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Mohite SV, Sharma KK. Gut microbial metalloproteins and its role in xenobiotics degradation and ROS scavenging. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:495-538. [PMID: 38960484 DOI: 10.1016/bs.apcsb.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The gut microbial metalloenzymes play an important role in maintaining the balance between gut microbial ecosystem, human physiologically processes and immune system. The metals coordinated into active site contribute in various detoxification and defense strategies to avoid unfavourable environment and ensure bacterial survival in human gut. Metallo-β-lactamase is a potent degrader of antibiotics present in periplasmic space of both commensals and pathogenic bacteria. The resistance to anti-microbial agents developed in this enzyme is one of the global threats for human health. The organophosphorus eliminator, organophosphorus hydrolases have evolved over a course of time to hydrolyze toxic organophosphorus compounds and decrease its effect on human health. Further, the redox stress responders namely superoxide dismutase and catalase are key metalloenzymes in reducing both endogenous and exogenous oxidative stress. They hold a great importance for pathogens as they contribute in pathogenesis in human gut along with reduction of oxidative stress. The in-silico study on these enzymes reveals the importance of point mutation for the evolution of these enzymes in order to enhance their enzyme activity and stability. Various mutation studies were conducted to investigate the catalytic activity of these enzymes. By using the "directed evolution" method, the enzymes involved in detoxification and defense system can be engineered to produce new variants with enhance catalytic features, which may be used to predict the severity due to multi-drug resistance and degradation pattern of organophosphorus compounds in human gut.
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Affiliation(s)
- Shreya Vishwas Mohite
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
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2
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Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
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Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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3
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The activity and mechanism of vidofludimus as a potent enzyme inhibitor against NDM-1-positive E. coli. Eur J Med Chem 2023; 250:115225. [PMID: 36870273 DOI: 10.1016/j.ejmech.2023.115225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/11/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is the most important and prevalent enzyme among all metallo-β-lactamases. NDM-1 can hydrolyze almost all-available β-lactam antibiotics including carbapenems, resulting in multidrug resistance, which poses an increasing clinical threat. However, there is no NDM-1 inhibitor approved for clinical treatment. Therefore, identifying a novel and potential enzyme inhibitor against NDM-1-mediated infections is an urgent need. In this study, vidofludimus was identified as a potential NDM-1 inhibitor by structure-based virtual screening and an enzyme activity inhibition assay. Vidofludimus significantly inhibited NDM-1 hydrolysis activity with a significant dose-dependent effect. When the vidofludimus concentration was 10 μg/ml, the inhibition rate and 50% inhibitory concentration were 93.3% and 13.8 ± 0.5 μM, respectively. In vitro, vidofludimus effectively restored the antibacterial activity of meropenem against NDM-1-positive Escherichia coli (E. coli), and the minimum inhibitory concentration of meropenem was decreased from 64 μg/ml to 4 μg/ml, a 16-fold reduction. The combination of vidofludimus and meropenem showed a significant synergistic effect with a fractional inhibitory concentration index of 0.125 and almost all the NDM-1-positive E. coli were killed within 12 h. Furthermore, the synergistic therapeutic effect of vidofludimus and meropenem in vivo was evaluated in mice infected with NDM-1 positive E. coli. Compared with the control treatment, vidofludimus combined with meropenem significantly improved the survival rate of mice infected with NDM-1-positive E. coli (P < 0.05), decreased the white blood cell count, the bacterial burden and inflammatory response induced by NDM-1-positive E. coli (P < 0.05), and alleviated histopathological damage in infected mice. It was demonstrated by molecular dynamic simulation, site-directed mutagenesis and biomolecular interaction that vidofludimus could interact directly with the key amino acids (Met67, His120, His122 and His250) and Zn2+ in the active site of NDM-1, thereby competitively inhibiting the hydrolysis activity of NDM-1 on meropenem. In summary, vidofludimus holds promise as anNDM-1 inhibitor, and the combination of vidofludimus and meropenem has potential as a therapeutic strategy for NDM-1-mediated infections.
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4
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Omolabi KF, Reddy N, Mdanda S, Ntshangase S, Singh SD, Kruger HG, Naicker T, Govender T, Bajinath S. The in vitro and in vivo potential of metal-chelating agents as metallo-beta-lactamase inhibitors against carbapenem-resistant Enterobacterales. FEMS Microbiol Lett 2023; 370:6912242. [PMID: 36521842 DOI: 10.1093/femsle/fnac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/28/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The recent surge in beta-lactamase resistance has created superbugs, which pose a current and significant threat to public healthcare. This has created an urgent need to keep pace with the discovery of inhibitors that can inactivate these beta-lactamase producers. In this study, the in vitro and in vivo activity of 1,4,7-triazacyclononane-1,4,7 triacetic acid (NOTA)-a potential metallo-beta-lactamase (MBL) inhibitor was evaluated in combination with meropenem against MBL producing bacteria. Time-kill studies showed that NOTA restored the efficacy of meropenem against all bacterial strains tested. A murine infection model was then used to study the in vivo pharmacokinetics and efficacy of this metal chelator. The coadministration of NOTA and meropenem (100 mg/kg.bw each) resulted in a significant decrease in the colony-forming units of Klebsiella pneumoniae NDM-1 over an 8-h treatment period (>3 log10 units). The findings suggest that chelators, such as NOTA, hold strong potential for use as a MBL inhibitor in treating carbapenem-resistant Enterobacterale infections.
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Affiliation(s)
- Kehinde F Omolabi
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Private Bag X54001,Durban 4000, South Africa
| | - Nakita Reddy
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Private Bag X54001,Durban 4000, South Africa
| | - Sipho Mdanda
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Private Bag X54001,Durban 4000, South Africa
| | - Sphamandla Ntshangase
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Private Bag X54001,Durban 4000, South Africa
| | - Sanil D Singh
- Department of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4000, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Private Bag X54001,Durban 4000, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Private Bag X54001,Durban 4000, South Africa
| | - Thavendran Govender
- Department of Chemistry, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa
| | - Sooraj Bajinath
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Private Bag X54001,Durban 4000, South Africa.,Department of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4000, South Africa.,School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
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5
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Kong WP, Chen YW, Wong KY. The crystal structure of the H116Q mutant of NDM-1: An enzyme devoid of zinc ions. J Struct Biol 2022; 214:107922. [PMID: 36375744 DOI: 10.1016/j.jsb.2022.107922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
New Delhi metallo-β-lactamase 1 (NDM-1) is an important causative factor of antimicrobial resistance due to its efficient hydrolysis of a broad range of β-lactam compounds. The two zinc ions at the active site play essential roles in the NDM-1 catalytic activities. In a previous work, H116, one of the three ligands at the Zn1 site, was mutated in order to investigate the nature of zinc ion chelation. We report here the crystal structure of the NDM-1 H116Q mutant, that was designed to convert a B1 di-zinc enzyme into a B3 type, which either still binds two zinc ions or binds only one at the Zn2 site. The effect of mutation on the overall structure is minimal. Unexpectedly, no zinc ion was observed in the crystal structure. The Zn2-site ligating residue C221 forms a covalent bond with the nearby K121, a residue important in maintaining the active-site structure. The largest conformational changes were found at main-chain and side-chain atoms at residues 232-236 (loop 10), the proper configuration of which is known to be essential for substrate binding. The catalytic-site mutation caused little local changes, yet the effects were amplified and propagated to the substrate binding residues. There were big changes in the ψ angles of residues G232 and L234, which resulted in the side chain of N233 being displaced away from the substrate-binding site. In summary, we failed in turning a B1 enzyme into a B3 enzyme, yet we produced a zinc-less NDM-1 with residual activities.
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Affiliation(s)
- Wai-Po Kong
- 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
- 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
- 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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Antimicrobial Susceptibility Profile and Whole-Genome Analysis of a Strong Biofilm-Forming Bacillus Sp. B87 Strain Isolated from Food. Microorganisms 2022; 10:microorganisms10020252. [PMID: 35208707 PMCID: PMC8876208 DOI: 10.3390/microorganisms10020252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Members of the Bacillus cereus group are considered to be foodborne pathogens commonly associated with diarrheal and emetic gastrointestinal syndromes. Biofilm formation is a major virulence determinant of various pathogenic bacteria, including the B. cereus strains, since it can protect the bacteria against antimicrobial agents and the host immune response. Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. Based on the analysis of the phylogenetic relationship, the isolate was phylogenetically mapped close to Bacillus pacificus. Antimicrobial susceptibility testing revealed that the isolate was resistant to tetracycline and β-lactam antimicrobial agents, which corresponded with the genotypic characterization using the whole-genome analysis. The genome of Bacillus sp. B87 carried the three-component non-hemolytic enterotoxin (NHE), which is a type of enterotoxin that causes diarrheal symptoms. In addition, the genome also contained several genes that participate in biofilm formation, including the pelDEADAFG operon. These findings expand our understanding of antimicrobial resistance and virulence in Bacillus species based on the link between genotypic and phenotypic characterization.
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7
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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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8
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Menz BD, Charani E, Gordon DL, Leather AJM, Moonesinghe SR, Phillips CJ. Surgical Antibiotic Prophylaxis in an Era of Antibiotic Resistance: Common Resistant Bacteria and Wider Considerations for Practice. Infect Drug Resist 2021; 14:5235-5252. [PMID: 34908856 PMCID: PMC8665887 DOI: 10.2147/idr.s319780] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/19/2021] [Indexed: 01/19/2023] Open
Abstract
The increasing incidence of antimicrobial resistance (AMR) presents a global crisis to healthcare, with longstanding antimicrobial agents becoming less effective at treating and preventing infection. In the surgical setting, antibiotic prophylaxis has long been established as routine standard of care to prevent surgical site infection (SSI), which remains one of the most common hospital-acquired infections. The growing incidence of AMR increases the risk of SSI complicated with resistant bacteria, resulting in poorer surgical outcomes (prolonged hospitalisation, extended durations of antibiotic therapy, higher rates of surgical revision and mortality). Despite these increasing challenges, more data are required on approaches at the institutional and patient level to optimise surgical antibiotic prophylaxis in the era of antibiotic resistance (AR). This review provides an overview of the common resistant bacteria encountered in the surgical setting and covers wider considerations for practice to optimise surgical antibiotic prophylaxis in the perioperative setting.
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Affiliation(s)
- Bradley D Menz
- SA Pharmacy, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Esmita Charani
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,National Institute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Medicine, Imperial College London, London, UK
| | - David L Gordon
- Flinders Health & Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia.,Division of Medicine, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Andrew J M Leather
- Centre for Global Health and Health Partnerships, School of Population Health and Environmental Science, Kings College London, London, UK
| | - S Ramani Moonesinghe
- Centre for Perioperative Medicine, UCL Division of Surgery and Interventional Science, London, UK.,UCL Hospitals NIHR Biomedical Research Centre, London, UK
| | - Cameron J Phillips
- SA Pharmacy, Flinders Medical Centre, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia.,Flinders Health & Medical Research Institute, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia.,Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
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9
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Medina FE, Jaña GA. QM/MM Study of a VIM-1 Metallo-β-Lactamase Enzyme: The Catalytic Reaction Mechanism. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Fabiola E. Medina
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
- Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, 4051381 Concepción, Chile
| | - Gonzalo A. Jaña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano, 7100 Talcahuano, Chile
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10
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Fathollahi M, Fathollahi A, Motamedi H, Moradi J, Alvandi A, Abiri R. In silico vaccine design and epitope mapping of New Delhi metallo-beta-lactamase (NDM): an immunoinformatics approach. BMC Bioinformatics 2021; 22:458. [PMID: 34563132 PMCID: PMC8465709 DOI: 10.1186/s12859-021-04378-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/17/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Antibiotic resistance is a global health crisis. The adage that "prevention is better than cure" is especially true regarding antibiotic resistance because the resistance appears and spreads much faster than the production of new antibiotics. Vaccination is an important strategy to fight infectious agents; however, this strategy has not attracted sufficient attention in antibiotic resistance prevention. New Delhi metallo-beta-lactamase (NDM) confers resistance to many beta-lactamases, including important carbapenems like imipenem. Our goal in this study is to use an immunoinformatics approach to develop a vaccine that can elicit strong and specific immune responses against NDMs that prevent the development of antibiotic-resistant bacteria. RESULTS In this study, 2194 NDM sequences were aligned to obtain a conserved sequence. One continuous B cell epitope and three T cell CD4+ epitopes were selected from NDMs conserved sequence. Epitope conservancy for B cell and HLA-DR, HLA-DQ, and HLA-DP epitopes was 100.00%, 99.82%, 99.41%, and 99.86%, respectively, and population coverage of MHC II epitopes for the world was 99.91%. Permutation of the four epitope fragments resulted in 24 different peptides, of which 6 peptides were selected after toxicity, allergenicity, and antigenicity assessment. After primary vaccine design, only one vaccine sequence with the highest similarity with discontinuous B cell epitope in NDMs was selected. The final vaccine can bind to various Toll-like receptors (TLRs). The prediction implied that the vaccine would be stable with a good half-life. An immune simulation performed by the C-IMMSIM server predicted that two doses of vaccine injection can induce a strong immune response to NDMs. Finally, the GC-Content of the vaccine was designed very similar to E. coli K12. CONCLUSIONS In this study, immunoinformatics strategies were used to design a vaccine against different NDM variants that could produce an effective immune response against this antibiotic-resistant factor.
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Affiliation(s)
- Matin Fathollahi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Anwar Fathollahi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Motamedi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Jale Moradi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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11
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Foley W, Arman H, Musie GT. Homodinuclear copper(II) and zinc(II) complexes of a carboxylate-rich ligand as synthetic mimics of phosphoester hydrolase in aqueous solutions. J Inorg Biochem 2021; 225:111589. [PMID: 34530333 DOI: 10.1016/j.jinorgbio.2021.111589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/14/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
The synthesis, characterization and catalytic activities of two homodinuclear Cu(II) and Zn(II) complexes of a carboxylate-rich ligand, N,N'-Bis[2-carboxybenzomethyl]-N,N' -Bis[carboxymethyl]-1,3-diaminopropan-2-ol (H5ccdp) ligand towards the hydrolysis of (p-nitrophenyl phosphate) (PNPP) and bis(p-nitrophenyl) phosphate (BNPP) substrates in aqueous systems are described. Kinetic investigations were carried out using UV-Vis spectrophotometric techniques at 25 °C and 37 °C and different pH (7-10) conditions. The kinetic studies revealed that the turnover rate (kcat) values among the PNPP hydrolysis systems, the highest and the lowest kcat values were displayed by [Cu2(ccdp)(μ-OAc)]2- at 2.34 × 10-6 s-1 (pH 8 and 37 °C) and 2.13 × 10-8 s-1 (pH 8 and 25 °C), respectively. However, similar comparisons among the BNPP hydrolysis revealed that highest and the lowest kcat values were displayed by [Zn2(ccdp)(μ-OAc)]2- at 4.64 × 10-8 s-1 (pH 9 and 37 °C) and 2.38 × 10-9 (pH 9 and 25 °C). Significantly enough, the catalyst-substrate adduct species containing a metal bound PNPP and BNPP have been detected by ESI-MS techniques. Additionally, a PNPP-bound copper complex has been isolated and crystalized using single crystal X-ray diffraction technique. Based on the structural and activity information obtained in this study, reaction mechanisms for the hydrolysis of PNPP have been proposed.
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Affiliation(s)
- William Foley
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, United States
| | - Hadi Arman
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, United States
| | - Ghezai T Musie
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX 78249, United States.
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12
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Biswal HS, Kumar Sahu A, Frontera A, Bauzá A. Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function. J Chem Inf Model 2021; 61:3945-3954. [PMID: 34375103 PMCID: PMC8525862 DOI: 10.1021/acs.jcim.1c00594] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Understanding the structural and functional implications of metal ions is of pivotal significance to chemical biology. Herein, we report first time the evidence of spodium bonds (SpB's, an attractive noncovalent force involving elements from group 12 and electron-rich species) in tetrahedral Zn-binding sites. Through a combined crystallographic (PDB analysis) and computational (ab initio calculations) study, we demonstrate that Zn SpB's are abundant and might be involved in protein structure and enzyme inhibition.
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Affiliation(s)
- Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Akshay Kumar Sahu
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhimpur-Padanpur, Via-Jatni, Khurda, 752050 Bhubaneswar, India.,Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, 400094 Mumbai, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain
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13
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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14
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Gallique M, Wei K, Maisuria VB, Okshevsky M, McKay G, Nguyen D, Tufenkji N. Cranberry-Derived Proanthocyanidins Potentiate β-Lactam Antibiotics against Resistant Bacteria. Appl Environ Microbiol 2021; 87:e00127-21. [PMID: 33712420 PMCID: PMC8117774 DOI: 10.1128/aem.00127-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence and spread of extended-spectrum β-lactamases (ESBLs), metallo-β-lactamases (MBLs), or variant low-affinity penicillin-binding proteins (PBPs) pose a major threat to our ability to treat bacterial infection using β-lactam antibiotics. Although combinations of β-lactamase inhibitors with β-lactam agents have been clinically successful, there are no MBL inhibitors in current therapeutic use. Furthermore, recent clinical use of new-generation cephalosporins targeting PBP2a, an altered PBP, has led to the emergence of resistance to these antimicrobial agents. Previous work shows that natural polyphenols such as cranberry-extracted proanthocyanidins (cPAC) can potentiate non-β-lactam antibiotics against Gram-negative bacteria. This study extends beyond previous work by investigating the in vitro effect of cPAC in overcoming ESBL-, MBL-, and PBP2a-mediated β-lactam resistance. The results show that cPAC exhibit variable potentiation of different β-lactams against β-lactam-resistant Enterobacteriaceae clinical isolates as well as ESBL- and MBL-producing E. coli We also discovered that cPAC have broad-spectrum inhibitory properties in vitro on the activity of different classes of β-lactamases, including CTX-M3 ESBL and IMP-1 MBL. Furthermore, we observe that cPAC selectively potentiate oxacillin and carbenicillin against methicillin-resistant but not methicillin-sensitive staphylococci, suggesting that cPAC also interfere with PBP2a-mediated resistance. This study motivates the need for future work to identify the most bioactive compounds in cPAC and to evaluate their antibiotic-potentiating efficacy in vivoIMPORTANCE The emergence of β-lactam-resistant Enterobacteriaceae and staphylococci compromises the effectiveness of β-lactam-based therapy. By acquisition of ESBLs, MBLs, or PBPs, it is highly likely that bacteria may become completely resistant to the most effective β-lactam agents in the near future. In this study, we described a natural extract rich in proanthocyanidins which exerts adjuvant properties by interfering with two different resistance mechanisms. By their broad-spectrum inhibitory ability, cranberry-extracted proanthocyanidins could have the potential to enhance the effectiveness of existing β-lactam agents.
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Affiliation(s)
- Mathias Gallique
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Kuan Wei
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Vimal B Maisuria
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
| | - Mira Okshevsky
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
| | - Geoffrey McKay
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Nathalie Tufenkji
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
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15
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Taylor IR, Paczkowski JE, Jeffrey PD, Henke BR, Smith CD, Bassler BL. Inhibitor Mimetic Mutations in the Pseudomonas aeruginosa PqsE Enzyme Reveal a Protein-Protein Interaction with the Quorum-Sensing Receptor RhlR That Is Vital for Virulence Factor Production. ACS Chem Biol 2021; 16:740-752. [PMID: 33793200 PMCID: PMC8056388 DOI: 10.1021/acschembio.1c00049] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
Pseudomonas
aeruginosa is an opportunistic human
pathogen that causes fatal infections. There exists an urgent need
for new antimicrobial agents to combat P. aeruginosa. We conducted a screen for molecules that bind the virulence-controlling
protein PqsE and characterized hit compounds for inhibition of PqsE
enzymatic activity. The binding conformations of two inhibitory molecules,
BB391 and BB393, were identified by crystallography, and inhibitor
binding was mimicked by the substitution of PqsE residues E182 and
S285 with tryptophan. Comparison of the inhibitor-mimetic mutations
to the catalytically inactive PqsE D73A protein demonstrated that
catalysis is not responsible for the role PqsE plays in driving virulence
factor production. Rather, the PqsE E182W protein fails to interact
with the quorum-sensing receptor, RhlR, and our results suggest that
it is this interaction that is responsible for promoting virulence
factor production in P. aeruginosa. These findings
provide a new route for drug discovery efforts targeting PqsE.
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Affiliation(s)
- Isabelle R. Taylor
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Jon E. Paczkowski
- Department of Health, Wadsworth Center, Albany, New York 12208, United States
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York 12201, United States
| | - Philip D. Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Brad R. Henke
- Opti-Mol Consulting, LLC, Cary, North Carolina 27518, United States
| | - Chari D. Smith
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
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16
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Kullappan M, Mallavarapu Ambrose J, Surapaneni KM. Understanding the binding conformation of ceftolozane/tazobactam with Metallo-β-lactamases VIM-5 and IMP-7 of Pseudomonas aeruginosa: A molecular docking and virtual screening process. J Mol Recognit 2021; 34:e2898. [PMID: 33780080 DOI: 10.1002/jmr.2898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 11/11/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is one of the community-acquired and healthcare-associated infections causing organisms. It has become resistant to most of the available antibiotics and is termed multi-drug resistance (MDR). There are a limited number of antibiotics are available to treat such MDR organism causing infections. The ceftolozane/tazobactam is one among the combination drug therapy (CDT) prescribed for the treatment of MDR causing infections. The resistance for the same CDT was observed in the MDR P. aeruginosa harboring VIM-5 and IMP-7 Metallo beta (β)-lactamases (MBLs). To explore the resistance mechanism at the molecular level, docking studies were carried out for antibiotics against VIM-5 and IMP-7 MBLs. The Zn2 metal ions carry out the nucleophile attack on the carbonyl carbon of the β-lactam ring along with conserved water molecules. To find lead compounds against the MBLs, a virtual screening process was carried out. We have employed MODELLER for structure modeling, AutoDock for molecular docking and AutoDock Vina, Molinspiration, PASS prediction & admetSAR in virtual screening. The search of low binding energy ceftolozane analogs against VIM-5 and IMP-7 MBLs has resulted in the ZINC000029060075 and ZINC000009163636 analogs. Similarly, the screening of high binding energy inhibitors against VIM-5 and IMP-7 MBLs has resulted in ZINC000003831503 and ZINC000000897247 tazobactam analogs respectively. The ADMET prediction results in the non-toxicity of the lead compounds. Our study may provide new insights for the scientist who are designing novel drugs against MDR P. aeruginosa causing infections.
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Affiliation(s)
- Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, Tamil Nadu, India
| | - Jenifer Mallavarapu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, Tamil Nadu, India
| | - Krishna Mohan Surapaneni
- Departments of Biochemistry, Clinical Skills & Simulation and Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, Tamil Nadu, India
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17
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Lima LM, Silva BNMD, Barbosa G, Barreiro EJ. β-lactam antibiotics: An overview from a medicinal chemistry perspective. Eur J Med Chem 2020; 208:112829. [DOI: 10.1016/j.ejmech.2020.112829] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 11/27/2022]
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18
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Variability in Zinc Concentration among Mueller-Hinton Broth Brands: Impact on Antimicrobial Susceptibility Testing of Metallo-β-Lactamase-Producing Enterobacteriaceae. J Clin Microbiol 2020; 58:JCM.02019-20. [PMID: 32999009 DOI: 10.1128/jcm.02019-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/27/2020] [Indexed: 01/13/2023] Open
Abstract
Zinc concentrations in cation-adjusted Mueller-Hinton broth (caMHB) from different manufacturers have been found to differ. Here, we evaluated the impact of utilizing different brands and lots of commercially available caMHB on the classification of the antimicrobial susceptibility of metallo-β-lactamase (MBL)-harboring Enterobacteriaceae We also evaluated the addition of EDTA to caMHB as a means of achieving zinc-limited media. Fifteen clinical Enterobacteriaceae isolates (harboring NDM [n = 7], VIM [n = 3], IMP [n = 2], or KPC [n = 3]) and nine different commercial lots from three caMHB manufacturers (Becton, Dickinson; Oxoid; and Sigma-Aldrich) were utilized. Zinc-limited media were prepared by the addition of EDTA at concentrations ranging from 3 to 300 μg/ml. Meropenem MICs were determined in triplicate for each lot of conventional caMHB and zinc-limited media by broth microdilution. The zinc concentration in each lot of conventional caMHB was determined by inductively coupled plasma mass spectrometry. Up to 8-fold differences in meropenem MICs were observed between the commercial lots, resulting in different classifications of susceptibility among MBL-harboring isolates. Mean zinc concentrations were highest among conventional Becton, Dickinson caMHB lots relative to those for Oxoid and Sigma-Aldrich broth. Among MBL-harboring isolates, the impact of EDTA on MICs was dependent on the lot, correlating with initial zinc availability (i.e., less MIC reduction with higher initial zinc concentrations), while MICs for KPC-harboring isolates were unchanged. In summary, zinc variability was observed among commercial lots of caMHB, resulting in different classifications of susceptibility among MBL-harboring Enterobacteriaceae The addition of EDTA at concentrations of ≥30 μg/ml was sufficient to provide a zinc-limited medium, resulting in MICs that reflect in vivo meropenem activity.
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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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Softley CA, Zak KM, Bostock MJ, Fino R, Zhou RX, Kolonko M, Mejdi-Nitiu R, Meyer H, Sattler M, Popowicz GM. Structure and Molecular Recognition Mechanism of IMP-13 Metallo-β-Lactamase. Antimicrob Agents Chemother 2020; 64:e00123-20. [PMID: 32205343 PMCID: PMC7269475 DOI: 10.1128/aac.00123-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/17/2020] [Indexed: 12/31/2022] Open
Abstract
Multidrug resistance among Gram-negative bacteria is a major global public health threat. Metallo-β-lactamases (MBLs) target the most widely used antibiotic class, the β-lactams, including the most recent generation of carbapenems. Interspecies spread renders these enzymes a serious clinical threat, and there are no clinically available inhibitors. We present the crystal structures of IMP-13, a structurally uncharacterized MBL from the Gram-negative bacterium Pseudomonas aeruginosa found in clinical outbreaks globally, and characterize the binding using solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The crystal structures of apo IMP-13 and IMP-13 bound to four clinically relevant carbapenem antibiotics (doripenem, ertapenem, imipenem, and meropenem) are presented. Active-site plasticity and the active-site loop, where a tryptophan residue stabilizes the antibiotic core scaffold, are essential to the substrate-binding mechanism. The conserved carbapenem scaffold plays the most significant role in IMP-13 binding, explaining the broad substrate specificity. The observed plasticity and substrate-locking mechanism provide opportunities for rational drug design of novel metallo-β-lactamase inhibitors, essential in the fight against antibiotic resistance.
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Affiliation(s)
- Charlotte A Softley
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Krzysztof M Zak
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mark J Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Roberto Fino
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Richard Xu Zhou
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marta Kolonko
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Ramona Mejdi-Nitiu
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Hannelore Meyer
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Munich, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
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21
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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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22
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Kim Y, Maltseva N, Wilamowski M, Tesar C, Endres M, Joachimiak A. Structural and biochemical analysis of the metallo-β-lactamase L1 from emerging pathogen Stenotrophomonas maltophilia revealed the subtle but distinct di-metal scaffold for catalytic activity. Protein Sci 2019; 29:723-743. [PMID: 31846104 PMCID: PMC7020990 DOI: 10.1002/pro.3804] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023]
Abstract
Emergence of Enterobacteriaceae harboring metallo‐β‐lactamases (MBL) has raised global threats due to their broad antibiotic resistance profiles and the lack of effective inhibitors against them. We have been studied one of the emerging environmental MBL, the L1 from Stenotrophomonas maltophilia K279a. We determined several crystal structures of L1 complexes with three different classes of β‐lactam antibiotics (penicillin G, moxalactam, meropenem, and imipenem), with the inhibitor captopril and different metal ions (Zn+2, Cd+2, and Cu+2). All hydrolyzed antibiotics and the inhibitor were found binding to two Zn+2 ions mainly through the opened lactam ring and some hydrophobic interactions with the binding pocket atoms. Without a metal ion, the active site is very similarly maintained as that of the native form with two Zn+2 ions, however, the protein does not bind the substrate moxalactam. When two Zn+2 ions were replaced with other metal ions, the same di‐metal scaffold was maintained and the added moxalactam was found hydrolyzed in the active site. Differential scanning fluorimetry and isothermal titration calorimetry were used to study thermodynamic properties of L1 MBL compared with New Deli Metallo‐β‐lactamase‐1 (NDM‐1). Both enzymes are significantly stabilized by Zn+2 and other divalent metals but showed different dependency. These studies also suggest that moxalactam and its hydrolyzed form may bind and dissociate with different kinetic modes with or without Zn+2 for each of L1 and NDM‐1. Our analysis implicates metal ions, in forming a distinct di‐metal scaffold, which is central to the enzyme stability, promiscuous substrate binding and versatile catalytic activity. Statement The L1 metallo‐β‐lactamase from an environmental multidrug‐resistant opportunistic pathogen Stenotrophomonas maltophilia K279a has been studied by determining 3D structures of L1 enzyme in the complexes with several β‐lactam antibiotics and different divalent metals and characterizing its biochemical and ligand binding properties. We found that the two‐metal center in the active site is critical in the enzymatic process including antibiotics recognition and binding, which explains the enzyme's activity toward diverse antibiotic substrates. This study provides the critical information for understanding the ligand recognition and for advanced drug development.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Mateusz Wilamowski
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois
| | - Christine Tesar
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Michael Endres
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, the University of Chicago, Chicago, Illinois.,Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois
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23
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Khalili Arjomandi O, Kavoosi M, Adibi H. Synthesis and investigation of inhibitory activities of imidazole derivatives against the metallo-β-lactamase IMP-1. Bioorg Chem 2019; 92:103277. [PMID: 31539743 DOI: 10.1016/j.bioorg.2019.103277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 12/21/2022]
Abstract
Mutations in bacteria can result in antibiotic resistance due to the overuse or abuse of β-lactam antibiotics. One strategy which bacteria can become resistance toward antibiotics is secreting of metallo β-lactamase enzymes that can open the lactam ring of the β-lactam antibiotic and inactivate them. This issue is a threat for human health and one strategy to overcome this situation is co-administration of β-lactam antibiotics with an inhibitor. So far, no clinically available inhibitors of metallo β-lactamases (MBLs) reported and the clinically inhibitors of serine β-lactamase are useless for MBLs. Accordingly, finding a potent inhibitor of the MBLs being very important. In this study, imidazole derivatives primarily were synthesized and their inhibitory activity were measured. Later in silico binding model was used to predict the configuration and conformation of the ligands into the active site of enzyme. Two molecules demonstrated with IC50 of 39 µM and 46 µM against MBL (IMP-1).
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Affiliation(s)
- Omid Khalili Arjomandi
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Qld 4072, Australia; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mahboubeh Kavoosi
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.
| | - Hadi Adibi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Khalili Arjomandi O, Kavoosi M, Adibi H. Synthesis and enzyme-based evaluation of analogues L-tyrosine thiol carboxylic acid inhibitor of metallo-β-lactamase IMP-1. J Enzyme Inhib Med Chem 2019; 34:1414-1425. [PMID: 31401901 PMCID: PMC8853707 DOI: 10.1080/14756366.2019.1651314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The emergence of drug-resistant pathogenic bacteria is occurring due to the global overuse and misuse of β-lactam antibiotics. Infections caused by some bacteria which secrete metallo-β-lactamases (enzymes that inactivate β-lactam antibiotics) are increasingly prevalent and have become a major worldwide threat to human health. These bacteria are resistant to β-lactam antibiotics and MBL-inhibitor/β-lactam antibiotic combination therapy can be a strategy to overcome this problem. So far, no clinically available inhibitors of metallo-β-lactamases (MBLs) have been reported. In this study, L-benzyl tyrosine thiol carboxylic acid analogues (2a–2k) were synthesized after the study of computational simulation by adding of methyl, chloro, bromo and nitro groups to the benzyl ring for investigation of SAR analysis. Although the synthesized molecules 2a–k shows the potent inhibitory effects against metallo-β-lactamase (IMP-1) with the range of Kic values of 1.04–4.77 µM, they are not as potent as the candidate inhibitor.
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Affiliation(s)
- Omid Khalili Arjomandi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Australia
| | | | - Hadi Adibi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Abstract
Natural and nonnatural amino acids represent important building blocks for the development of peptidomimetic scaffolds, especially for targeting proteolytic enzymes and for addressing protein–protein interactions. Among all the different amino acids derivatives, proline is particularly relevant in chemical biology and medicinal chemistry due to its secondary structure’s inducing and stabilizing properties. Also, the pyrrolidine ring is a conformationally constrained template that can direct appendages into specific clefts of the enzyme binding site. Thus, many papers have appeared in the literature focusing on the use of proline and its derivatives as scaffolds for medicinal chemistry applications. In this review paper, an insight into the different biological outcomes of d-proline and l-proline in enzyme inhibitors is presented, especially when associated with matrix metalloprotease and metallo-β-lactamase enzymes.
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High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1. Int J Mol Sci 2019; 20:ijms20040819. [PMID: 30769822 PMCID: PMC6412273 DOI: 10.3390/ijms20040819] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/10/2019] [Indexed: 01/04/2023] Open
Abstract
The bacteria expressing New Delhi Metallo-β-lactamase-1 (NDM-1) can hydrolyze all β-lactam antibiotics including carbapenems, causing multi-drug resistance. The worldwide emergence and dissemination of gene blaNDM-1 (produces NDM-1) in hospital and community settings, rising problems for public health. Indeed, there is an urgent need for NDM-1 inhibitors to manage antibiotic resistance. Here, we have identified novel non-β-lactam ring-containing inhibitors of NDM-1 by applying a high-throughput virtual screening of lead-like subset of ZINC database. The screened compounds were followed for the molecular docking, the molecular dynamics simulation, and then enzyme kinetics assessment. The adopted screening procedure funnels out five novel inhibitors of NDM-1 including ZINC10936382, ZINC30479078, ZINC41493045, ZINC7424911, and ZINC84525623. The molecular mechanics-generalized born surface area and molecular dynamics (MD) simulation showed that ZINC84525623 formed the most stable complex with NDM-1. Furthermore, analyses of the binding pose after MD simulation revealed that ZINC84525623 formed two hydrogen bonds (electrostatic and hydrophobic interaction) with key amino acid residues of the NDM-1 active site. The docking binding free energy and docking binding constant for the ZINC84525623 and NDM-1 interaction were estimated to be −11.234 kcal/mol, and 1.74 × 108 M−1 respectively. Steady-state enzyme kinetics in the presence of ZINC84525623 show the decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics. The findings of this study would be helpful in identifying novel inhibitors against other β-lactamases from a pool of large databases. Furthermore, the identified inhibitor (ZINC84525623) could be developed as efficient drug candidates.
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Yarlagadda V, Sarkar P, Samaddar S, Manjunath GB, Mitra SD, Paramanandham K, Shome BR, Haldar J. Vancomycin Analogue Restores Meropenem Activity against NDM-1 Gram-Negative Pathogens. ACS Infect Dis 2018; 4:1093-1101. [PMID: 29726673 DOI: 10.1021/acsinfecdis.8b00011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is the major contributor to the emergence of carbapenem resistance in Gram-negative pathogens (GNPs) and has caused many clinically available β-lactam antibiotics to become obsolete. A clinically approved inhibitor of metallo-β-lactamase (MBL) that could restore the activity of carbapenems against resistant GNPs has not yet been found, making NDM-1 a serious threat to human health. Here, we have rationally developed an inhibitor for the NDM-1 enzyme, which has the ability to penetrate the outer membrane of GNPs and inactivate the enzyme by depleting the metal ion (Zn2+) from the active site. The inhibitor reinstated the activity of meropenem against NDM-1 producing clinical isolates of GNPs like Klebsiella pneumoniae and Escherichia coli. Further, the inhibitor efficiently restored meropenem activity against NDM-1 producing K. pneumoniae in a murine sepsis infection model. These findings demonstrate that a combination of the present inhibitor and meropenem has high potential to be translated clinically to combat carbapenem-resistant GNPs.
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Affiliation(s)
- Venkateswarlu Yarlagadda
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Paramita Sarkar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Sandip Samaddar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Goutham Belagula Manjunath
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
| | - Susweta Das Mitra
- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560064, India
| | - Krishnamoorthy Paramanandham
- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560064, India
| | - Bibek Ranjan Shome
- National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka 560064, India
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru, Karnataka 560064, India
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28
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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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Abboud MI, Kosmopoulou M, Krismanich AP, Johnson JW, Hinchliffe P, Brem J, Claridge TDW, Spencer J, Schofield CJ, Dmitrienko GI. Cyclobutanone Mimics of Intermediates in Metallo-β-Lactamase Catalysis. Chemistry 2018; 24:5734-5737. [PMID: 29250863 PMCID: PMC5947706 DOI: 10.1002/chem.201705886] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Indexed: 01/25/2023]
Abstract
The most important resistance mechanism to β-lactam antibiotics involves hydrolysis by two β-lactamase categories: the nucleophilic serine and the metallo-β-lactamases (SBLs and MBLs, respectively). Cyclobutanones are hydrolytically stable β-lactam analogues with potential to inhibit both SBLs and MBLs. We describe solution and crystallographic studies on the interaction of a cyclobutanone penem analogue with the clinically important MBL SPM-1. NMR experiments using 19 F-labeled SPM-1 imply the cyclobutanone binds to SPM-1 with micromolar affinity. A crystal structure of the SPM-1:cyclobutanone complex reveals binding of the hydrated cyclobutanone through interactions with one of the zinc ions, stabilisation of the hydrate by hydrogen bonding to zinc-bound water, and hydrophobic contacts with aromatic residues. NMR analyses using a 13 C-labeled cyclobutanone support assignment of the bound species as the hydrated ketone. The results inform on how MBLs bind substrates and stabilize tetrahedral intermediates. They support further investigations on the use of transition-state and/or intermediate analogues as inhibitors of all β-lactamase classes.
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Affiliation(s)
- Martine I. Abboud
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Magda Kosmopoulou
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | - Anthony P. Krismanich
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
| | - Jarrod W. Johnson
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
| | - Philip Hinchliffe
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | - Jürgen Brem
- Department of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | | | - James Spencer
- School of Cellular and Molecular MedicineUniversity of Bristol, Medical Sciences BuildingBristolBS8 1TDUK
| | | | - Gary I. Dmitrienko
- Department of ChemistryUniversity of Waterloo200 University Ave. W.Waterloo, OntarioN2L 3G1Canada
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30
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Grauffel C, Lim C. Factors governing when a metal-bound water is deprotonated in proteins. Phys Chem Chem Phys 2018; 20:29625-29636. [DOI: 10.1039/c8cp04776f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We evaluate the extent to which the pKw depends on the type, number, and metal-binding mode of the first-shell ligands, the metal–ligand bond distances, first-shell⋯second-shell H-bonding interactions, and the protein environment.
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Affiliation(s)
- Cédric Grauffel
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 115
- Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences
- Academia Sinica
- Taipei 115
- Taiwan
- Department of Chemistry
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31
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Di Pisa F, Pozzi C, Benvenuti M, Docquier JD, De Luca F, Mangani S. Boric acid and acetate anion binding to subclass B3 metallo-β-lactamase BJP-1 provides clues for mechanism of action and inhibitor design. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.07.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Tan SH, Normi YM, Leow ATC, Salleh AB, Murad AMA, Mahadi NM, Rahman MBA. Danger lurking in the "unknowns": structure-to-function studies of hypothetical protein Bleg1_2437 from Bacillus lehensis G1 alkaliphile revealed an evolutionary divergent B3 metallo-beta-lactamase. J Biochem 2017; 161:167-186. [PMID: 28175318 DOI: 10.1093/jb/mvw058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/22/2016] [Indexed: 11/12/2022] Open
Abstract
The effectiveness of β-lactam antibiotics as chemotherapeutic agents to treat bacterial infections is gradually threatened with the emergence of antibiotic resistance mechanism among pathogenic bacteria through the production metallo-β-lactamase (MBL). In this study, we discovered a novel hypothetical protein (HP) termed Bleg1_2437 from the genome of alkaliphilic Bacillus lehensis G1 which exhibited MBL-like properties of B3 subclass; but evolutionary divergent from other circulating B3 MBLs. Domain and sequence analysis of HP Bleg1_2437 revealed that it contains highly conserved Zn2+-binding residues such as H54, H56, D58, H59, H131 and H191, important for catalysis, similar with the subclass B3 of MBL. Built 3-D Bleg1_2437 structure exhibited an αββα sandwich layer similar to the well-conserved global topology of MBL superfamily. Other features include a ceiling and floor in the model which are important for accommodation and orientation of β-lactam antibiotics docked to the protein model showed interactions at varying degrees with residues in the binding pocket of Bleg1_2437. Hydrolysis activity towards several β-lactam antibiotics was proven through an in vitro assay using purified recombinant Bleg1_2437 protein. These findings highlight the presence of a clinically important and evolutionary divergent antibiotics-degrading enzyme within the pools of uncharacterized HPs.
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Affiliation(s)
- Soo Huei Tan
- Center for Enzyme and Microbial Technology (EMTECH), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Center for Enzyme and Microbial Technology (EMTECH), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Center for Enzyme and Microbial Technology (EMTECH), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Center for Enzyme and Microbial Technology (EMTECH), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Kajang, Selangor, Malaysia
| | - Mohd Basyaruddin Abdul Rahman
- Center for Enzyme and Microbial Technology (EMTECH), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Kajang, Selangor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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33
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Li GB, Abboud MI, Brem J, Someya H, Lohans CT, Yang SY, Spencer J, Wareham DW, McDonough MA, Schofield CJ. NMR-filtered virtual screening leads to non-metal chelating metallo-β-lactamase inhibitors. Chem Sci 2016; 8:928-937. [PMID: 28451231 PMCID: PMC5369532 DOI: 10.1039/c6sc04524c] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023] Open
Abstract
There are no clinically useful inhibitors of metallo-β-lactamases (MBLs), which are a growing problem because they hydrolyse almost all β-lactam antibacterials. Inhibition by most reported MBL inhibitors involves zinc ion chelation. A structure-based virtual screening approach combined with NMR filtering led to the identification of inhibitors of the clinically relevant Verona Integron-encoded MBL (VIM)-2. Crystallographic analyses reveal a new mode of MBL inhibition involving binding adjacent to the active site zinc ions, but which does not involve metal chelation. The results will aid efforts to develop new types of clinically useful inhibitors targeting MBLs/MBL-fold metallo-enzymes involved in antibacterial and anticancer drug resistance.
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Affiliation(s)
- Guo-Bo Li
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education , West China School of Pharmacy , Sichuan University , Chengdu , 610041 , China
| | - Martine I Abboud
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Jürgen Brem
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Hidenori Someya
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ; .,Medicinal Chemistry Research Laboratories , New Drug Research Division , Otsuka Pharmaceutical Co., Ltd. , 463-10 Kagasuno, Kawauchi-cho , Tokushima 771-0192 , Japan
| | - Christopher T Lohans
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy , West China Hospital , West China Medical School , Sichuan University , Sichuan 610041 , China
| | - James Spencer
- School of Cellular and Molecular Medicine , Biomedical Sciences Building , University of Bristol , Bristol BS8 1TD , UK
| | - David W Wareham
- Antimicrobial Research Group , Barts & The London School of Medicine and Dentistry , Queen Mary University of London , London , E1 2AT , UK
| | - Michael A McDonough
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
| | - Christopher J Schofield
- Department of Chemistry , University of Oxford , 12 Mansfield Road , Oxford , OX1 3TA , UK . ;
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34
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Salimraj R, Zhang L, Hinchliffe P, Wellington EMH, Brem J, Schofield CJ, Gaze WH, Spencer J. Structural and Biochemical Characterization of Rm3, a Subclass B3 Metallo-β-Lactamase Identified from a Functional Metagenomic Study. Antimicrob Agents Chemother 2016; 60:5828-40. [PMID: 27431213 PMCID: PMC5038237 DOI: 10.1128/aac.00750-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 07/08/2016] [Indexed: 11/20/2022] Open
Abstract
β-Lactamase production increasingly threatens the effectiveness of β-lactams, which remain a mainstay of antimicrobial chemotherapy. New activities emerge through both mutation of previously known β-lactamases and mobilization from environmental reservoirs. The spread of metallo-β-lactamases (MBLs) represents a particular challenge because of their typically broad-spectrum activities encompassing carbapenems, in addition to other β-lactam classes. Increasingly, genomic and metagenomic studies have revealed the distribution of putative MBLs in the environment, but in most cases their activity against clinically relevant β-lactams and, hence, the extent to which they can be considered a resistance reservoir remain uncharacterized. Here we characterize the product of one such gene, blaRm3, identified through functional metagenomic sampling of an environment with high levels of biocide exposure. blaRm3 encodes a subclass B3 MBL that, when expressed in a recombinant Escherichia coli strain, is exported to the bacterial periplasm and hydrolyzes clinically used penicillins, cephalosporins, and carbapenems with an efficiency limited by high Km values. An Rm3 crystal structure reveals the MBL superfamily αβ/βα fold, which more closely resembles that in mobilized B3 MBLs (AIM-1 and SMB-1) than other chromosomal enzymes (L1 or FEZ-1). A binuclear zinc site sits in a deep channel that is in part defined by a relatively extended N terminus. Structural comparisons suggest that the steric constraints imposed by the N terminus may limit its affinity for β-lactams. Sequence comparisons identify Rm3-like MBLs in numerous other environmental samples and species. Our data suggest that Rm3-like enzymes represent a distinct group of B3 MBLs with a wide distribution and can be considered an environmental reservoir of determinants of β-lactam resistance.
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Affiliation(s)
- Ramya Salimraj
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Lihong Zhang
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - William H Gaze
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
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35
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Brem J, Cain R, Cahill S, McDonough MA, Clifton IJ, Jiménez-Castellanos JC, Avison MB, Spencer J, Fishwick CWG, Schofield CJ. Structural basis of metallo-β-lactamase, serine-β-lactamase and penicillin-binding protein inhibition by cyclic boronates. Nat Commun 2016; 7:12406. [PMID: 27499424 PMCID: PMC4979060 DOI: 10.1038/ncomms12406] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/29/2016] [Indexed: 12/24/2022] Open
Abstract
β-Lactamases enable resistance to almost all β-lactam antibiotics. Pioneering work revealed that acyclic boronic acids can act as 'transition state analogue' inhibitors of nucleophilic serine enzymes, including serine-β-lactamases. Here we report biochemical and biophysical analyses revealing that cyclic boronates potently inhibit both nucleophilic serine and zinc-dependent β-lactamases by a mechanism involving mimicking of the common tetrahedral intermediate. Cyclic boronates also potently inhibit the non-essential penicillin-binding protein PBP 5 by the same mechanism of action. The results open the way for development of dual action inhibitors effective against both serine- and metallo-β-lactamases, and which could also have antimicrobial activity through inhibition of PBPs.
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Affiliation(s)
- Jürgen Brem
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ricky Cain
- School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Samuel Cahill
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Michael A. McDonough
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ian J. Clifton
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | | | - Matthew B. Avison
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
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Structural Insights into Recognition of Hydrolyzed Carbapenems and Inhibitors by Subclass B3 Metallo-β-Lactamase SMB-1. Antimicrob Agents Chemother 2016; 60:4274-82. [PMID: 27161644 DOI: 10.1128/aac.03108-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 04/27/2016] [Indexed: 11/20/2022] Open
Abstract
Metallo-β-lactamases (MBLs) confer resistance to carbapenems, and their increasing global prevalence is a growing clinical concern. To elucidate the mechanisms by which these enzymes recognize and hydrolyze carbapenems, we solved 1.4 to 1.6 Å crystal structures of SMB-1 (Serratia metallo-β-lactamase 1), a subclass B3 MBL, bound to hydrolyzed carbapenems (doripenem, meropenem, and imipenem). In these structures, SMB-1 interacts mainly with the carbapenem core structure via elements in the active site, including a zinc ion (Zn-2), Q157[113] (where the position in the SMB-1 sequence is in brackets after the BBL number), S221[175], and T223[177]. There is less contact with the carbapenem R2 side chains, strongly indicating that SMB-1 primarily recognizes the carbapenem core structure. This is the first report describing how a subclass B3 MBL recognizes carbapenems. We also solved the crystal structure of SMB-1 in complex with the approved drugs captopril, an inhibitor of the angiotensin-converting enzyme, and 2-mercaptoethanesulfonate, a chemoprotectant. These drugs are inhibitors of SMB-1 with Ki values of 8.9 and 184 μM, respectively. Like carbapenems, these inhibitors interact with Q157[113] and T223[177] and their thiol groups coordinate the zinc ions in the active site. Taken together, the data indicate that Q157[113], S221[175], T223[177], and the two zinc ions in the active site are key targets in the design of SMB-1 inhibitors with enhanced affinity. The structural data provide a solid foundation for the development of effective inhibitors that would overcome the carbapenem resistance of MBL-producing multidrug-resistant microbes.
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37
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Wang DY, Abboud MI, Markoulides MS, Brem J, Schofield CJ. The road to avibactam: the first clinically useful non-β-lactam working somewhat like a β-lactam. Future Med Chem 2016; 8:1063-84. [PMID: 27327972 DOI: 10.4155/fmc-2016-0078] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Avibactam, which is the first non-β-lactam β-lactamase inhibitor to be introduced for clinical use, is a broad-spectrum serine β-lactamase inhibitor with activity against class A, class C, and, some, class D β-lactamases. We provide an overview of efforts, which extend to the period soon after the discovery of the penicillins, to develop clinically useful non-β-lactam compounds as antibacterials, and, subsequently, penicillin-binding protein and β-lactamase inhibitors. Like the β-lactam inhibitors, avibactam works via a mechanism involving covalent modification of a catalytically important nucleophilic serine residue. However, unlike the β-lactam inhibitors, avibactam reacts reversibly with its β-lactamase targets. We discuss chemical factors that may account for the apparently special nature of β-lactams and related compounds as antibacterials and β-lactamase inhibitors, including with respect to resistance. Avenues for future research including non-β-lactam antibacterials acting similarly to β-lactams are discussed.
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Affiliation(s)
| | | | | | - Jürgen Brem
- Department of Chemistry, University of Oxford, UK
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38
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Prombhul S, Tribuddharat C, Laikijrung P, Aranya C, Bamrungsri N, Mekviwattanawong S. New variant of an imipenemase, IMP-32, in Klebsiella pneumoniae from a fatal case of a Thai patient. J Med Microbiol 2016; 65:572-573. [DOI: 10.1099/jmm.0.000252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sasiprapa Prombhul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanwit Tribuddharat
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Patsorn Laikijrung
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
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Montagner C, Nigen M, Jacquin O, Willet N, Dumoulin M, Karsisiotis AI, Roberts GCK, Damblon C, Redfield C, Matagne A. The Role of Active Site Flexible Loops in Catalysis and of Zinc in Conformational Stability of Bacillus cereus 569/H/9 β-Lactamase. J Biol Chem 2016; 291:16124-37. [PMID: 27235401 DOI: 10.1074/jbc.m116.719005] [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: 03/03/2016] [Indexed: 11/06/2022] Open
Abstract
Metallo-β-lactamases catalyze the hydrolysis of most β-lactam antibiotics and hence represent a major clinical concern. The development of inhibitors for these enzymes is complicated by the diversity and flexibility of their substrate-binding sites, motivating research into their structure and function. In this study, we examined the conformational properties of the Bacillus cereus β-lactamase II in the presence of chemical denaturants using a variety of biochemical and biophysical techniques. The apoenzyme was found to unfold cooperatively, with a Gibbs free energy of stabilization (ΔG(0)) of 32 ± 2 kJ·mol(-1) For holoBcII, a first non-cooperative transition leads to multiple interconverting native-like states, in which both zinc atoms remain bound in an apparently unaltered active site, and the protein displays a well organized compact hydrophobic core with structural changes confined to the enzyme surface, but with no catalytic activity. Two-dimensional NMR data revealed that the loss of activity occurs concomitantly with perturbations in two loops that border the enzyme active site. A second cooperative transition, corresponding to global unfolding, is observed at higher denaturant concentrations, with ΔG(0) value of 65 ± 1.4 kJ·mol(-1) These combined data highlight the importance of the two zinc ions in maintaining structure as well as a relatively well defined conformation for both active site loops to maintain enzymatic activity.
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Affiliation(s)
- Caroline Montagner
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Michaël Nigen
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Olivier Jacquin
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Nicolas Willet
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Mireille Dumoulin
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
| | - Andreas Ioannis Karsisiotis
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, United Kingdom
| | - Gordon C K Roberts
- the Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom, and
| | - Christian Damblon
- Département de Chimie, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
| | - Christina Redfield
- the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - André Matagne
- From the Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, and
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Lee SY, Brem J, Pettinati I, Claridge TDW, Gileadi O, Schofield CJ, McHugh PJ. Cephalosporins inhibit human metallo β-lactamase fold DNA repair nucleases SNM1A and SNM1B/apollo. Chem Commun (Camb) 2016; 52:6727-30. [PMID: 27121860 PMCID: PMC5063058 DOI: 10.1039/c6cc00529b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/18/2016] [Indexed: 12/19/2022]
Abstract
Bacterial metallo-β-lactamases (MBLs) are involved in resistance to β-lactam antibiotics including cephalosporins. Human SNM1A and SNM1B are MBL superfamily exonucleases that play a key role in the repair of DNA interstrand cross-links, which are induced by antitumour chemotherapeutics, and are therefore targets for cancer chemosensitization. We report that cephalosporins are competitive inhibitors of SNM1A and SNM1B exonuclease activity; both the intact β-lactam and their hydrolysed products are active. This discovery provides a lead for the development of potent and selective SNM1A and SNM1B inhibitors.
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Affiliation(s)
- Sook Y Lee
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK. and Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Jürgen Brem
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Ilaria Pettinati
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Timothy D W Claridge
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Opher Gileadi
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, OX3 7DQ, UK
| | | | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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41
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Kinetic Study of Laboratory Mutants of NDM-1 Metallo-β-Lactamase and the Importance of an Isoleucine at Position 35. Antimicrob Agents Chemother 2016; 60:2366-72. [PMID: 26856833 DOI: 10.1128/aac.00531-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 01/25/2016] [Indexed: 01/27/2023] Open
Abstract
Two laboratory mutants of NDM-1 were generated by replacing the isoleucine at position 35 with threonine and serine residues: the NDM-1(I35T)and NDM-1(I35S)enzymes. These mutants were well characterized, and their kinetic parameters were compared with those of the NDM-1 wild type. Thekcat,Km, andkcat/Kmvalues calculated for the two mutants were slightly different from those of the wild-type enzyme. Interestingly, thekcat/Kmof NDM-1(I35S)for loracarbef was about 14-fold higher than that of NDM-1. Far-UV circular dichroism (CD) spectra of NDM-1 and NDM-1(I35T)and NDM-1(I35S)enzymes suggest local structural rearrangements in the secondary structure with a marked reduction of α-helix content in the mutants.
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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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Rotondo CM, Marrone L, Goodfellow VJ, Ghavami A, Labbé G, Spencer J, Dmitrienko GI, Siemann S. Arginine-containing peptides as potent inhibitors of VIM-2 metallo-β-lactamase. Biochim Biophys Acta Gen Subj 2015; 1850:2228-38. [DOI: 10.1016/j.bbagen.2015.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
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Amolegbe SA, Adewuyi S, Akinremi CA, Adediji JF, Lawal A, Atayese AO, Obaleye JA. Iron(III) and copper(II) complexes bearing 8-quinolinol with amino-acids mixed ligands: Synthesis, characterization and antibacterial investigation. ARAB J CHEM 2015. [DOI: 10.1016/j.arabjc.2014.11.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Abstract
Swarming bacteria are challenged by the need to invade hostile environments. Swarms of the flagellated bacterium Paenibacillus vortex can collectively transport other microorganisms. Here we show that P. vortex can invade toxic environments by carrying antibiotic-degrading bacteria; this transport is mediated by a specialized, phenotypic subpopulation utilizing a process not dependent on cargo motility. Swarms of beta-lactam antibiotic (BLA)-sensitive P. vortex used beta-lactamase-producing, resistant, cargo bacteria to detoxify BLAs in their path. In the presence of BLAs, both transporter and cargo bacteria gained from this temporary cooperation; there was a positive correlation between BLA resistance and dispersal. P. vortex transported only the most beneficial antibiotic-resistant cargo (including environmental and clinical isolates) in a sustained way. P. vortex displayed a bet-hedging strategy that promoted the colonization of nontoxic niches by P. vortex alone; when detoxifying cargo bacteria were not needed, they were lost. This work has relevance for the dispersal of antibiotic-resistant microorganisms and for strategies for asymmetric cooperation with agricultural and medical implications. Antibiotic resistance is a major health threat. We show a novel mechanism for the local spread of antibiotic resistance. This involves interactions between different bacteria: one species provides an enzyme that detoxifies the antibiotic (a sessile cargo bacterium carrying a resistance gene), while the other (Paenibacillus vortex) moves itself and transports the cargo. P. vortex used a bet-hedging strategy, colonizing new environments alone when the cargo added no benefit, but cooperating when the cargo was needed. This work is of interest in an evolutionary context and sheds light on fundamental questions, such as how environmental antibiotic resistance may lead to clinical resistance and also microbial social organization, as well as the costs, benefits, and risks of dispersal in the environment.
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Affiliation(s)
- Ravi Tripathi
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department
of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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47
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Miraula M, Whitaker JJ, Schenk G, Mitić N. β-Lactam antibiotic-degrading enzymes from non-pathogenic marine organisms: a potential threat to human health. J Biol Inorg Chem 2015; 20:639-51. [PMID: 25773168 DOI: 10.1007/s00775-015-1250-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Metallo-β-lactamases (MBLs) are a family of Zn(II)-dependent enzymes that inactivate most of the commonly used β-lactam antibiotics. They have emerged as a major threat to global healthcare. Recently, we identified two novel MBL-like proteins, Maynooth IMipenemase-1 (MIM-1) and Maynooth IMipenemase-2 (MIM-2), in the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans, respectively. Here, we demonstrate that MIM-1 and MIM-2 have catalytic activities comparable to those of known MBLs, but from the pH dependence of their catalytic parameters it is evident that both enzymes differ with respect to their mechanisms, with MIM-1 preferring alkaline and MIM-2 acidic conditions. Both enzymes require Zn(II) but activity can also be reconstituted with other metal ions including Co(II), Mn(II), Cu(II) and Ca(II). Importantly, the substrate preference of MIM-1 and MIM-2 appears to be influenced by their metal ion composition. Since neither N. pentaromativorans nor S. agarivorans are human pathogens, the precise biological role(s) of MIM-1 and MIM-2 remains to be established. However, due to the similarity of at least some of their in vitro functional properties to those of known MBLs, MIM-1 and MIM-2 may provide essential structural insight that may guide the design of as of yet elusive clinically useful MBL inhibitors.
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Affiliation(s)
- Manfredi Miraula
- Department of Chemistry, Maynooth University, Maynooth, Co., Kildare, Ireland
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Sahuquillo-Arce JM, Hernández-Cabezas A, Yarad-Auad F, Ibáñez-Martínez E, Falomir-Salcedo P, Ruiz-Gaitán A. Carbapenemases: A worldwide threat to antimicrobial therapy. World J Pharmacol 2015; 4:75-95. [DOI: 10.5497/wjp.v4.i1.75] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 11/07/2014] [Accepted: 12/01/2014] [Indexed: 02/07/2023] Open
Abstract
Carbapenems are potent β-lactams with activity against extended-spectrum cephalosporinases and β-lactamases. These antibiotics, derived from thienamycn, a carbapenem produced by the environmental bacterium Streptomyces cattleya, were initially used as last-resort treatments for severe Gram-negative bacterial infections presenting resistance to most β-lactams but have become an empirical option in countries with high prevalence of Extended Spectrum β-lactamase-producing bacterial infections. Imipenem, the first commercially available carbapenem, was approved for clinical use in 1985. Since then, a wide variety of carbapenem-resistant bacteria has appeared, primarily Enterobacteriaceae such as Escherichia coli or Klebsiella pneumoniae (K. pneumoniae), Pseudomonas aeruginosa and Acinetobacter baumannii, presenting different resistance mechanisms. The most relevant mechanism is the production of carbapenem-hydrolyzing β-lactamases, also known as carbapenemases. These enzymes also inactivate all known β-lactams, and some of these enzymes can be acquired through horizontal gene transfer. Moreover, plasmids, transposons and integrons harboring these genes typically carry other resistance determinants, rendering the recipient bacteria resistant to almost all currently used antimicrobials, as is the case for K. pneumoniae carbapenemase - or New Delhi metallo-β-lactamases-type enzymes. The recent advent of these enzymes in the health landscape presents a serious challenge. First, the emergence of carbapenemases limits the currently available treatment options; second, these enzymes pose a risk to patients, as some studies have demonstrated high mortality associated with carbapenemase-producing bacterial infections; and third, these circumstances require an extra cost to sanitary systems, which are particularly cumbersome in developing countries. Therefore, emphasis should be placed on the early detection of these enzymes, the prevention of the spread of carbapenemase-producing bacteria and the development of new drugs resistant to carbapenemase hydrolysis.
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49
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Sgrignani J, Novati B, Colombo G, Grazioso G. Covalent docking of selected boron-based serine beta-lactamase inhibitors. J Comput Aided Mol Des 2015; 29:441-50. [DOI: 10.1007/s10822-015-9834-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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50
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Rhodanine hydrolysis leads to potent thioenolate mediated metallo-β-lactamase inhibition. Nat Chem 2014; 6:1084-90. [DOI: 10.1038/nchem.2110] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 10/08/2014] [Indexed: 12/29/2022]
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