/2021] [Indexed: 12/13/2022]
Abstract
Metallo-β-lactamases (MBLs) are zinc-containing carbapenemases that inactivate a broad range of β-lactam antibiotics. There is a lack of β-lactamase inhibitors for restoring existing β-lactam antibiotics arsenals against common bacterial infections. Fragment-based screening of a non-specific metal chelator library demonstrates 8-hydroxyquinoline as a broad-spectrum nanomolar inhibitor against VIM-2 and NDM-1. A hit-based substructure search provided an early structure-activity relationship of 8-hydroxyquinolines and identified 8-hydroxyquinoline-7-carboxylic acid as a low-cytotoxic β-lactamase inhibitor that can restore β-lactam activity against VIM-2-expressing E. coli. Molecular modeling further shed structural insight into its potential mode of binding within the dinuclear zinc active site. 8-Hydroxyquinoline-7-carboxylic acid is highly stable in human plasma and human liver microsomal study, making it an ideal lead candidate for further development.
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Affiliation(s)
- Woo Shik Shin
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Megin E Nguyen
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | | | - Isabella R Jennings
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Ramaiah Muthyala
- Department of Experimental & Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Yuk Yin Sham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA.,Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN, USA
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13
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Mehta R, Rivera DD, Reilley DJ, Tan D, Thomas PW, Hinojosa A, Stewart AC, Cheng Z, Thomas CA, Crowder MW, Alexandrova AN, Fast W, Que EL. Visualizing the Dynamic Metalation State of New Delhi Metallo-β-lactamase-1 in Bacteria Using a Reversible Fluorescent Probe. J Am Chem Soc 2021; 143:8314-8323. [PMID: 34038127 DOI: 10.1021/jacs.1c00290] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) grants resistance to a broad spectrum of β-lactam antibiotics, including last-resort carbapenems, and is emerging as a global antibiotic resistance threat. Limited zinc availability adversely impacts the ability of NDM-1 to provide resistance, but a number of clinical variants have emerged that are more resistant to zinc scarcity (e.g., NDM-15). To provide a novel tool to better study metal ion sequestration in host-pathogen interactions, we describe the development of a fluorescent probe that reports on the dynamic metalation state of NDM within Escherichia coli. The thiol-containing probe selectively coordinates the dizinc metal cluster of NDM and results in a 17-fold increase in fluorescence intensity. Reversible binding enables competition and time-dependent studies that reveal fluorescence changes used to detect enzyme localization, substrate and inhibitor engagement, and changes to metalation state through the imaging of live E. coli using confocal microscopy. NDM-1 is shown to be susceptible to demetalation by intracellular and extracellular metal chelators in a live-cell model of zinc dyshomeostasis, whereas the NDM-15 metalation state is shown to be more resistant to zinc flux. The development of this reversible turn-on fluorescent probe for the metalation state of NDM provides a new tool for monitoring the impact of metal ion sequestration by host defense mechanisms and for detecting inhibitor-target engagement during the development of therapeutics to counter this resistance determinant.
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Affiliation(s)
- Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Dann D Rivera
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - David J Reilley
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Dominique Tan
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Pei W Thomas
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Abigail Hinojosa
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
| | - Alesha C Stewart
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California-Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Walter Fast
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Emily L Que
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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14
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Ali A, Gupta D, Khan AU. Role of non-active site residues in maintaining New Delhi metallo-β-lactamase-1(NDM-1) function: an approach of site-directed mutagenesis and docking. FEMS Microbiol Lett 2021; 368:fnz003. [PMID: 30624634 DOI: 10.1093/femsle/fnz003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/05/2019] [Indexed: 12/17/2023] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) has been known to hydrolyze nearly all β-lactam antibiotics, leading to a multidrug-resistant state. Hence, it is important to study its structure and function in relation to controlling infections caused by such resistant bacterial strains. Mutagenesis is one of the approaches used to explore it. No study has been performed to explore the role of non-active site residues in the enzyme activity. This study includes mutations of three non-active site residues to comprehend its structure and function simultaneously. Three non-active site laboratory mutants of NDM-1 were generated by site-directed mutagenesis. The minimum inhibitory concentrations of cefotaxime, cefoxitin, imipenem and meropenem were reduced by up to 4-fold for these mutants compared with wild-type. The hydrolytic activity of mutants was also found to be reduced. Mutants showed a significant change in secondary structure compared with wild-type, as determined by CD spectrophotometry. The catalytic properties and stability of these mutants were found to be reduced. Hence, it revealed an imperative role of non-active site residues in the enzymatic activity of NDM-1.
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15
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Carbapenem Use Is Driving the Evolution of Imipenemase 1 Variants. Antimicrob Agents Chemother 2021; 65:AAC.01714-20. [PMID: 33468463 DOI: 10.1128/aac.01714-20] [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: 08/10/2020] [Accepted: 12/07/2020] [Indexed: 12/18/2022] Open
Abstract
Metallo-β-lactamases (MBLs) are a growing clinical threat because they inactivate nearly all β-lactam-containing antibiotics, and there are no clinically available inhibitors. A significant number of variants have already emerged for each MBL subfamily. To understand the evolution of imipenemase (IMP) genes (bla IMP) and their clinical impact, 20 clinically derived IMP-1 like variants were obtained using site-directed mutagenesis and expressed in a uniform genetic background in Escherichia coli strain DH10B. Strains of IMP-1-like variants harboring S262G or V67F substitutions exhibited increased resistance toward carbapenems and decreased resistance toward ampicillin. Strains expressing IMP-78 (S262G/V67F) exhibited the largest changes in MIC values compared to IMP-1. In order to understand the molecular mechanisms of increased resistance, biochemical, biophysical, and molecular modeling studies were conducted to compare IMP-1, IMP-6 (S262G), IMP-10 (V67F), and IMP-78 (S262G/V67F). Finally, unlike most New Delhi metallo-β-lactamase (NDM) and Verona integron-encoded metallo-β-lactamase (VIM) variants, the IMP-1-like variants do not confer any additional survival advantage if zinc availability is limited. Therefore, the evolution of MBL subfamilies (i.e., IMP-6, -10, and -78) appears to be driven by different selective pressures.
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16
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Tietgen M, Leukert L, Sommer J, Kramer JS, Brunst S, Wittig I, Proschak E, Göttig S. Characterization of the novel OXA-213-like β-lactamase OXA-822 from Acinetobacter calcoaceticus. J Antimicrob Chemother 2021; 76:626-634. [PMID: 33201995 DOI: 10.1093/jac/dkaa488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/29/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This study analysed the novel carbapenem-hydrolysing class D β-lactamase OXA-822 identified in the clinical Acinetobacter calcoaceticus isolate AC_2117. METHODS WGS was employed for identification of β-lactamases. Micro-broth dilution was used for evaluation of antibiotic susceptibility of AC_2117 and transformants containing blaOXA-822. After heterologous purification of OXA-822, OXA-359 and OXA-213, enzyme kinetics were determined using spectrometry. The effect of OXA-822 upon meropenem treatment was analysed in the Galleria mellonella in vivo infection model. RESULTS OXA-822 is a member of the intrinsic OXA-213-like family found in A. calcoaceticus and Acinetobacter pittii. Amino acid sequence similarity to the nearest related OXA-359 was 97%. Production of OXA-822, OXA-359 and OXA-213 in Acinetobacter baumannii ATCC® 19606T resulted in elevated MICs for carbapenems (up to 16-fold). Penicillinase activity of the purified OXA-822 revealed high KM values, in the millimolar range, combined with high turnover numbers. OXA-822 showed the highest affinity to carbapenems, but affinity to imipenem was ∼10-fold lower compared with other carbapenems. Molecular modelling revealed that imipenem does not interact with a negatively charged side chain of OXA-822, as doripenem does, leading to the lower affinity. Presence of OXA-822 decreased survival of infected Galleria mellonella larvae after treatment with meropenem. Only 52.7% ± 7.7% of the larvae survived after 24 h compared with 90.9% ± 3.7% survival in the control group. CONCLUSIONS The novel OXA-822 from a clinical A. calcoaceticus isolate displayed penicillinase and carbapenemase activity in vitro, elevated MICs in different species and decreased carbapenem susceptibility in A. baumannii in vivo.
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Affiliation(s)
- Manuela Tietgen
- Institute for Medical Microbiology and Infection Control, Hospital of the Goethe University, Frankfurt am Main, Germany.,Faculty of Biological Sciences of the Goethe University, Frankfurt am Main, Germany.,University Center of Competence for Infection Control of the State of Hesse, Frankfurt am Main, Germany
| | - Laura Leukert
- Institute for Medical Microbiology and Infection Control, Hospital of the Goethe University, Frankfurt am Main, Germany
| | - Julian Sommer
- Institute for Medical Microbiology and Infection Control, Hospital of the Goethe University, Frankfurt am Main, Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, Hospital of the Goethe University, Frankfurt am Main, Germany
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17
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Aertker KMJ, Chan HTH, Lohans CT, Schofield CJ. Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism. J Biol Chem 2020; 295:16604-16613. [PMID: 32963107 PMCID: PMC7864059 DOI: 10.1074/jbc.ra120.014607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase-catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.
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Affiliation(s)
| | - H T Henry Chan
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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18
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Farhat N, Khan AU. Evolving trends of New Delhi Metallo-betalactamse (NDM) variants: A threat to antimicrobial resistance. INFECTION GENETICS AND EVOLUTION 2020; 86:104588. [PMID: 33038522 DOI: 10.1016/j.meegid.2020.104588] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 01/15/2023]
Abstract
The rapid emergence of carbapenemase producing Gram-negative bacterial strains exhibit broad-spectrum β-lactam resistance, especially New Delhi metallo-β-lactamase (NDM-1). It is a major public health threat as it catalyses the hydrolysis of a vast variety of β-lactam antibiotics, including carbapenems, which is the last choice for physicians to treat infections. NDM-1 and its variants are continuously spreading worldwide, in spite of constant efforts to control. Its clinical treatment remains challenging due to continuous evolution of new variants. A thorough structural study of all variants is required to develop new and effective inhibitors. This review focuses on the dissemination, position of substitution and carbapenemases activity of all the 28 NDM variants so far reported.
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Affiliation(s)
- Nabeela Farhat
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India.
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19
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Boyd SE, Livermore DM, Hooper DC, Hope WW. Metallo-β-Lactamases: Structure, Function, Epidemiology, Treatment Options, and the Development Pipeline. Antimicrob Agents Chemother 2020; 64:e00397-20. [PMID: 32690645 PMCID: PMC7508574 DOI: 10.1128/aac.00397-20] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Modern medicine is threatened by the global rise of antibiotic resistance, especially among Gram-negative bacteria. Metallo-β-lactamase (MBL) enzymes are a particular concern and are increasingly disseminated worldwide, though particularly in Asia. Many MBL producers have multiple further drug resistances, leaving few obvious treatment options. Nonetheless, and more encouragingly, MBLs may be less effective agents of carbapenem resistance in vivo, under zinc limitation, than in vitro Owing to their unique structure and function and their diversity, MBLs pose a particular challenge for drug development. They evade all recently licensed β-lactam-β-lactamase inhibitor combinations, although several stable agents and inhibitor combinations are at various stages in the development pipeline. These potential therapies, along with the epidemiology of producers and current treatment options, are the focus of this review.
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Affiliation(s)
- Sara E Boyd
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, United Kingdom
| | - David M Livermore
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - William W Hope
- Antimicrobial Pharmacodynamics and Therapeutics, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
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20
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Mehaffey MR, Ahn YC, Rivera DD, Thomas PW, Cheng Z, Crowder MW, Pratt RF, Fast W, Brodbelt JS. Elusive structural changes of New Delhi metallo-β-lactamase revealed by ultraviolet photodissociation mass spectrometry. Chem Sci 2020; 11:8999-9010. [PMID: 34123154 PMCID: PMC8163344 DOI: 10.1039/d0sc02503h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We use mass spectrometry (MS), under denaturing and non-denaturing solution conditions, along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation. Mapping changes in the abundances and distributions of fragment ions enables sensitive detection of structural alterations throughout the protein. Binding of three covalent inhibitors was characterized: a pentafluorphenyl ester, an O-aryloxycarbonyl hydroxamate, and ebselen. The first two inhibitors modify Lys211 and maintain dizinc binding, although the pentafluorophenyl ester is not selective (Lys214 and Lys216 are also modified). Ebselen reacts with the sole Cys (Cys208) and ejects Zn2 from the active site. For each inhibitor, native UVPD-MS enabled simultaneous detection of the closing of a substrate-binding beta-hairpin loop, identification of covalently-modified residue(s), reporting of the metalation state of the enzyme, and in the case of ebselen, observation of the induction of partial disorder in the C-terminus of the protein. Owing to the ability of native UVPD-MS to track structural changes and metalation state with high sensitivity, we further used this method to evaluate the impact of mutations found in NDM clinical variants. Changes introduced by NDM-4 (M154L) and NDM-6 (A233V) are revealed to propagate through separate networks of interactions to direct zinc ligands, and the combination of these two mutations in NDM-15 (M154L, A233V) results in additive as well as additional structural changes. Insight from UVPD-MS helps to elucidate how distant mutations impact zinc affinity in the evolution of this antibiotic resistance determinant. UVPD-MS is a powerful tool capable of simultaneous reporting of ligand binding, conformational changes and metalation state of NDM, revealing structural aspects of ligand recognition and clinical variants that have proven difficult to probe. We use mass spectrometry (MS) along with ultraviolet photodissociation (UVPD) to characterize structural variations in New Delhi metallo-β-lactamase (NDM) upon perturbation by ligands or mutation.![]()
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin Austin TX 78712 USA
| | - Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Dann D Rivera
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Pei W Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University Oxford OH 45056 USA
| | - R F Pratt
- Department of Chemistry, Wesleyan University Middletown CT 06459 USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin Austin TX 78712 USA
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21
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Behzadi P, García-Perdomo HA, Karpiński TM, Issakhanian L. Metallo-ß-lactamases: a review. Mol Biol Rep 2020; 47:6281-6294. [PMID: 32654052 DOI: 10.1007/s11033-020-05651-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/08/2020] [Indexed: 01/09/2023]
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22
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Raczynska JE, Imiolczyk B, Komorowska M, Sliwiak J, Czyrko-Horczak J, Brzezinski K, Jaskolski M. Flexible loops of New Delhi metallo-β-lactamase modulate its activity towards different substrates. Int J Biol Macromol 2020; 158:104-115. [PMID: 32353499 DOI: 10.1016/j.ijbiomac.2020.04.219] [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: 03/05/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 12/26/2022]
Abstract
Two accessory loop regions that are present in numerous variants of New Delhi metallo-β-lactamases (NDM) are important for the enzymatic activity. The first one is a flexible loop L3 that is located near the active site and is thought to play an important role in the catalytic process. The second region, Ω loop is located close to a structural element that coordinates two essential zinc ions. Both loops are not involved in any specific interactions with a substrate. Herein, we investigated how the length and hydrophobicity of loop L3 influence the enzymatic activity of NDMs, by analyzing mutants of NDM-1 with various deletions/point mutations within the L3 loop. We also investigated NDM variants with sequence variations/artificial deletions within the Ω loop. For all these variants we determined kinetic parameters for the hydrolysis of ampicillin, imipenem, and a chromogenic cephalosporin (CENTA). None of the mutations in the L3 loop completely abolished the enzymatic activity of NDM-1. Our results suggest that various elements of the loop play different roles in the hydrolysis of different substrates and the flexibility of the loop seems necessary to fulfill the requirements imposed by various substrates. Deletions within the Ω loop usually enhanced the enzymatic activity, particularly for the hydrolysis of ampicillin and imipenem. However, the exact role of the Ω loop in the catalytic reaction remains unclear. In our kinetic tests, the NDM enzymes were inhibited in the β-lactamase reaction by the CENTA substrate. We also present the X-ray crystal structures of the NDM-1, NDM-9 and NDM-12 proteins.
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Affiliation(s)
- Joanna E Raczynska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Imiolczyk
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marlena Komorowska
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Justyna Czyrko-Horczak
- Laboratory of Biochemistry and Structural Biology, Faculty of Chemistry, University of Bialystok, Poland
| | - Krzysztof Brzezinski
- Laboratory of Biochemistry and Structural Biology, Faculty of Chemistry, University of Bialystok, Poland.
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.
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23
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Zalucki YM, Jen FEC, Pegg CL, Nouwens AS, Schulz BL, Jennings MP. Evolution for improved secretion and fitness may be the selective pressures leading to the emergence of two NDM alleles. Biochem Biophys Res Commun 2020; 524:555-560. [DOI: 10.1016/j.bbrc.2020.01.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/24/2020] [Indexed: 01/07/2023]
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24
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Giannini E, González LJ, Vila AJ. A simple protocol to characterize bacterial cell-envelope lipoproteins in a native-like environment. Protein Sci 2019; 28:2004-2010. [PMID: 31518027 DOI: 10.1002/pro.3728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/04/2023]
Abstract
Physiological conditions in living cells are strictly regulated to allow, optimize, and coordinate biological processes. The bacterial cell envelope is the compartment where the communication with the external environment takes place. This involves membrane proteins, key players in many biological processes that ensure bacterial survival. The biochemical characterization of membrane proteins, either integral, lipidated or peripheral is challenging due to their mixed protein-lipid nature, making it difficult to purify and obtain considerable amounts of samples. In contrast to integral membrane proteins, lipidated proteins are usually purified as truncated soluble versions, neglecting the impact of the membrane environment. Here we report a simple and robust protocol to characterize bacterial lipidated proteins in spheroplasts from Escherichia coli using a β-lactamase as a model. The Metallo-β-lactamase NDM-1 is an enzyme anchored to the inner leaflet of the outer membrane of Gram-negative bacteria. Kinetic parameters and stability of the lipidated NDM-1 and the soluble unbound version (NDM-1 C26A) were measured in spheroplasts and periplasm, respectively. These studies revealed that membrane anchoring increases the KM of the enzyme, consequently decreasing the catalytic efficiency, while not affecting its kinetic stability. This approach can be used to characterize lipidated proteins avoiding the purification step while mimicking its native environment. This approach also helps in filling the gap between in vitro and in vivo studies.
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Affiliation(s)
- Estefanía Giannini
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
| | - Lisandro J González
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Alejandro J Vila
- Laboratorio de Metaloproteínas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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25
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Singha M, Kumar G, Jain D, Kumar N G, Ray D, Ghosh AS, Basak A. Rapid Fluorescent-Based Detection of New Delhi Metallo-β-Lactamases by Photo-Cross-Linking Using Conjugates of Azidonaphthalimide and Zinc(II)-Chelating Motifs. ACS OMEGA 2019; 4:10891-10898. [PMID: 31460186 PMCID: PMC6648899 DOI: 10.1021/acsomega.9b01145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A method for rapid detection of metallo-β-lactamases NDM-5 and NDM-7 using conjugates of azidonaphthalimide and Zn(II) chelating motifs (like sulfonamides, hydroxamate, and terpyridine) is described. Incubation and irradiation, followed by gel electrophoresis, clearly show the presence of NDMs. The o-sulfonamide-based probe has the highest efficiency of detection for both the NDMs. The proteins are detectable at nM concentrations, and the method is also selective, works both in vitro and in vivo, as revealed by cellular imaging and also with clinical isolates.
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Affiliation(s)
- Monisha Singha
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Gaurav Kumar
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Diamond Jain
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Ganesh Kumar N
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Debashis Ray
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Anindya S. Ghosh
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
| | - Amit Basak
- Department
of Chemistry, Department of Biotechnology, and School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur 721302 India
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26
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Maryam L, Khalid S, Ali A, Khan AU. Synergistic effect of doripenem in combination with cefoxitin and tetracycline in inhibiting NDM-1 producing bacteria. Future Microbiol 2019; 14:671-689. [PMID: 31161792 DOI: 10.2217/fmb-2019-0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Aim: To propose newer combinations of antibiotics effective against NDM-1-producing bacterial strains. Materials & methods: Antibiotics combinations were tested by checkerboard assay. NDM-1 protein/enzyme was expressed and purified to perform enzyme kinetics, circular dichroism and fluorescence spectroscopic studies. Results: Doripenem-cefoxitin combination and doripenem-tetracycline combination showed synergistic effect toward NDM-1-producing strains. The catalytic efficiency of NDM-1 enzyme was decreased drastically by 96.6% upon doripenem-cefoxitin treatment and by 35.54% after doripenem-tetracycline treatment. Conformational changes were observed in NDM-1 upon combination treatment. Conclusion: NDM-1-producing bacterial strains show resistance to multiple antibiotics but the combination of doripenem-cefoxitin and doripenem-tetracycline are effective against them. The combination of a carbapenem and cephamycin antibiotic is proposed for future treatment options against bacteria-producing NDM-1.
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Affiliation(s)
- Lubna Maryam
- Medical Microbiology & Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Shamsi Khalid
- Medical Microbiology & Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Abid Ali
- Medical Microbiology & Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Asad U Khan
- Medical Microbiology & Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
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27
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Chen C, Kramer JS, Brunst S, Proschak E, Scriba GK. Capillary electrophoresis‐based enzyme assays for β‐lactamase enzymes. Electrophoresis 2019; 40:2375-2381. [DOI: 10.1002/elps.201900104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Chunyang Chen
- Friedrich Schiller UniversityDepartment of Pharmaceutical/Medicinal Chemistry Jena Germany
| | - Jan S. Kramer
- Goethe UniversityInstitute of Pharmaceutical Chemistry Frankfurt Germany
| | - Steffen Brunst
- Goethe UniversityInstitute of Pharmaceutical Chemistry Frankfurt Germany
| | - Ewgenij Proschak
- Goethe UniversityInstitute of Pharmaceutical Chemistry Frankfurt Germany
| | - Gerhard K.E. Scriba
- Friedrich Schiller UniversityDepartment of Pharmaceutical/Medicinal Chemistry Jena Germany
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28
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Duan H, Liu X, Zhuo W, Meng J, Gu J, Sun X, Zuo K, Luo Q, Luo Y, Tang D, Shi H, Cao S, Hu J. 3D-QSAR and molecular recognition of Klebsiella pneumoniae NDM-1 inhibitors. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1579327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Huaichuan Duan
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Xinyu Liu
- Laboratory of tumor targeted and immune therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, People’s Republic of China
| | - Wei Zhuo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Jian Meng
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, People’s Republic of China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, People’s Republic of China
| | - Xin Sun
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Ke Zuo
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Qing Luo
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
| | - Yafei Luo
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, Chongqing, People’s Republic of China
| | - Dianyong Tang
- International Academy of Targeted Therapeutics and Innovation, Chongqing University of Arts and Sciences, Chongqing, People’s Republic of China
| | - Hubing Shi
- Laboratory of tumor targeted and immune therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, People’s Republic of China
| | - Shenghua Cao
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, People’s Republic of China
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, People’s Republic of China
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29
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Ali A, Kumar R, Iquebal MA, Jaiswal S, Kumar D, Khan AU. The role of conserved residues in the catalytic activity of NDM-1: an approach involving site directed mutagenesis and molecular dynamics. Phys Chem Chem Phys 2019; 21:17821-17835. [DOI: 10.1039/c9cp02734c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Drug degraded by enzyme and hence not targeted on to the cell leading to cell survival. After mutation leading to conformational changes and loss of function hence drug was not degraded and remained available for the target to lyse the cell.
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Affiliation(s)
- Abid Ali
- Medical Microbiology and Molecular Biology Lab
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University
- Aligarh 202002
- India
| | - Rakesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Mir Asif Iquebal
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Sarika Jaiswal
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Dinesh Kumar
- ICAR-Indian Agricultural Statistics Research Institute (IASRI)
- Library Avenue
- PUSA
- New Delhi –110012
- India
| | - Asad U. Khan
- Medical Microbiology and Molecular Biology Lab
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University
- Aligarh 202002
- India
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30
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Liu Z, Zhang R, Li W, Yang L, Liu D, Wang S, Shen J, Wang Y. Amino acid changes at the VIM-48 C-terminus result in increased carbapenem resistance, enzyme activity and protein stability. J Antimicrob Chemother 2018; 74:885-893. [DOI: 10.1093/jac/dky536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/17/2018] [Accepted: 11/23/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- Zhihai Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Agricultural Bio-pharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, China
| | - Rongmin Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wan Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Yang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Dejun Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
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31
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Wang Y, Tong MK, Chow KH, Cheng VCC, Tse CWS, Wu AKL, Lai RWM, Luk WK, Tsang DNC, Ho PL. Occurrence of Highly Conjugative IncX3 Epidemic Plasmid Carrying bla NDM in Enterobacteriaceae Isolates in Geographically Widespread Areas. Front Microbiol 2018; 9:2272. [PMID: 30294321 PMCID: PMC6158458 DOI: 10.3389/fmicb.2018.02272] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/05/2018] [Indexed: 11/13/2022] Open
Abstract
The emergence of New Delhi metallo-β-lactamase (NDM) in common enterobacterial species is a major concern for healthcare. Early reports have revealed that the spread of NDM involved diverse and heterogeneous plasmids. Recently, the involvement of a rare, IncX3 subtype plasmid has been increasingly recognized. Here, we studied the prevalence of IncX plasmid subtypes in 198 carbapenem-resistant Enterobacteriaceae, originating from a territory-wide active surveillance in Hong Kong in 2016. The complete sequences and biological features of the bla NDM-carrying plasmids were investigated. A total of 62 NDM-type, 21 OXA-48 type, 14 IMP-type, 8 KPC-type, 4 IMI-type producers, and 89 non-carbapenemase-producers were tested for presence of IncX subtypes. IncX3 (n = 60) was the most common subtype, followed by IncX4 (n = 6) and IncX1 (n = 2). The prevalence of IncX3 subtype in isolates producing NDM, other carbapenemase types and non-carbapenemase producers were 75.8, 21.3, and 3.4%, respectively (P < 0.001). An IncX3 plasmid (size ∼50 kb) was confirmed to carry bla NDM in 47 isolates of different enterobacterial species. Thirteen IncX3 plasmids originating from six healthcare regions in Hong Kong were completely sequenced. The results showed that the IncX3 plasmids carrying bla NDM share a high degree of sequence identity with a previously reported plasmid, pNDM-HN380 (GenBank accession JX104760), over the backbone and genetic load regions. A blast search further revealed the occurrence of identical or nearly identical IncX3 plasmids carrying bla NDM in other part of China, Korea, Myanmar, India, Oman, Kuwait, Italy, and Canada. Two IncX3 carrying bla NDM were investigated further. Conjugation experiments demonstrated that the IncX3 plasmids could be efficiently transferred to multiple enterobacterial species at frequencies that are comparable or higher than the epidemic IncFII plasmid carrying bla CTX-M (pHK01). In addition, efficient transfer of the NDM plasmids occurred over a range of temperatures. In conclusion, this study demonstrated the important role played by IncX3 in the dissemination of NDM and the occurrence of pNDM-HN380-like plasmids in geographically widespread areas. The high mobility of IncX3 plasmid across different enterobacterial species highlights the ability of this plasmid replicon to be an important vehicle in worldwide dissemination of NDM.
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Affiliation(s)
- Ya Wang
- Department of Microbiology, Queen Mary Hospital, Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Man-Ki Tong
- Department of Microbiology, Queen Mary Hospital, Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Kin-Hung Chow
- Department of Microbiology, Queen Mary Hospital, Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
| | - Cindy Wing-Sze Tse
- Department of Clinical Pathology, Kwong Wah Hospital, Hospital Authority, Hong Kong, China
| | - Alan Ka-Lun Wu
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hospital Authority, Hong Kong, China
| | - Raymond Wai-Man Lai
- Department of Microbiology, Prince of Wales Hospital, Hospital Authority, Hong Kong, China
| | - Wei-Kwang Luk
- Department of Pathology, Tseung Kwan O Hospital, Hospital Authority, Hong Kong, China
| | - Dominic Ngai-Chong Tsang
- Department of Clinical Pathology, Queen Elizabeth Hospital, Hospital Authority, Hong Kong, China
| | - Pak-Leung Ho
- Department of Microbiology, Queen Mary Hospital, Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
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32
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Kang JS, Zhang AL, Faheem M, Zhang CJ, Ai N, Buynak JD, Welsh WJ, Oelschlaeger P. Virtual Screening and Experimental Testing of B1 Metallo-β-lactamase Inhibitors. J Chem Inf Model 2018; 58:1902-1914. [PMID: 30107123 DOI: 10.1021/acs.jcim.8b00133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The global rise of metallo-β-lactamases (MBLs) is problematic due to their ability to inactivate most β-lactam antibiotics. MBL inhibitors that could be coadministered with and restore the efficacy of β-lactams are highly sought after. In this study, we employ virtual screening of candidate MBL inhibitors without thiols or carboxylates to avoid off-target effects using the Avalanche software package, followed by experimental validation of the selected compounds. As target enzymes, we chose the clinically relevant B1 MBLs NDM-1, IMP-1, and VIM-2. Among 32 compounds selected from an approximately 1.5 million compound library, 6 exhibited IC50 values less than 40 μM against NDM-1 and/or IMP-1. The most potent inhibitors of NDM-1, IMP-1, and VIM-2 had IC50 values of 19 ± 2, 14 ± 1, and 50 ± 20 μM, respectively. While chemically diverse, the most potent inhibitors all contain combinations of hydroxyl, ketone, ester, amide, or sulfonyl groups. Docking studies suggest that these electron-dense moieties are involved in Zn(II) coordination and interaction with protein residues. These novel scaffolds could serve as the basis for further development of MBL inhibitors. A procedure for renaming NDM-1 residues to conform to the class B β-lactamase (BBL) numbering scheme is also included.
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Affiliation(s)
- Joon S Kang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States.,Department of Biological Sciences , California State Polytechnic University , Pomona , California 91768-2557 , United States
| | - Antonia L Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Mohammad Faheem
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Charles J Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
| | - Ni Ai
- Pharmaceutical Informatics Institute, School of Pharmaceutical Sciences , Zhejiang University , Zhejiang 31005 , People's Republic of China
| | - John D Buynak
- Department of Chemistry , Southern Methodist University , Dallas , Texas 75275-0314 , United States
| | - William J Welsh
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, and Division of Chem Informatics, Biomedical Informatics Shared Resource, Rutgers-Cancer Institute of New Jersey , The State University of New Jersey , Piscataway , New Jersey 08854-8021 , United States
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy , Western University of Health Sciences , Pomona , California 91766-1854 , United States
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33
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Cheng Z, Thomas PW, Ju L, Bergstrom A, Mason K, Clayton D, Miller C, Bethel CR, VanPelt J, Tierney DL, Page RC, Bonomo RA, Fast W, Crowder MW. Evolution of New Delhi metallo-β-lactamase (NDM) in the clinic: Effects of NDM mutations on stability, zinc affinity, and mono-zinc activity. J Biol Chem 2018; 293:12606-12618. [PMID: 29909397 PMCID: PMC6093243 DOI: 10.1074/jbc.ra118.003835] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/07/2018] [Indexed: 11/06/2022] Open
Abstract
Infections by carbapenem-resistant Enterobacteriaceae are difficult to manage owing to broad antibiotic resistance profiles and because of the inability of clinically used β-lactamase inhibitors to counter the activity of metallo-β-lactamases often harbored by these pathogens. Of particular importance is New Delhi metallo-β-lactamase (NDM), which requires a di-nuclear zinc ion cluster for catalytic activity. Here, we compare the structures and functions of clinical NDM variants 1-17. The impact of NDM variants on structure is probed by comparing melting temperature and refolding efficiency and also by spectroscopy (UV-visible, 1H NMR, and EPR) of di-cobalt metalloforms. The impact of NDM variants on function is probed by determining the minimum inhibitory concentrations of various antibiotics, pre-steady-state and steady-state kinetics, inhibitor binding, and zinc dependence of resistance and activity. We observed only minor differences among the fully loaded di-zinc enzymes, but most NDM variants had more distinguishable selective advantages in experiments that mimicked zinc scarcity imposed by typical host defenses. Most NDM variants exhibited improved thermostability (up to ∼10 °C increased Tm ) and improved zinc affinity (up to ∼10-fold decreased Kd, Zn2). We also provide first evidence that some NDM variants have evolved the ability to function as mono-zinc enzymes with high catalytic efficiency (NDM-15, ampicillin: kcat/Km = 5 × 106 m-1 s-1). These findings reveal the molecular mechanisms that NDM variants have evolved to overcome the combined selective pressures of β-lactam antibiotics and zinc deprivation.
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Affiliation(s)
- Zishuo Cheng
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Pei W Thomas
- the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center of Infectious Disease, University of Texas, Austin, Texas 78712
| | - Lincheng Ju
- the Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Alexander Bergstrom
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Kelly Mason
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Delaney Clayton
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Callie Miller
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Christopher R Bethel
- the Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, and
| | - Jamie VanPelt
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - David L Tierney
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056,
| | - Richard C Page
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056,
| | - Robert A Bonomo
- the Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, and
- the Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics, and Bioinformatics, Case Western Reserve University (CWRU)-Cleveland Veterans Administration Medical Center (VAMC) Center of Antimicrobial Resistance and Epidemiology (CARES), Cleveland, Ohio 44106
| | - Walter Fast
- the Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne Center of Infectious Disease, University of Texas, Austin, Texas 78712,
| | - Michael W Crowder
- From the Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056,
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34
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Non-active site mutation (Q123A) in New Delhi metallo-β-lactamase (NDM-1) enhanced its enzyme activity. Int J Biol Macromol 2018; 112:1272-1277. [DOI: 10.1016/j.ijbiomac.2018.02.091] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 11/18/2022]
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35
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Ju LC, Cheng Z, Fast W, Bonomo RA, Crowder MW. The Continuing Challenge of Metallo-β-Lactamase Inhibition: Mechanism Matters. Trends Pharmacol Sci 2018; 39:635-647. [PMID: 29680579 DOI: 10.1016/j.tips.2018.03.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/16/2018] [Accepted: 03/22/2018] [Indexed: 01/16/2023]
Abstract
Metallo-β-lactamases (MBLs) are a significant clinical problem because they hydrolyze and inactivate nearly all β-lactam-containing antibiotics. These 'lifesaving drugs' constitute >50% of the available contemporary antibiotic arsenal. Despite the global spread of MBLs, MBL inhibitors have not yet appeared in clinical trials. Most MBL inhibitors target active site zinc ions and vary in mechanism from ternary complex formation to metal ion stripping. Importantly, differences in mechanism can impact pharmacology in terms of reversibility, target selectivity, and structure-activity relationship interpretation. This review surveys the mechanisms of MBL inhibitors and describes methods that determine the mechanism of inhibition to guide development of future therapeutics.
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Affiliation(s)
- Lin-Cheng Ju
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, PR China; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA.
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
| | - Robert A Bonomo
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics, and Bioinformatics and the CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, OH 44106, USA
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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Structural and functional insight of New Delhi Metallo β-lactamase-1 variants. Future Med Chem 2018; 10:221-229. [DOI: 10.4155/fmc-2017-0143] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
New Delhi Metallo β-lactamase-1 (NDM-1) is a member of the Metallo-β-lactamase family, capable of catalyzing the hydrolysis of all β-lactam antibiotics. The rapid dissemination of NDM producers, ‘superbugs’, has become a worldwide concern to health workers. Seventeen different variants of NDM have been reported so far, across the world. These variants varied in their sequences either by single or multiple amino acid substitutions. This review summarizes the crystal structure of NDM and provides a comparative analysis of all variants. Moreover, we have for the first time highlighted the role of α-helix, β-sheet and loop structures of NDM enzyme, having different mutations occurred in these regions. The effect of these substitutions on its structure and functional aspect has to be thoroughly understood to design effective inhibitors in future.
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Clinical Evolution of New Delhi Metallo-β-Lactamase (NDM) Optimizes Resistance under Zn(II) Deprivation. Antimicrob Agents Chemother 2017; 62:AAC.01849-17. [PMID: 29038264 DOI: 10.1128/aac.01849-17] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/10/2017] [Indexed: 11/20/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are rapidly spreading and taking a staggering toll on all health care systems, largely due to the dissemination of genes coding for potent carbapenemases. An important family of carbapenemases are the Zn(II)-dependent β-lactamases, known as metallo-β-lactamases (MBLs). Among them, the New Delhi metallo-β-lactamase (NDM) has experienced the fastest and widest geographical spread. While other clinically important MBLs are soluble periplasmic enzymes, NDMs are lipoproteins anchored to the outer membrane in Gram-negative bacteria. This unique cellular localization endows NDMs with enhanced stability upon the Zn(II) starvation elicited by the immune system response at the sites of infection. Since the first report of NDM-1, new allelic variants (16 in total) have been identified in clinical isolates differing by a limited number of substitutions. Here, we show that these variants have evolved by accumulating mutations that enhance their stability or the Zn(II) binding affinity in vivo, overriding the most common evolutionary pressure acting on catalytic efficiency. We identified the ubiquitous substitution M154L as responsible for improving the Zn(II) binding capabilities of the NDM variants. These results also reveal that Zn(II) deprivation imposes a strict constraint on the evolution of this MBL, overriding the most common pressures acting on catalytic performance, and shed light on possible inhibitory strategies.
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Stewart AC, Bethel CR, VanPelt J, Bergstrom A, Cheng Z, Miller CG, Williams C, Poth R, Morris M, Lahey O, Nix JC, Tierney DL, Page RC, Crowder MW, Bonomo RA, Fast W. Clinical Variants of New Delhi Metallo-β-Lactamase Are Evolving To Overcome Zinc Scarcity. ACS Infect Dis 2017; 3:927-940. [PMID: 28965402 DOI: 10.1021/acsinfecdis.7b00128] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Use and misuse of antibiotics have driven the evolution of serine β-lactamases to better recognize new generations of β-lactam drugs, but the selective pressures driving evolution of metallo-β-lactamases are less clear. Here, we present evidence that New Delhi metallo-β-lactamase (NDM) is evolving to overcome the selective pressure of zinc(II) scarcity. Studies of NDM-1, NDM-4 (M154L), and NDM-12 (M154L, G222D) demonstrate that the point mutant M154L, contained in 50% of clinical NDM variants, selectively enhances resistance to the penam ampicillin at low zinc(II) concentrations relevant to infection sites. Each of the clinical variants is shown to be progressively more thermostable and to bind zinc(II) more tightly than NDM-1, but a selective enhancement of penam turnover at low zinc(II) concentrations indicates that most of the improvement derives from catalysis rather than stability. X-ray crystallography of NDM-4 and NDM-12, as well as bioinorganic spectroscopy of dizinc(II), zinc(II)/cobalt(II), and dicobalt(II) metalloforms probe the mechanism of enhanced resistance and reveal perturbations of the dinuclear metal cluster that underlie improved catalysis. These studies support the proposal that zinc(II) scarcity, rather than changes in antibiotic structure, is driving the evolution of new NDM variants in clinical settings.
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Affiliation(s)
- Alesha C. Stewart
- Division of Chemical
Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne
Center for Infectious Disease, University of Texas, Austin, Texas 78712, United States
| | - Christopher R. Bethel
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Jamie VanPelt
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Alex Bergstrom
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Zishuo Cheng
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Callie G. Miller
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Cameron Williams
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert Poth
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Matthew Morris
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Olivia Lahey
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Jay C. Nix
- Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Richard C. Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert A. Bonomo
- Research Services, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Departments
of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry,
Proteomics and Bioinformatics, and the CWRU-Cleveland VAMC Center
for Antimicrobial Resistance and Epidemiology, Cleveland, Ohio 44106, United States
| | - Walter Fast
- Division of Chemical
Biology and Medicinal Chemistry, College of Pharmacy, and the LaMontagne
Center for Infectious Disease, University of Texas, Austin, Texas 78712, United States
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Mojica MF, Bonomo RA, Fast W. B1-Metallo-β-Lactamases: Where Do We Stand? Curr Drug Targets 2017; 17:1029-50. [PMID: 26424398 DOI: 10.2174/1389450116666151001105622] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 12/31/1969] [Accepted: 09/14/2015] [Indexed: 11/22/2022]
Abstract
Metallo-β-Lactamases (MBLs) are class Bβ-lactamases that hydrolyze almost all clinically-availableβ-lactam antibiotics. MBLs feature the distinctive αβ/βα sandwich fold of the metallo-hydrolase/oxidoreductase superfamily and possess a shallow active-site groove containing one or two divalent zinc ions, flanked by flexible loops. According to sequence identity and zinc ion dependence, MBLs are classified into three subclasses (B1, B2 and B3), of which the B1 subclass enzymes have emerged as the most clinically significant. Differences among the active site architectures, the nature of zinc ligands, and the catalytic mechanisms have limited the development of a common inhibitor. In this review, we will describe the molecular epidemiology and structural studies of the most prominent representatives of class B1 MBLs (NDM-1, IMP-1 and VIM-2) and describe the implications for inhibitor design to counter this growing clinical threat.
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Affiliation(s)
| | - Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Blvd., Cleveland, OH 44106, USA.
| | - Walter Fast
- Division of Medicinal Chemistry, College of Pharmacy, University of Texas, Austin TX, 78712, USA.
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Plasmid-Mediated Novel blaNDM-17 Gene Encoding a Carbapenemase with Enhanced Activity in a Sequence Type 48 Escherichia coli Strain. Antimicrob Agents Chemother 2017; 61:AAC.02233-16. [PMID: 28242668 DOI: 10.1128/aac.02233-16] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/26/2017] [Indexed: 01/25/2023] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have spread worldwide, leaving very few treatment options available. New Delhi metallo-beta-lactamase (NDM) is the main carbapenemase mediating CRE resistance and is of increasing concern. NDM-positive Enterobacteriaceae of human origin are frequently identified; however, the emergence of NDM, and particularly novel variants, in bacteria of food animal origin has never been reported. Here, we characterize a novel NDM variant (assigned NDM-17) identified in a β-lactam-resistant sequence type 48 (ST48) Escherichia coli strain that was isolated from a chicken in China. Compared to NDM-1, NDM-17 had three amino acid substitutions (V88L, M154L, and E170K) that confer significantly enhanced carbapenemase activity. Compared to NDM-5, NDM-17 had only one amino acid substitution (E170K) and slightly increased isolate resistance to carbapenem, as indicated by increased MIC values. The gene encoding NDM-17 (blaNDM-17) was located on an IncX3 plasmid, which was readily transferrable to recipient E. coli strain J53 by conjugation, suggesting the possibility of the rapid dissemination of blaNDM-17 Enzyme kinetics showed that NDM-17 could hydrolyze all β-lactams tested, except for aztreonam, and had a significantly higher affinity for all β-lactams tested than did NDM-5. The emergence of this novel NDM variant could pose a threat to public health because of its transferability and enhanced carbapenemase activity.
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Thakur P, Chawla R, Narula A, Sharma RK. Protective effect of Berberis aristata against peritonitis induced by carbapenem-resistant Escherichia coli in a mammalian model. J Glob Antimicrob Resist 2017; 9:21-29. [PMID: 28323228 DOI: 10.1016/j.jgar.2016.12.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/18/2016] [Accepted: 12/22/2016] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVES Berberis aristata is known to contain a variety of phenolic compounds contributing to its holistic capability of mitigating bacterial multidrug resistance. METHODS B. aristata stem bark extract was prepared and was characterised using liquid chromatography-mass spectrometry (LC-MS). The antimicrobial efficacy of the extract against carbapenem-resistant Escherichia coli was assessed in vivo in an animal model using Sprague Dawley rats. Microbial counts in blood and urine, physical health status, haematological and biochemical analysis of blood, and histopathology of the kidney were assessed as the study endpoints. RESULTS An aquo-alcoholic extract of B. aristata (PTRC-2111-A) was found to effectively manage peritonitis induced by carbapenem-resistant E. coli in a rat model at a single post-exposure prophylactic dose of 0.5mg/kg body weight (BW). The extract was also found to show a no observed adverse effect level (NOAEL) up to a dose of 2000mg/kg BW. Physical, immunological, haematological, biochemical and histopathological aberrations were found to be restored to normal in the herbal-treated group at a dose of 0.5mg/kg BW. CONCLUSIONS The antimicrobial and hepatorenal protective ability of PTRC-2111-A could be attributed to the presence of isoquinoline alkaloids.
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Affiliation(s)
- Pallavi Thakur
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, New Delhi 110054, India
| | - Raman Chawla
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, New Delhi 110054, India.
| | - Alka Narula
- Department of Biotechnology, Jamia Hamdard, New Delhi, India
| | - Rakesh Kumar Sharma
- Division of CBRN Defence, Institute of Nuclear Medicine and Allied Sciences, New Delhi 110054, India
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42
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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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43
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Hsu LY, Apisarnthanarak A, Khan E, Suwantarat N, Ghafur A, Tambyah PA. Carbapenem-Resistant Acinetobacter baumannii and Enterobacteriaceae in South and Southeast Asia. Clin Microbiol Rev 2017; 30:1-22. [PMID: 27795305 PMCID: PMC5217790 DOI: 10.1128/cmr.masthead.30-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Carbapenem-resistant Gram-negative bacteria, in particular the Acinetobacter baumannii-calcoaceticus complex and Enterobacteriaceae, are escalating global public health threats. We review the epidemiology and prevalence of these carbapenem-resistant Gram-negative bacteria among countries in South and Southeast Asia, where the rates of resistance are some of the highest in the world. These countries house more than a third of the world's population, and several are also major medical tourism destinations. There are significant data gaps, and the almost universal lack of comprehensive surveillance programs that include molecular epidemiologic testing has made it difficult to understand the origins and extent of the problem in depth. A complex combination of factors such as inappropriate prescription of antibiotics, overstretched health systems, and international travel (including the phenomenon of medical tourism) probably led to the rapid rise and spread of these bacteria in hospitals in South and Southeast Asia. In India, Pakistan, and Vietnam, carbapenem-resistant Enterobacteriaceae have also been found in the environment and community, likely as a consequence of poor environmental hygiene and sanitation. Considerable political will and effort, including from countries outside these regions, are vital in order to reduce the prevalence of such bacteria in South and Southeast Asia and prevent their global spread.
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Affiliation(s)
- Li-Yang Hsu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Tan Tock Seng Hospital, Singapore
| | | | - Erum Khan
- Aga Khan University, Karachi, Pakistan
| | - Nuntra Suwantarat
- Chulabhorn International College of Medicine, Thammasat University, Pathum Thani, Thailand
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44
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Pedroso MM, Selleck C, Enculescu C, Harmer JR, Mitić N, Craig WR, Helweh W, Hugenholtz P, Tyson GW, Tierney DL, Larrabee JA, Schenk G. Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics 2017; 9:1157-1168. [DOI: 10.1039/c7mt00195a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microorganisms in the permafrost contain a potent mechanism to inactivate antibiotics.
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45
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Carbapenem-Resistant Acinetobacter baumannii and Enterobacteriaceae in South and Southeast Asia. Clin Microbiol Rev 2016. [PMID: 27795305 DOI: 10.1128/cmr.00042-16] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Carbapenem-resistant Gram-negative bacteria, in particular the Acinetobacter baumannii-calcoaceticus complex and Enterobacteriaceae, are escalating global public health threats. We review the epidemiology and prevalence of these carbapenem-resistant Gram-negative bacteria among countries in South and Southeast Asia, where the rates of resistance are some of the highest in the world. These countries house more than a third of the world's population, and several are also major medical tourism destinations. There are significant data gaps, and the almost universal lack of comprehensive surveillance programs that include molecular epidemiologic testing has made it difficult to understand the origins and extent of the problem in depth. A complex combination of factors such as inappropriate prescription of antibiotics, overstretched health systems, and international travel (including the phenomenon of medical tourism) probably led to the rapid rise and spread of these bacteria in hospitals in South and Southeast Asia. In India, Pakistan, and Vietnam, carbapenem-resistant Enterobacteriaceae have also been found in the environment and community, likely as a consequence of poor environmental hygiene and sanitation. Considerable political will and effort, including from countries outside these regions, are vital in order to reduce the prevalence of such bacteria in South and Southeast Asia and prevent their global spread.
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46
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Molecular Characterization and Computational Modelling of New Delhi Metallo-β-Lactamase-5 from an Escherichia coli Isolate (KOEC3) of Bovine Origin. Indian J Microbiol 2016; 56:182-189. [PMID: 27570310 DOI: 10.1007/s12088-016-0569-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 02/04/2016] [Indexed: 10/22/2022] Open
Abstract
Emergence of antimicrobial resistance mediated through New Delhi metallo-β-lactamases (NDMs) is a serious therapeutic challenge. Till date, 16 different NDMs have been described. In this study, we report the molecular and structural characteristics of NDM-5 isolated from an Escherichia coli isolate (KOEC3) of bovine origin. Using PCR amplification, cloning and sequencing of full blaNDM gene, we identified the NDM type as NDM-5. Cloning of full gene in E. coli DH5α and subsequent assessment of antibiotic susceptibility of the transformed cells indicated possible role of native promoter in expression blaNDM-5. Translated amino acid sequence had two substitutions (Val88Leu and Met154Leu) compared to NDM-1. Theoretically deduced isoelectric pH of NDM-5 was 5.88 and instability index was 36.99, indicating a stable protein. From the amino acids sequence, a 3D model of the protein was computed. Analysis of the protein structure elucidated zinc coordination and also revealed a large binding cleft and flexible nature of the protein, which might be the reason for broad substrate range. Docking experiments revealed plausible binding poses for five carbapenem drugs in the vicinity of metal ions. In conclusion, results provided possible explanation for wide range of antibiotics catalyzed by NDM-5 and likely interaction modes with five carbapenem drugs.
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47
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Comparison of Verona Integron-Borne Metallo-β-Lactamase (VIM) Variants Reveals Differences in Stability and Inhibition Profiles. Antimicrob Agents Chemother 2015; 60:1377-84. [PMID: 26666919 PMCID: PMC4775916 DOI: 10.1128/aac.01768-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/05/2015] [Indexed: 01/28/2023] Open
Abstract
Metallo-β-lactamases (MBLs) are of increasing clinical significance; the development of clinically useful MBL inhibitors is challenged by the rapid evolution of variant MBLs. The Verona integron-borne metallo-β-lactamase (VIM) enzymes are among the most widely distributed MBLs, with >40 VIM variants having been reported. We report on the crystallographic analysis of VIM-5 and comparison of biochemical and biophysical properties of VIM-1, VIM-2, VIM-4, VIM-5, and VIM-38. Recombinant VIM variants were produced and purified, and their secondary structure and thermal stabilities were investigated by circular dichroism analyses. Steady-state kinetic analyses with a representative panel of β-lactam substrates were carried out to compare the catalytic efficiencies of the VIM variants. Furthermore, a set of metalloenzyme inhibitors were screened to compare their effects on the different VIM variants. The results reveal only small variations in the kinetic parameters of the VIM variants but substantial differences in their thermal stabilities and inhibition profiles. Overall, these results support the proposal that protein stability may be a factor in MBL evolution and highlight the importance of screening MBL variants during inhibitor development programs.
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48
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Role of Non-Active-Site Residue Trp-93 in the Function and Stability of New Delhi Metallo-β-Lactamase 1. Antimicrob Agents Chemother 2015; 60:356-60. [PMID: 26525789 DOI: 10.1128/aac.01194-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 10/18/2015] [Indexed: 01/25/2023] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is expressed by various members of Enterobacteriaceae as a defense mechanism to hydrolyze β-lactam antibiotics. Despite various studies showing the significance of active-site residues in the catalytic mechanism, there is a paucity of reports addressing the role of non-active-site residues in the structure and function of NDM-1. In this study, we investigated the significance of non-active-site residue Trp-93 in the structure and function of NDM-1. We cloned blaNDM-1 from an Enterobacter cloacae clinical strain (EC-15) and introduced the mutation of Trp-93 to Ala (yielding the Trp93Ala mutant) by PCR-based site-directed mutagenesis. Proteins were expressed and purified to homogeneity by affinity chromatography. The MICs of the Trp93Ala mutant were reduced 4- to 8-fold for ampicillin, cefotaxime, ceftazidime, cefoxitin, imipenem, and meropenem. The poor hydrolytic activity of the Trp93Ala mutant was also reflected by its reduced catalytic efficiency. The overall catalytic efficiency of the Trp93Ala mutant was reduced by 40 to 55% (the Km was reduced, while the kcat was similar to that of wild-type NDM-1 [wtNDM-1]). Heat-induced denaturation showed that the ΔGD (o) and Tm of Trp93Ala mutant were reduced by 1.8 kcal/mol and 4.8°C, respectively. Far-UV circular dichroism (CD) analysis showed that the α-helical content of the Trp93Ala mutant was reduced by 2.9%. The decrease in stability and catalytic efficiency of the Trp93Ala mutant was due to the loss of two hydrogen bonds with Ser-63 and Val-73 and hydrophobic interactions with Leu-65, Val-73, Gln-123, and Asp-124. The study provided insight into the role of non-active-site amino acid residues in the hydrolytic mechanism of NDM-1.
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49
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A novel New Delhi metallo-β-lactamase variant, NDM-14, isolated in a Chinese Hospital possesses increased enzymatic activity against carbapenems. Antimicrob Agents Chemother 2015; 59:2450-3. [PMID: 25645836 DOI: 10.1128/aac.05168-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel New Delhi metallo-β-lactamase (NDM) variant, NDM-14, was identified in clinical isolate Acinetobacter lwoffii JN49-1, which was recovered from an intensive care unit patient at a local hospital in China. NDM-14, which differs from other existing enzymes by an amino acid substitution at position 130 (Asp130Gly), possesses enzymatic activity toward carbapenems that is greater than that of NDM-1. Kinetic data indicate that NDM-14 has a higher affinity for imipenem and meropenem.
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