1
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van den Berg DF, Costa AR, Esser JQ, Stanciu I, Geissler JQ, Zoumaro-Djayoon AD, Haas PJ, Brouns SJJ. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe 2024; 32:1427-1443.e8. [PMID: 39094584 DOI: 10.1016/j.chom.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Prokaryotes have evolved a multitude of defense systems to protect against phage predation. Some of these resemble eukaryotic genes involved in antiviral responses. Here, we set out to systematically project the current knowledge of eukaryotic-like antiviral defense systems onto prokaryotic genomes, using Pseudomonas aeruginosa as a model organism. Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates. We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling. Collectively, these defense systems support the concept of deep evolutionary links and shared antiviral mechanisms between prokaryotes and eukaryotes.
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Affiliation(s)
- Daan F van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Jelger Q Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Ilinka Stanciu
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Jasper Q Geissler
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | | | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
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2
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Swift LP, Lagerholm BC, Henderson LR, Ratnaweera M, Baddock HT, Sengerova B, Lee S, Cruz-Migoni A, Waithe D, Renz C, Ulrich HD, Newman JA, Schofield CJ, McHugh PJ. SNM1A is crucial for efficient repair of complex DNA breaks in human cells. Nat Commun 2024; 15:5392. [PMID: 38918391 PMCID: PMC11199599 DOI: 10.1038/s41467-024-49583-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
DNA double-strand breaks (DSBs), such as those produced by radiation and radiomimetics, are amongst the most toxic forms of cellular damage, in part because they involve extensive oxidative modifications at the break termini. Prior to completion of DSB repair, the chemically modified termini must be removed. Various DNA processing enzymes have been implicated in the processing of these dirty ends, but molecular knowledge of this process is limited. Here, we demonstrate a role for the metallo-β-lactamase fold 5'-3' exonuclease SNM1A in this vital process. Cells disrupted for SNM1A manifest increased sensitivity to radiation and radiomimetic agents and show defects in DSB damage repair. SNM1A is recruited and is retained at the sites of DSB damage via the concerted action of its three highly conserved PBZ, PIP box and UBZ interaction domains, which mediate interactions with poly-ADP-ribose chains, PCNA and the ubiquitinated form of PCNA, respectively. SNM1A can resect DNA containing oxidative lesions induced by radiation damage at break termini. The combined results reveal a crucial role for SNM1A to digest chemically modified DNA during the repair of DSBs and imply that the catalytic domain of SNM1A is an attractive target for potentiation of radiotherapy.
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Affiliation(s)
- Lonnie P Swift
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Cell Imaging and Cytometry Core, Turku Bioscience Centre, University of Turku and Åbo Akademi, ku, Finland
| | - Lucy R Henderson
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Malitha Ratnaweera
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hannah T Baddock
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Calico Life Sciences, South San Francisco, CA, USA
| | - Blanka Sengerova
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sook Lee
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Abimael Cruz-Migoni
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Dominic Waithe
- Wolfson Imaging Centre, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Christian Renz
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Mainz, Germany
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Peter J McHugh
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom.
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3
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Rodriguez P, Blakely RD. Sink or swim: Does a worm paralysis phenotype hold clues to neurodegenerative disease? J Cell Physiol 2024; 239:e31125. [PMID: 37795580 DOI: 10.1002/jcp.31125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
Receiving a neurodegenerative disease (NDD) diagnosis, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, or amyotrophic lateral sclerosis, is devastating, particularly given the limited options for treatment. Advances in genetic technologies have allowed for efficient modeling of NDDs in animals and brought hope for new disease-modifying medications. The complexity of the mammalian brain and the costs and time needed to identify and develop therapeutic leads limits progress. Modeling NDDs in invertebrates, such as the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans, offers orders of magnitude increases in speed of genetic analysis and manipulation, and can be pursued at substantially reduced cost, providing an important, platform complement and inform research with mammalian NDD models. In this review, we describe how our efforts to exploit C. elegans for the study of neural signaling and health led to the discovery of a paralytic phenotype (swimming-induced paralysis) associated with altered dopamine signaling and, surprisingly, to the discovery of a novel gene and pathway whose dysfunction in glial cells triggers neurodegeneration. Research to date on swip-10 and its putative mammalian ortholog MBLAC1, suggests that a tandem analysis will offer insights into NDD mechanisms and insights into novel, disease-modifying therapeutics.
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Affiliation(s)
- Peter Rodriguez
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Boca Raton, Florida, USA
| | - Randy D Blakely
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Boca Raton, Florida, USA
- Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, Florida, USA
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4
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Bielinski M, Henderson LR, Yosaatmadja Y, Swift LP, Baddock HT, Bowen MJ, Brem J, Jones PS, McElroy SP, Morrison A, Speake M, van Boeckel S, van Doornmalen E, van Groningen J, van den Hurk H, Gileadi O, Newman JA, McHugh PJ, Schofield CJ. Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target. Chem Sci 2024; 15:8227-8241. [PMID: 38817593 PMCID: PMC11134331 DOI: 10.1039/d4sc00367e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/30/2024] [Indexed: 06/01/2024] Open
Abstract
The three human SNM1 metallo-β-lactamase fold nucleases (SNM1A-C) play key roles in DNA damage repair and in maintaining telomere integrity. Genetic studies indicate that they are attractive targets for cancer treatment and to potentiate chemo- and radiation-therapy. A high-throughput screen for SNM1A inhibitors identified diverse pharmacophores, some of which were shown by crystallography to coordinate to the di-metal ion centre at the SNM1A active site. Structure and turnover assay-guided optimization enabled the identification of potent quinazoline-hydroxamic acid containing inhibitors, which bind in a manner where the hydroxamic acid displaces the hydrolytic water and the quinazoline ring occupies a substrate nucleobase binding site. Cellular assays reveal that SNM1A inhibitors cause sensitisation to, and defects in the resolution of, cisplatin-induced DNA damage, validating the tractability of MBL fold nucleases as cancer drug targets.
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Affiliation(s)
- Marcin Bielinski
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Lucy R Henderson
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Yuliana Yosaatmadja
- Centre for Medicines Discovery, NDM Research Building, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Lonnie P Swift
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Matthew J Bowen
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jürgen Brem
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Philip S Jones
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | - Stuart P McElroy
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | - Angus Morrison
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | - Michael Speake
- University of Dundee, European Screening Centre Newhouse ML1 5UH UK
| | | | | | | | | | - Opher Gileadi
- Centre for Medicines Discovery, NDM Research Building, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Joseph A Newman
- Centre for Medicines Discovery, NDM Research Building, University of Oxford Old Road Campus Research Building, Roosevelt Drive Oxford OX3 7DQ UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital Oxford OX3 9DS UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford Mansfield Road Oxford OX1 3TA UK
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5
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de Souza J, Vieira AZ, Dos Santos HG, Faoro H. Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group. BMC Genomics 2024; 25:508. [PMID: 38778284 PMCID: PMC11112869 DOI: 10.1186/s12864-024-10410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher's exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems. We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.
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Affiliation(s)
- Joyce de Souza
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | - Alexandre Zanatta Vieira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil
| | | | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Paraná, 81350-010, Brazil.
- Department of Microbiology, Infectious Disease and Immunology, CHU de Quebec Research Center, University Laval, Quebec, QC, G1V 0A6, Canada.
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6
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Diaz A, G S, Balaji S, Ramakrishnan J, Thamotharan S, Ramakrishnan V. Comprehensive screening of marine metabolites against class B1 metallo-β-lactamases of Klebsiella pneumoniae using two-pronged in silico approach. J Biomol Struct Dyn 2023; 41:10930-10943. [PMID: 36541935 DOI: 10.1080/07391102.2022.2159532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
The emergence of antibiotic resistance is one of the major global threats in healthcare. Metallo-β-Lactamases (MBL) are a class of enzymes in bacteria that cleave β-lactam antibiotics and confer resistance. MBLs are further divided into subclasses B1, B2 and B3. Of these, subclasses B1-MBLs (including NDM-1, VIM-2 and IMP-1) constitute the clinically prevalent lactamases conferring resistance. To date, no effective drugs are available clinically against MBLs. In this work, we aim to identify potent inhibitors for the B1 subclass of MBL from available marine metabolites in Comprehensive Marine Natural Product database through integrated in silico approaches. We have used two methods, namely, the high-throughput strategy and the pharmacophore-based strategy to identify potential inhibitors from marine metabolites. High-throughput virtual screening identified N-methyl mycosporine-Ser, which had the highest binding affinity to NDM-1. The pharmacophore-based approach based on co-crystallized ligands identified makaluvic acid and didymellamide with higher binding affinity across B1-MBLs. Taking into account of the advantage of a pharmacophore model-based approach with higher binding affinity, we conclude that both makaluvic acid and didymellamide show potential broad-spectrum effects by binding to all three B1-MBL receptors. The study also indicates the need to take multiple in silico approaches to screen and identify novel inhibitors. Together, our study reveals promising inhibitors that can be identified from marine systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aathithya Diaz
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Shripushkar G
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Shruti Balaji
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | | | - Subbiah Thamotharan
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Vigneshwar Ramakrishnan
- School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, India
- Bioinformatics Center, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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7
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Thore S, Raoelijaona F, Talenton V, Fribourg S, Mackereth CD. Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin. Open Biol 2023; 13:230221. [PMID: 37989222 PMCID: PMC10688271 DOI: 10.1098/rsob.230221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 11/23/2023] Open
Abstract
Eukaryotic pre-mRNA is processed by a large multiprotein complex to accurately cleave the 3' end, and to catalyse the addition of the poly(A) tail. Within this cleavage and polyadenylation specificity factor (CPSF) machinery, the CPSF73/CPSF3 endonuclease subunit directly contacts both CPSF100/CPSF2 and the scaffold protein Symplekin to form a subcomplex known as the core cleavage complex or mammalian cleavage factor. Here we have taken advantage of a stable CPSF73-CPSF100 minimal heterodimer from Encephalitozoon cuniculi to determine the solution structure formed by the first and second C-terminal domain (CTD1 and CTD2) of both proteins. We find a large number of contacts between both proteins in the complex, and notably in the region between CTD1 and CTD2. A similarity is also observed between CTD2 and the TATA-box binding protein (TBP) domains. Separately, we have determined the structure of the terminal CTD3 domain of CPSF73, which also belongs to the TBP domain family and is connected by a flexible linker to the rest of CPSF73. Biochemical assays demonstrate a key role for the CTD3 of CPSF73 in binding Symplekin, and structural models of the trimeric complex from other species allow for comparative analysis and support an overall conserved architecture.
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Affiliation(s)
- Stéphane Thore
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Finaritra Raoelijaona
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Vincent Talenton
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, Institut Européen de Chimie et Biologie, U1212, UMR 5320, 33600 Pessac, France
| | - Sébastien Fribourg
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, U1212, UMR 5320, 33000 Bordeaux, France
| | - Cameron D. Mackereth
- Inserm, CNRS, ARNA Laboratory, Univ. Bordeaux, Institut Européen de Chimie et Biologie, U1212, UMR 5320, 33600 Pessac, France
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8
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Ayipo YO, Ahmad I, Alananzeh W, Lawal A, Patel H, Mordi MN. Computational modelling of potential Zn-sensitive non-β-lactam inhibitors of imipenemase-1 (IMP-1). J Biomol Struct Dyn 2023; 41:10096-10116. [PMID: 36476097 DOI: 10.1080/07391102.2022.2153168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance (AR) remains one of the leading global health challenges, mostly implicated in disease-related deaths. The Enterobacteriaceae-producing metallo-β-lactamases (MBLs) are critically involved in AR pathogenesis through Zn-dependent catalytic destruction of β-lactam antibiotics, yet with limited successful clinical inhibitors. The efficacy of relevant broad-spectrum β-lactams including imipenem and meropenem are seriously challenged by their susceptibility to the Zn-dependent carbapenemase hydrolysis, as such, searching for alternatives remains imperative. In this study, computational molecular modelling and virtual screening methods were extensively applied to identify new putative Zn-sensitive broad-spectrum inhibitors of MBLs, specifically imipenemase-1 (IMP-1) from the IBScreen database. Three ligands, STOCK3S-30154, STOCK3S-30418 and STOCK3S-30514 selectively displayed stronger binding interactions with the enzymes compared to reference inhibitors, imipenem and meropenem. For instance, the ligands showed molecular docking scores of -9.450, -8.005 and -10.159 kcal/mol, and MM-GBSA values of -40.404, -31.902 and -33.680 kcal/mol respectively against the IMP-1. Whereas, imipenem and meropenem showed docking scores of -9.038 and -10.875 kcal/mol, and MM-GBSA of -31.184 and -32.330 kcal/mol respectively against the enzyme. The ligands demonstrated good thermodynamic stability and compactness in complexes with IMP-1 throughout the 100 ns molecular dynamics (MD) trajectories. Interestingly, their binding affinities and stabilities were significantly affected in contacts with the remodelled Zn-deficient IMP-1, indicating sensitivity to the carbapenemase active Zn site, however, with non-β-lactam scaffolds, tenable to resist catalytic hydrolysis. They displayed ideal drug-like ADMET properties, thus, representing putative Zn-sensitive non-β-lactam inhibitors of IMP-1 amenable for further experimental studies.
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Affiliation(s)
- Yusuf Oloruntoyin Ayipo
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
- Department of Chemistry and Industrial Chemistry, Kwara State University, Ilorin, Nigeria
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Waleed Alananzeh
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
| | - Amudat Lawal
- Department of Chemistry, University of Ilorin, Ilorin, Nigeria
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Mohd Nizam Mordi
- Centre for Drug Research, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
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9
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Ji P, Yang K, Xu Q, Qin G, Zhu Q, Qian Y, Yao W. Mechanisms and Application of Gas-Based Anticancer Therapies. Pharmaceuticals (Basel) 2023; 16:1394. [PMID: 37895865 PMCID: PMC10609769 DOI: 10.3390/ph16101394] [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: 08/15/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Cancer is still one of the major factors threatening public health, with morbidity and mortality rates at the forefront of the world. Clinical drawbacks, such as high toxicity and side effects of drug therapy, and easy recurrence after surgery affect its therapeutic effect. Gas signaling molecules are essential in maintaining biological homeostasis and physiological functions as specific chemical substances for biological information transfer. In recent years, the physiological regulatory functions of gas molecules in the cancer process have been gradually revealed and have shown broad application prospects in tumor therapy. In this paper, standard gas therapies are classified and introduced. Taking H2, CO2, NO, CO, H2S, and SO2 gases as examples, the research progress and application of gas therapies in malignant tumors are mainly introduced in terms of biological characteristics, anticancer mechanisms, and treatment strategies. Finally, the problems and prospects for developing gases as anticancer drugs are outlined.
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Affiliation(s)
- Peng Ji
- College of Pharmacy and Chemistry & Chemical Engineering, Jiangsu Provincial Key Laboratory of Chiral Pharmaceutical Chemicals Biologically Manufacturing, Taizhou University, Taizhou 225300, China
| | - Kexin Yang
- College of Pharmacy and Chemistry & Chemical Engineering, Jiangsu Provincial Key Laboratory of Chiral Pharmaceutical Chemicals Biologically Manufacturing, Taizhou University, Taizhou 225300, China
| | - Qingqing Xu
- College of Pharmacy and Chemistry & Chemical Engineering, Jiangsu Provincial Key Laboratory of Chiral Pharmaceutical Chemicals Biologically Manufacturing, Taizhou University, Taizhou 225300, China
| | - Guilin Qin
- College of Pharmacy and Chemistry & Chemical Engineering, Jiangsu Provincial Key Laboratory of Chiral Pharmaceutical Chemicals Biologically Manufacturing, Taizhou University, Taizhou 225300, China
| | - Qianyu Zhu
- College of Pharmacy and Chemistry & Chemical Engineering, Jiangsu Provincial Key Laboratory of Chiral Pharmaceutical Chemicals Biologically Manufacturing, Taizhou University, Taizhou 225300, China
| | - Ying Qian
- College of Pharmacy and Chemistry & Chemical Engineering, Jiangsu Provincial Key Laboratory of Chiral Pharmaceutical Chemicals Biologically Manufacturing, Taizhou University, Taizhou 225300, China
| | - Wenshui Yao
- Department of Anesthesiology, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou 350001, China
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10
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Yang SY, Liao L, Hu SY, Deng L, Andriani L, Zhang TM, Zhang YL, Ma XY, Zhang FL, Liu YY, Li DQ. ETHE1 Accelerates Triple-Negative Breast Cancer Metastasis by Activating GCN2/eIF2α/ATF4 Signaling. Int J Mol Sci 2023; 24:14566. [PMID: 37834012 PMCID: PMC10572406 DOI: 10.3390/ijms241914566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most fatal subtype of breast cancer; however, effective treatment strategies for TNBC are lacking. Therefore, it is important to explore the mechanism of TNBC metastasis and identify its therapeutic targets. Dysregulation of ETHE1 leads to ethylmalonic encephalopathy in humans; however, the role of ETHE1 in TNBC remains elusive. Stable cell lines with ETHE1 overexpression or knockdown were constructed to explore the biological functions of ETHE1 during TNBC progression in vitro and in vivo. Mass spectrometry was used to analyze the molecular mechanism through which ETHE1 functions in TNBC progression. ETHE1 had no impact on TNBC cell proliferation and xenograft tumor growth but promoted TNBC cell migration and invasion in vitro and lung metastasis in vivo. The effect of ETHE1 on TNBC cell migratory potential was independent of its enzymatic activity. Mechanistic investigations revealed that ETHE1 interacted with eIF2α and enhanced its phosphorylation by promoting the interaction between eIF2α and GCN2. Phosphorylated eIF2α in turn upregulated the expression of ATF4, a transcriptional activator of genes involved in cell migration and tumor metastasis. Notably, inhibition of eIF2α phosphorylation through ISRIB or ATF4 knockdown partially abolished the tumor-promoting effect of ETHE1 overexpression. ETHE1 has a functional and mechanistic role in TNBC metastasis and offers a new therapeutic strategy for targeting ETHE1-propelled TNBC using ISRIB.
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Affiliation(s)
- Shao-Ying Yang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; (S.-Y.Y.); (L.L.); (S.-Y.H.); (L.D.); (T.-M.Z.)
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China; (Y.-L.Z.); (F.-L.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li Liao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; (S.-Y.Y.); (L.L.); (S.-Y.H.); (L.D.); (T.-M.Z.)
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China; (Y.-L.Z.); (F.-L.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Shu-Yuan Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; (S.-Y.Y.); (L.L.); (S.-Y.H.); (L.D.); (T.-M.Z.)
| | - Ling Deng
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; (S.-Y.Y.); (L.L.); (S.-Y.H.); (L.D.); (T.-M.Z.)
| | - Lisa Andriani
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China; (L.A.); (X.-Y.M.)
| | - Tai-Mei Zhang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; (S.-Y.Y.); (L.L.); (S.-Y.H.); (L.D.); (T.-M.Z.)
| | - Yin-Ling Zhang
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China; (Y.-L.Z.); (F.-L.Z.)
| | - Xiao-Yan Ma
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China; (L.A.); (X.-Y.M.)
| | - Fang-Lin Zhang
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China; (Y.-L.Z.); (F.-L.Z.)
| | - Ying-Ying Liu
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China; (L.A.); (X.-Y.M.)
| | - Da-Qiang Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; (S.-Y.Y.); (L.L.); (S.-Y.H.); (L.D.); (T.-M.Z.)
- Cancer Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China; (Y.-L.Z.); (F.-L.Z.)
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Department of Breast Surgery, Shanghai Medical College, Fudan University, Shanghai 200032, China; (L.A.); (X.-Y.M.)
- Shanghai Key Laboratory of Breast Cancer, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Radiation Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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11
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Deschênes T, Tohoundjona FWE, Plante PL, Di Marzo V, Raymond F. Gene-based microbiome representation enhances host phenotype classification. mSystems 2023; 8:e0053123. [PMID: 37404032 PMCID: PMC10469787 DOI: 10.1128/msystems.00531-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023] Open
Abstract
With the concomitant advances in both the microbiome and machine learning fields, the gut microbiome has become of great interest for the potential discovery of biomarkers to be used in the classification of the host health status. Shotgun metagenomics data derived from the human microbiome is composed of a high-dimensional set of microbial features. The use of such complex data for the modeling of host-microbiome interactions remains a challenge as retaining de novo content yields a highly granular set of microbial features. In this study, we compared the prediction performances of machine learning approaches according to different types of data representations derived from shotgun metagenomics. These representations include commonly used taxonomic and functional profiles and the more granular gene cluster approach. For the five case-control datasets used in this study (Type 2 diabetes, obesity, liver cirrhosis, colorectal cancer, and inflammatory bowel disease), gene-based approaches, whether used alone or in combination with reference-based data types, allowed improved or similar classification performances as the taxonomic and functional profiles. In addition, we show that using subsets of gene families from specific functional categories of genes highlight the importance of these functions on the host phenotype. This study demonstrates that both reference-free microbiome representations and curated metagenomic annotations can provide relevant representations for machine learning based on metagenomic data. IMPORTANCE Data representation is an essential part of machine learning performance when using metagenomic data. In this work, we show that different microbiome representations provide varied host phenotype classification performance depending on the dataset. In classification tasks, untargeted microbiome gene content can provide similar or improved classification compared to taxonomical profiling. Feature selection based on biological function also improves classification performance for some pathologies. Function-based feature selection combined with interpretable machine learning algorithms can generate new hypotheses that can potentially be assayed mechanistically. This work thus proposes new approaches to represent microbiome data for machine learning that can potentiate the findings associated with metagenomic data.
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Affiliation(s)
- Thomas Deschênes
- Centre Nutrition, Santé et Société (NUTRISS) – Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
- Canada Research Excellence Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND), Quebec City, Quebec, Canada
- Institut Intelligence et Données, Université Laval, Québec, Canada
| | - Fred Wilfried Elom Tohoundjona
- Centre Nutrition, Santé et Société (NUTRISS) – Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
- Canada Research Excellence Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND), Quebec City, Quebec, Canada
| | - Pier-Luc Plante
- Centre Nutrition, Santé et Société (NUTRISS) – Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
- Canada Research Excellence Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND), Quebec City, Quebec, Canada
- Institut Intelligence et Données, Université Laval, Québec, Canada
| | - Vincenzo Di Marzo
- Centre Nutrition, Santé et Société (NUTRISS) – Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
- Canada Research Excellence Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND), Quebec City, Quebec, Canada
- École de nutrition, Faculté des sciences de l’agriculture et de l’alimentation (FSAA), Université Laval, Québec, Canada
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Québec, Canada
- Département de médecine, Faculté de Médecine, Université Laval, Québec, Canada
- Joint International Unit on Chemical and Biomolecular Research on the Microbiome and its Impact on Metabolic Health and Nutrition (UMI-MicroMeNu), Quebec City, Canada
| | - Frédéric Raymond
- Centre Nutrition, Santé et Société (NUTRISS) – Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Université Laval, Québec, Canada
- Canada Research Excellence Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND), Quebec City, Quebec, Canada
- Institut Intelligence et Données, Université Laval, Québec, Canada
- École de nutrition, Faculté des sciences de l’agriculture et de l’alimentation (FSAA), Université Laval, Québec, Canada
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12
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Geraffi N, Gupta P, Wagner N, Barash I, Pupko T, Sessa G. Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria. FRONTIERS IN PLANT SCIENCE 2023; 14:1198160. [PMID: 37583594 PMCID: PMC10425158 DOI: 10.3389/fpls.2023.1198160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
Acquisition of the pathogenicity plasmid pPATH that encodes a type III secretion system (T3SS) and effectors (T3Es) has likely led to the transition of a non-pathogenic bacterium into the tumorigenic pathogen Pantoea agglomerans. P. agglomerans pv. gypsophilae (Pag) forms galls on gypsophila (Gypsophila paniculata) and triggers immunity on sugar beet (Beta vulgaris), while P. agglomerans pv. betae (Pab) causes galls on both gypsophila and sugar beet. Draft sequences of the Pag and Pab genomes were previously generated using the MiSeq Illumina technology and used to determine partial T3E inventories of Pab and Pag. Here, we fully assembled the Pab and Pag genomes following sequencing with PacBio technology and carried out a comparative sequence analysis of the Pab and Pag pathogenicity plasmids pPATHpag and pPATHpab. Assembly of Pab and Pag genomes revealed a ~4 Mbp chromosome with a 55% GC content, and three and four plasmids in Pab and Pag, respectively. pPATHpag and pPATHpab share 97% identity within a 74% coverage, and a similar GC content (51%); they are ~156 kb and ~131 kb in size and consist of 198 and 155 coding sequences (CDSs), respectively. In both plasmids, we confirmed the presence of highly similar gene clusters encoding a T3SS, as well as auxin and cytokinins biosynthetic enzymes. Three putative novel T3Es were identified in Pab and one in Pag. Among T3SS-associated proteins encoded by Pag and Pab, we identified two novel chaperons of the ShcV and CesT families that are present in both pathovars with high similarity. We also identified insertion sequences (ISs) and transposons (Tns) that may have contributed to the evolution of the two pathovars. These include seven shared IS elements, and three ISs and two transposons unique to Pab. Finally, comparative sequence analysis revealed plasmid regions and CDSs that are present only in pPATHpab or in pPATHpag. The high similarity and common features of the pPATH plasmids support the hypothesis that the two strains recently evolved into host-specific pathogens.
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Affiliation(s)
- Naama Geraffi
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Priya Gupta
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Isaac Barash
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Guido Sessa
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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13
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Diene SM, Pontarotti P, Azza S, Armstrong N, Pinault L, Chabrière E, Colson P, Rolain JM, Raoult D. Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms. Cells 2023; 12:1752. [PMID: 37443786 PMCID: PMC10340364 DOI: 10.3390/cells12131752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities.
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Affiliation(s)
- Seydina M. Diene
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Pierre Pontarotti
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- CNRS SNC5039, 13005 Marseille, France
| | - Saïd Azza
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Nicholas Armstrong
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Lucile Pinault
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Eric Chabrière
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Philippe Colson
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Jean-Marc Rolain
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Didier Raoult
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
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14
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Krco S, Davis SJ, Joshi P, Wilson LA, Monteiro Pedroso M, Douw A, Schofield CJ, Hugenholtz P, Schenk G, Morris MT. Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup-emerging targets to combat antibiotic resistance. Front Chem 2023; 11:1196073. [PMID: 37408556 PMCID: PMC10318434 DOI: 10.3389/fchem.2023.1196073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis. Although nucleophilic serine-β-lactamases have long been clinically important, most broad-spectrum β-lactamases employ one or two metal ions (likely Zn2+) in catalysis. To date, potent and clinically useful inhibitors of these metallo-β-lactamases (MBLs) have not been available, exacerbating their negative impact on healthcare. MBLs are categorised into three subgroups: B1, B2, and B3 MBLs, depending on their sequence similarities, active site structures, interactions with metal ions, and substrate preferences. The majority of MBLs associated with the spread of antibiotic resistance belong to the B1 subgroup. Most characterized B3 MBLs have been discovered in environmental bacteria, but they are increasingly identified in clinical samples. B3-type MBLs display greater diversity in their active sites than other MBLs. Furthermore, at least one of the known B3-type MBLs is inhibited by the serine-β-lactamase inhibitor clavulanic acid, an observation that may promote the design of derivatives active against a broader range of MBLs. In this Mini Review, recent advances in structure-function relationships of B3-type MBLs will be discussed, with a view to inspiring inhibitor development to combat the growing spread of β-lactam resistance.
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Affiliation(s)
- Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Samuel J. Davis
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Pallav Joshi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Liam A. Wilson
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew Douw
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, The Ineos Oxford Institute for Antimicrobial Research, Oxford University, Oxford, United Kingdom
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Marc T. Morris
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
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15
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Russell ML, Simon N, Bradley P, Matsen FA. Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming. eLife 2023; 12:e85145. [PMID: 37227256 PMCID: PMC10212571 DOI: 10.7554/elife.85145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/11/2023] [Indexed: 05/26/2023] Open
Abstract
To appropriately defend against a wide array of pathogens, humans somatically generate highly diverse repertoires of B cell and T cell receptors (BCRs and TCRs) through a random process called V(D)J recombination. Receptor diversity is achieved during this process through both the combinatorial assembly of V(D)J-genes and the junctional deletion and insertion of nucleotides. While the Artemis protein is often regarded as the main nuclease involved in V(D)J recombination, the exact mechanism of nucleotide trimming is not understood. Using a previously published TCRβ repertoire sequencing data set, we have designed a flexible probabilistic model of nucleotide trimming that allows us to explore various mechanistically interpretable sequence-level features. We show that local sequence context, length, and GC nucleotide content in both directions of the wider sequence, together, can most accurately predict the trimming probabilities of a given V-gene sequence. Because GC nucleotide content is predictive of sequence-breathing, this model provides quantitative statistical evidence regarding the extent to which double-stranded DNA may need to be able to breathe for trimming to occur. We also see evidence of a sequence motif that appears to get preferentially trimmed, independent of GC-content-related effects. Further, we find that the inferred coefficients from this model provide accurate prediction for V- and J-gene sequences from other adaptive immune receptor loci. These results refine our understanding of how the Artemis nuclease may function to trim nucleotides during V(D)J recombination and provide another step toward understanding how V(D)J recombination generates diverse receptors and supports a powerful, unique immune response in healthy humans.
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Affiliation(s)
- Magdalena L Russell
- Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
- Molecular and Cellular Biology Program, University of WashingtonSeattleUnited States
| | - Noah Simon
- Department of Biostatistics, University of WashingtonSeattleUnited States
| | - Philip Bradley
- Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
- Institute for Protein Design, Department of Biochemistry, University of WashingtonSeattleUnited States
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Statistics, University of WashingtonSeattleUnited States
- Howard Hughes Medical InstituteSeattleUnited States
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16
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Luo Y, Zhang Y, Pang S, Min J, Wang T, Wu D, Lin C, Xiao Z, Xiang Q, Li Q, Ma L. PCBP1 protects bladder cancer cells from mitochondria injury and ferroptosis by inducing LACTB mRNA degradation. Mol Carcinog 2023. [PMID: 37157950 DOI: 10.1002/mc.23533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 05/10/2023]
Abstract
Although Poly C Binding Protein 1 (PCBP1) affects cellular ferroptosis and mitochondrial dysfunction, the mechanisms by which PCBP1 regulates bladder cancer (BC) cell functions are unknown. In this study, two BC cell lines (T24 and UMUC3) were treated with different doses of ferroptosis inducer erastin to analyze the effect of PCBP1. Online databases (RPISeq and CatRAPID) were used to predict the possible direct interaction between PCBP1 protein and serine β-lactamase-like protein (LACTB) mRNA, which was further validated via RNA pull-down, RNA immunoprecipitation, and luciferase reporter assays. Mitochondria injury and ferroptosis were evaluated using CCK-8 assay, TUNEL staining, flow cytometry, corresponding kits, and JC-1 staining. In vivo experiments were conducted using tumor xenograft models. Quantitative reverse-transcription polymerase chain reaction was used to detect transcript expression levels, while protein levels were analyzed using western blot and immunohistochemistry. PCBP1 expression was significantly upregulated in BC tissues and cell lines. Also, PCBP1 knockdown increased erastin-mediated ferroptosis in T24 and UMUC3 cells, while PCBP1 overexpression decreased erastin-mediated ferroptosis in T24 and UMUC3 cells. Mechanistic results showed that LACTB mRNA is a novel PCBP1-binding transcript. LACTB upregulation promoted erastin-induced ferroptosis and mitochondrial dysfunction. Furthermore, LACTB overexpression reversed PCBP1-mediated ferroptosis protection, including decreased ROS and enhanced mitochondrial function, which were further alleviated after phosphatidylserine decarboxylase (PISD) overexpression. Moreover, PCBP1 silencing significantly enhanced tumor inhibition effect of sulfasalazine in xenograft mice transplanted with T24 and UMUC3 cells, leading to LACTB upregulation and PISD downregulation. In conclusion, PCBP1 protects BC cells against mitochondria injury and ferroptosis via LACTB/PISD axis.
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Affiliation(s)
- Yang Luo
- Department of Urology, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Yunli Zhang
- Department of Pathology, Nanfang Hospital and School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shiyu Pang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jingxian Min
- Department of Health Management, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Wang
- Department of Urology, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Dali Wu
- Department of Urology, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Chun Lin
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zebin Xiao
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qi Xiang
- Department of Urology, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Qing Li
- Department of Urology, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Lili Ma
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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17
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Abstract
N-Acylphosphatidylethanolamine phospholipase D (NAPE-PLD) is regarded as the principal enzyme that generates N-acylethanolamines (NAEs), a family of signaling lipids that includes the endocannabinoid anandamide. To investigate the biological function and biosynthesis of NAEs, we sought to develop potent NAPE-PLD inhibitors. To this aim, we utilized a high-throughput screening-compatible NAPE-PLD activity assay, which uses the fluorescence-quenched substrate PED6. This assay conveniently uses membrane fractions of NAPE-PLD overexpressing HEK293T cell lysates, thus avoiding the need for protein purification. Here, we give a detailed description of the NAPE-PLD PED6 fluorescence activity assay, which has increased throughput compared to previous radioactivity- or mass-spectrometry-based assays.
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Affiliation(s)
- Elliot D Mock
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University & Oncode Institute, RA, Leiden, The Netherlands.
| | - Wouter P F Driever
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University & Oncode Institute, RA, Leiden, The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University & Oncode Institute, RA, Leiden, The Netherlands
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18
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Watanabe G, Lieber MR. Dynamics of the Artemis and DNA-PKcs Complex in the Repair of Double-Strand Breaks. J Mol Biol 2022; 434:167858. [PMID: 36270581 PMCID: PMC9940633 DOI: 10.1016/j.jmb.2022.167858] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
Pathologic chromosome breaks occur in human dividing cells ∼10 times per day, and physiologic breaks occur in each lymphoid cell many additional times per day. Nonhomologous DNA end joining (NHEJ) is the major pathway for the repair of all of these double-strand breaks (DSBs) during most of the cell cycle. Nearly all broken DNA ends require trimming before they can be suitable for joining by ligation. Artemis is the major nuclease for this purpose. Artemis is tightly regulated by one of the largest protein kinases, which tethers Artemis to its surface. This kinase is called DNA-dependent protein kinase catalytic subunit (or DNA-PKcs) because it is only active when it encounters a broken DNA end. With this activation, DNA-PKcs permits the Artemis catalytic domain to enter a large cavity in the center of DNA-PKcs. Given this remarkably tight supervision of Artemis by DNA-PKcs, it is an appropriate time to ask what we know about the Artemis:DNA-PKcs complex, as we integrate recent structural information with the biochemistry of the complex and how this relates to other NHEJ proteins and to V(D)J recombination in the immune system.
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Affiliation(s)
- Go Watanabe
- Department of Pathology, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Ave, Rm. 5428, Los Angeles, CA 90089, USA
| | - Michael R Lieber
- Department of Pathology, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Ave, Rm. 5428, Los Angeles, CA 90089, USA.
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19
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Inhibiting the metallo-β-lactamases: challenges and strategies to overcome bacterial β-lactam resistance. Future Med Chem 2022; 14:1021-1025. [DOI: 10.4155/fmc-2022-0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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20
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Metabolic Shades of S-D-Lactoylglutathione. Antioxidants (Basel) 2022; 11:antiox11051005. [PMID: 35624868 PMCID: PMC9138017 DOI: 10.3390/antiox11051005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
S-D-lactoylglutathione (SDL) is an intermediate of the glutathione-dependent metabolism of methylglyoxal (MGO) by glyoxalases. MGO is an electrophilic compound that is inevitably produced in conjunction with glucose breakdown and is essentially metabolized via the glyoxalase route. In the last decades, MGO metabolism and its cytotoxic effects have been under active investigation, while almost nothing is known about SDL. This article seeks to fill the gap by presenting an overview of the chemistry, biochemistry, physiological role and clinical importance of SDL. The effects of intracellular SDL are investigated in three main directions: as a substrate for post-translational protein modifications, as a reservoir for mitochondrial reduced glutathione and as an energy currency. In essence, all three approaches point to one direction, namely, a metabolism-related regulatory role, enhancing the cellular defense against insults. It is also suggested that an increased plasma concentration of SDL or its metabolites may possibly serve as marker molecules in hemolytic states, particularly when the cause of hemolysis is a disturbance of the pay-off phase of the glycolytic chain. Finally, SDL could also represent a useful marker in such metabolic disorders as diabetes mellitus or ketotic states, in which its formation is expected to be enhanced. Despite the lack of clear-cut evidence underlying the clinical and experimental findings, the investigation of SDL metabolism is a promising field of research.
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21
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Lamprey immunity protein enables detection for bladder cancer through recognizing N-hydroxyacetylneuraminic acid (Neu5Gc)-modified as a diagnostic marker and exploration of its production mechanism. Biochem Biophys Res Commun 2022; 614:153-160. [PMID: 35597152 DOI: 10.1016/j.bbrc.2022.04.121] [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: 04/12/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/23/2022]
Abstract
Previous studies have demonstrated that Neu5Gc is highly expressed in breast, ovarian, prostate, colon and lung cancers, but not in normal human cells. The presence of Neu5Gc is important for prognosis and is associated with aggressiveness, metastasis, and tumor grade. However, increased Neu5Gc in bladder cancer remains unclear. LIP from lamprey binds the carbohydrate receptor of N-glycolylneuraminic acid (Neu5Gc). The combination of Neu5Gc and LIP suggested that it might be used as a diagnostic tool for the detection of Neu5Gc tumor antigen. Here, the classical animal model of bladder cancer was successfully induced by MNU bladder perfusion. The ELISA results showed that the expression level of Neu5Gc in the urine of normal rats was 94.96 ± 21.01ng/mg, and that of bladder cancer rats was 158.28 ± 34.86 ng/mg. In addition, the results of SNA and LIP immunohistochemistry demonstrated the high expression of Neu5Gc in bladder cancer. After the addition of Neu5Gc to BIU-87 and SV-HUC-1 cells, transcriptomic sequencing and real-time quantitative PCR analysis demonstrated that the gene expression of Neu5Gc synthesis pathway was significantly increased. These data suggest that LIP provides a new tool for the detection of biological samples, especially urine from patients with bladder cancer or suspected cancer, and that revealing the mechanism of abnormal glycosylation can provide theoretical basis for clinical studies.
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22
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Brem J, Panduwawala T, Hansen JU, Hewitt J, Liepins E, Donets P, Espina L, Farley AJM, Shubin K, Campillos GG, Kiuru P, Shishodia S, Krahn D, Leśniak RK, Schmidt Adrian J, Calvopiña K, Turrientes MC, Kavanagh ME, Lubriks D, Hinchliffe P, Langley GW, Aboklaish AF, Eneroth A, Backlund M, Baran AG, Nielsen EI, Speake M, Kuka J, Robinson J, Grinberga S, Robinson L, McDonough MA, Rydzik AM, Leissing TM, Jimenez-Castellanos JC, Avison MB, Da Silva Pinto S, Pannifer AD, Martjuga M, Widlake E, Priede M, Hopkins Navratilova I, Gniadkowski M, Belfrage AK, Brandt P, Yli-Kauhaluoma J, Bacque E, Page MGP, Björkling F, Tyrrell JM, Spencer J, Lang PA, Baranczewski P, Cantón R, McElroy SP, Jones PS, Baquero F, Suna E, Morrison A, Walsh TR, Schofield CJ. Imitation of β-lactam binding enables broad-spectrum metallo-β-lactamase inhibitors. Nat Chem 2022; 14:15-24. [PMID: 34903857 DOI: 10.1038/s41557-021-00831-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 09/30/2021] [Indexed: 11/08/2022]
Abstract
Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.
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Affiliation(s)
- Jürgen Brem
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
| | - Tharindi Panduwawala
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | | | - Joanne Hewitt
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
| | | | - Pawel Donets
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Laura Espina
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Alistair J M Farley
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Kirill Shubin
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Gonzalo Gomez Campillos
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Paula Kiuru
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Shifali Shishodia
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Daniel Krahn
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Robert K Leśniak
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Juliane Schmidt Adrian
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Karina Calvopiña
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - María-Carmen Turrientes
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Madeline E Kavanagh
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Gareth W Langley
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Charles River Laboratories, Saffron Walden, UK
| | - Ali F Aboklaish
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Anders Eneroth
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Uppsala University, Uppsala, Sweden
| | - Maria Backlund
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Uppsala University, Uppsala, Sweden
| | | | | | - Michael Speake
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Janis Kuka
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - John Robinson
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | | | - Lindsay Robinson
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Michael A McDonough
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Anna M Rydzik
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
- Research and Early Development, Respiratory & Immunology, AstraZeneca, Mölndal, Sweden
| | - Thomas M Leissing
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Juan Carlos Jimenez-Castellanos
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Chemical Biology of Antibiotics, Centre for Infection & Immunity (CIIL), Pasteur Institute, INSERM U1019 - CNRS UMR 9017, Lille, France
| | - Matthew B Avison
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Solange Da Silva Pinto
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Andrew D Pannifer
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
| | | | - Emma Widlake
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | | | | | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Anna Karin Belfrage
- Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
- Beactica Therapeutics AB, Uppsala, Sweden
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Eric Bacque
- Evotec Infectious Diseases Lyon, Marcy l'Etoile, France
| | | | - Fredrik Björkling
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan M Tyrrell
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Pauline A Lang
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
| | - Pawel Baranczewski
- Department of Pharmacy, SciLifeLab Drug Discovery and Development Platform, ADME of Therapeutics Facility, Uppsala University, Uppsala, Sweden
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Stuart P McElroy
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Philip S Jones
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Edgars Suna
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Angus Morrison
- University of Dundee, European Screening Centre, BioCity Scotland, Newhouse, UK
- BioAscent Discovery Ltd, Newhouse, UK
| | - Timothy R Walsh
- Department of Medical Microbiology, Institute of infection & Immunity, Cardiff University, Cardiff, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK.
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23
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Ruiz CH, Osorio-Llanes E, Trespalacios MH, Mendoza-Torres E, Rosales W, Gómez CMM. Quorum Sensing Regulation as a Target for Antimicrobial Therapy. Mini Rev Med Chem 2021; 22:848-864. [PMID: 34856897 DOI: 10.2174/1389557521666211202115259] [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: 10/04/2020] [Revised: 05/20/2021] [Accepted: 09/04/2021] [Indexed: 11/22/2022]
Abstract
Some bacterial species use a cell-to-cell communication mechanism called Quorum Sensing (QS). Bacteria release small diffusible molecules, usually termed signals which allow the activation of beneficial phenotypes that guarantee bacterial survival and the expression of a diversity of virulence genes in response to an increase in population density. The study of the molecular mechanisms that relate signal molecules with bacterial pathogenesis is an area of growing interest due to its use as a possible therapeutic alternative through the development of synthetic analogues of autoinducers as a strategy to regulate bacterial communication as well as the study of bacterial resistance phenomena, the study of these relationships is based on the structural diversity of natural or synthetic autoinducers and their ability to inhibit bacterial QS, which can be approached with a molecular perspective from the following topics: i) Molecular signals and their role in QS regulation; ii) Strategies in the modulation of Quorum Sensing; iii) Analysis of Bacterial QS circuit regulation strategies; iv) Structural evolution of natural and synthetic autoinducers as QS regulators. This mini-review allows a molecular view of the QS systems, showing a perspective on the importance of the molecular diversity of autoinducer analogs as a strategy for the design of new antimicrobial agents.
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Affiliation(s)
- Caterine Henríquez Ruiz
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
| | - Estefanie Osorio-Llanes
- Faculty of Exact and Natural sciences. Grupo de Investigación Avanzada en Biomedicina. Universidad Libre. Barranquilla. Colombia
| | - Mayra Hernández Trespalacios
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
| | - Evelyn Mendoza-Torres
- Faculty of Health Sciences. Grupo de Investigación Avanzada en Biomedicina-Universidad Libre. Barranquilla. Colombia
| | - Wendy Rosales
- Faculty of Exact and Natural sciences. Grupo de Investigación Avanzada en Biomedicina. Universidad Libre. Barranquilla. Colombia
| | - Carlos Mario Meléndez Gómez
- Grupo de Investigación en Química Orgánica y Biomédica. Faculty of Basic Sciences. Universidad del Atlántico. Barranquilla. Colombia
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24
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Evolutionary Aspects of the Oxido-Reductive Network of Methylglyoxal. J Mol Evol 2021; 89:618-638. [PMID: 34718825 DOI: 10.1007/s00239-021-10031-3] [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: 05/18/2021] [Accepted: 10/08/2021] [Indexed: 10/19/2022]
Abstract
In the chemoautotrophic theory for the origin of life, offered as an alternative to broth theory, the archaic reductive citric acid cycle operating without enzymes is in the center. The non-enzymatic (methyl)glyoxalase pathway has been suggested to be the anaplerotic route for the reductive citric acid cycle. In the recent years, much has been learned about methylglyoxal, but its importance in the metabolic machinery is still uncovered. If methylglyoxal had been essential participant of the early stage of evolution, then it is a legitimate question whether it might have played a role in the early oxido-reduction network, too. Therefore, an oxido-reduction network of methylglyoxal that might have functioned under ancient circumstances without enzymes was constructed and analyzed by virtue of group contribution method. Taking methylglyoxal as input material, it turned out that the evolutionary value of reactions and biomolecules were not similar. Glycerol, glycerate, and tartonate, the output components, were conserved to different degrees. Although the tartonate route was similarly favorable from energetic point of view, its intermediates are almost not present in extant biochemistry. The presence of two carboxyl or aldehyde groups, or their combination in tricarbons of the constructed network seemed disadvantageous for selection, and the inductive effect, resulting in an asymmetry in electron cloud of chemicals, might have been important. The evolutionary role for cysteine, H2S, and formaldehyde in the emergence of high-energy bonds in the form of thioesters and in Fe-S cluster formation as well as in imidazole synthesis was shown to bridge the gap between prebiotic chemistry and contemporary biochemistry. Overall, the ideas developed here represent an approach fitting to chemoautotrophic origin of life and implying to the role of methylglyoxal in triose formation. The proposed network is expected to have an impact upon how one may think of prebiological chemical processes on methylglyoxal, too. Finally, along the evolutionary time line, the network functioning without enzymes is situated between the formation of simple organic compounds and primeval cells, being closer to the former and well preceding the last common metabolic ancestor developed after primitive cells emerged.
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25
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Melenotte C, Pontarotti P, Pinault L, Mège JL, Devaux C, Raoult D. Could β-Lactam Antibiotics Block Humoral Immunity? Front Immunol 2021; 12:680146. [PMID: 34603278 PMCID: PMC8480522 DOI: 10.3389/fimmu.2021.680146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
It has been reported that treatment with β-lactam antibiotics induces leukopenia and candidemia, worsens the clinical response to anticancer immunotherapy and decreases immune response to vaccination. β-lactamases can cleave β-lactam antibiotics by blocking their activity. Two distincts superfamilies of β-lactamases are described, the serine β-lactamases and the zinc ion dependent metallo-β-lactamases. In human, 18 metallo-β-lactamases encoding genes (hMBLs) have been identified. While the physiological role of most of them remains unknown, it is well established that the SNM1A, B and C proteins are involved in DNA repair. The SNM1C/Artemis protein is precisely associated in the V(D)J segments rearrangement, that leads to immunoglobulin (Ig) and T-cell receptor variable regions, which have a crucial role in the immune response. Thus in humans, SNM1C/Artemis mutation is associated with severe combined immunodeficiency characterized by hypogammaglobulinemia deficient cellular immunity and opportunistic infections. While catalytic site of hMBLs and especially that of the SNM1 family is highly conserved, in vitro studies showed that some β-lactam antibiotics, and precisely third generation of cephalosporin and ampicillin, inhibit the metallo-β-lactamase proteins SNM1A & B and the SNM1C/Artemis protein complex. By analogy, the question arises as to whether β-lactam antibiotics can block the SNM1C/Artemis protein in humans inducing transient immunodeficiency. We reviewed here the literature data supporting this hypothesis based on in silico, in vitro and in vivo evidences. Understanding the impact of β-lactam antibiotics on the immune cell will offer new therapeutic clues and new clinical approaches in oncology, immunology, and infectious diseases.
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Affiliation(s)
- Cléa Melenotte
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Pierre Pontarotti
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Lucile Pinault
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Jean-Louis Mège
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Christian Devaux
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Didier Raoult
- Aix-Marseille Univ, Institut de Recherche et Développement (IRD), Assistance Publique des Hpitaux de Marseille (APHM), Microbes, Evolution, Phylogénie et Infection (MEPHI), Marseille, France.,Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
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26
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Yosaatmadja Y, Baddock H, Newman J, Bielinski M, Gavard A, Mukhopadhyay SMM, Dannerfjord A, Schofield C, McHugh P, Gileadi O. Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition. Nucleic Acids Res 2021; 49:9310-9326. [PMID: 34387696 PMCID: PMC8450076 DOI: 10.1093/nar/gkab693] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 07/20/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
Artemis (SNM1C/DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in dsDNA break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Artemis deficiency leads to congenital radiosensitive severe acquired immune deficiency (RS-SCID). Artemis belongs to a superfamily of nucleases containing metallo-β-lactamase (MBL) and β-CASP (CPSF-Artemis-SNM1-Pso2) domains. We present crystal structures of the catalytic domain of wildtype and variant forms of Artemis, including one causing RS-SCID Omenn syndrome. The catalytic domain of the Artemis has similar endonuclease activity to the phosphorylated full-length protein. Our structures help explain the predominantly endonucleolytic activity of Artemis, which contrasts with the predominantly exonuclease activity of the closely related SNM1A and SNM1B MBL fold nucleases. The structures reveal a second metal binding site in its β-CASP domain unique to Artemis, which is amenable to inhibition by compounds including ebselen. By combining our structural data with that from a recently reported Artemis structure, we were able model the interaction of Artemis with DNA substrates. The structures, including one of Artemis with the cephalosporin ceftriaxone, will help enable the rational development of selective SNM1 nuclease inhibitors.
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Affiliation(s)
- Yuliana Yosaatmadja
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Hannah T Baddock
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Marcin Bielinski
- The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Angeline E Gavard
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | | | - Adam A Dannerfjord
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Christopher J Schofield
- The Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Peter J McHugh
- Department of Oncology, MRC-Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
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27
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Hussain HI, Aqib AI, Seleem MN, Shabbir MA, Hao H, Iqbal Z, Kulyar MFEA, Zaheer T, Li K. Genetic basis of molecular mechanisms in β-lactam resistant gram-negative bacteria. Microb Pathog 2021; 158:105040. [PMID: 34119627 PMCID: PMC8445154 DOI: 10.1016/j.micpath.2021.105040] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/25/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022]
Abstract
Antibiotic-resistant bacteria are considered one of the major global threats to human and animal health. The most harmful among the resistant bacteria are β-lactamase producing Gram-negative species (β-lactamases). β-lactamases constitute a paradigm shift in the evolution of antibiotic resistance. Therefore, it is imperative to present a comprehensive review of the mechanisms responsible for developing antimicrobial resistance. Resistance due to β-lactamases develops through a variety of mechanisms, and the number of resistant genes are involved that can be transferred between bacteria, mostly via plasmids. Over time, these new molecular-based resistance mechanisms have been progressively disclosed. The present review article provides information on the recent findings regarding the molecular mechanisms of resistance to β-lactams in Gram-negative bacteria, including CTX-M-type ESBLs with methylase activity, plasmids harbouring phages with β-lactam resistance genes, the co-presence of β-lactam resistant genes of unique combinations and the presence of β-lactam and non-β-lactam antibiotic-resistant genes in the same bacteria. Keeping in view, the molecular level resistance development, multifactorial and coordinated measures may be taken to counter the challenge of rapidly increasing β-lactam resistance.
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Affiliation(s)
- Hafiz Iftikhar Hussain
- Department of Pathology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan
| | - Amjad Islam Aqib
- Department of Medicine, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, 63100, Pakistan.
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, USA
| | | | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zahid Iqbal
- Department of Pharmacology, International Cancer Center, Shenzhen University Health Science Center, Shenzhen, 518055, China.
| | | | - Tean Zaheer
- Department of Parasitology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, PR China.
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Inverse association between use of broad spectrum penicllin with beta-lactamase inhibitors and prevalence of type 1 diabetes mellitus in Europe. Sci Rep 2021; 11:16768. [PMID: 34408224 PMCID: PMC8373876 DOI: 10.1038/s41598-021-96301-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 08/05/2021] [Indexed: 12/16/2022] Open
Abstract
Increasing incidence of type 1 diabetes is supposed to be induced by environmental factors. Microbiome modulated by antibiotics seems to serve as one of the environmental factors which could influence the development of T1DM. Mitochondria, as autochthonous environmental bacteria living in our cells, and other bacteria share many common enzymes including beta-lactamases and it is supported by evidence that some beta-lactamase inhibitors are able to interact with counterpart enzymes. Thus, antibiotics may utilize two different pathways influencing the development of T1DM; one through modulation of microbiome and a second one via the interaction of mitochondrial enzymes. Data of consumption of penicillin (both narrow and broad spectrum) and beta-lactamase inhibitors in 30 European countries were collected from the database of the European Centre for Disease Prevention and Control. These data were correlated with the prevalence reported by the International Diabetes Federation (2019) referring to type 1 diabetes in Europe. No correlation was found between total penicillin consumption or use of broad spectrum penicillin and the prevalence of type 1 diabetes. Nevertheless, broad spectrum penicillin, in combination with beta-lactamase inhibitor, was in inverse correlation with the prevalence of type 1 diabetes (r = − 0.573, p = 0.001). On the other hand, narrow spectrum penicillin was in positive correlation with type 1 diabetes (r = 0.523, p = 0.003). Prevalence of type 1 diabetes showed an inverse correlation with the use of beta-lactamase inhibitors and a positive one with that of narrow spectrum penicillin. Such a detailed analysis has not so far been provided referring to the penicillin group. In the background of this association either microbiomal or direct mitochondrial effects can be supposed.
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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Chen Q, Zheng W, Zhu L, Liu H, Song Y, Hu S, Bai Y, Pan Y, Zhang J, Guan J, Shao C. LACTB2 renders radioresistance by activating PINK1/Parkin-dependent mitophagy in nasopharyngeal carcinoma. Cancer Lett 2021; 518:127-139. [PMID: 34271102 DOI: 10.1016/j.canlet.2021.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 01/04/2023]
Abstract
Radiotherapy is a standard and conventional treatment strategy for nasopharyngeal carcinoma (NPC); however, radioresistance remains refractory to clinical outcomes. Understanding the molecular mechanism of radioresistance is crucial for advancing the efficacy of radiotherapy and improving the prognosis of NPC. In this study, β-lactamase-like-protein 2 (LACTB2) was identified as a potential biomarker for radioresistance using tandem mass tag proteomic analysis of NPC cells, gene chip analysis of NPC tissues, and differential gene analysis between NPC and normal nasopharyngeal tissues from the Gene Expression Omnibus database GSE68799. Meanwhile, LACTB2 levels were elevated in the serum of patients with NPC after radiotherapy. Inhibiting LACTB2 levels and mitophagy can sensitize NPC cells to ionizing radiation. In NPC cells, LACTB2 was augmented at the transcription and protein levels after radiation rather than nucleus-cytoplasm-mitochondria transposition to activate PTEN-induced kinase 1 (PINK1) and mitophagy. In addition, LACTB2 was first authenticated to co-locate with PINK1 by interacting with its N-terminal domain. Together, our findings indicate that overexpressed LACTB2 provoked PINK1-dependent mitophagy to promote radioresistance and thus might serve as a prognostic biomarker for NPC radiotherapy.
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Affiliation(s)
- Qianping Chen
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wang Zheng
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lin Zhu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hongxia Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yimeng Song
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Songling Hu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yang Bai
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yan Pan
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jianghong Zhang
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital of Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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31
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Farley AM, Ermolovich Y, Calvopiña K, Rabe P, Panduwawala T, Brem J, Björkling F, Schofield CJ. Structural Basis of Metallo-β-lactamase Inhibition by N-Sulfamoylpyrrole-2-carboxylates. ACS Infect Dis 2021; 7:1809-1817. [PMID: 34003651 PMCID: PMC8205225 DOI: 10.1021/acsinfecdis.1c00104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Indexed: 12/21/2022]
Abstract
Metallo-β-lactamases (MBLs) can efficiently catalyze the hydrolysis of all classes of β-lactam antibiotics except monobactams. While serine-β-lactamase (SBL) inhibitors (e.g., clavulanic acid, avibactam) are established for clinical use, no such MBL inhibitors are available. We report on the synthesis and mechanism of inhibition of N-sulfamoylpyrrole-2-carboxylates (NSPCs) which are potent inhibitors of clinically relevant B1 subclass MBLs, including NDM-1. Crystallography reveals that the N-sulfamoyl NH2 group displaces the dizinc bridging hydroxide/water of the B1 MBLs. Comparison of crystal structures of an NSPC and taniborbactam (VRNX-5133), presently in Phase III clinical trials, shows similar binding modes for the NSPC and the cyclic boronate ring systems. The presence of an NSPC restores meropenem efficacy in clinically derived E. coli and K. pneumoniae blaNDM-1. The results support the potential of NSPCs and related compounds as efficient MBL inhibitors, though further optimization is required for their clinical development.
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Affiliation(s)
- Alistair
J. M. Farley
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Yuri Ermolovich
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Karina Calvopiña
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Patrick Rabe
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Tharindi Panduwawala
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jürgen Brem
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Fredrik Björkling
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Christopher J. Schofield
- Department
of Chemistry, Chemistry Research Laboratory and the Ineos Institute
for Antimicrobial Research, University of
Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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32
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Antelo GT, Vila AJ, Giedroc DP, Capdevila DA. Molecular Evolution of Transition Metal Bioavailability at the Host-Pathogen Interface. Trends Microbiol 2021; 29:441-457. [PMID: 32951986 PMCID: PMC7969482 DOI: 10.1016/j.tim.2020.08.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/01/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022]
Abstract
The molecular evolution of the adaptive response at the host-pathogen interface has been frequently referred to as an 'arms race' between the host and bacterial pathogens. The innate immune system employs multiple strategies to starve microbes of metals. Pathogens, in turn, develop successful strategies to maintain access to bioavailable metal ions under conditions of extreme restriction of transition metals, or nutritional immunity. However, the processes by which evolution repurposes or re-engineers host and pathogen proteins to perform or refine new functions have been explored only recently. Here we review the molecular evolution of several human metalloproteins charged with restricting bacterial access to transition metals. These include the transition metal-chelating S100 proteins, natural resistance-associated macrophage protein-1 (NRAMP-1), transferrin, lactoferrin, and heme-binding proteins. We examine their coevolution with bacterial transition metal acquisition systems, involving siderophores and membrane-spanning metal importers, and the biological specificity of allosteric transcriptional regulatory proteins tasked with maintaining bacterial metallostasis. We also discuss the evolution of metallo-β-lactamases; this illustrates how rapid antibiotic-mediated evolution of a zinc metalloenzyme obligatorily occurs in the context of host-imposed nutritional immunity.
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Affiliation(s)
- Giuliano T Antelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, S2002LRK Rosario, Argentina; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
| | - Daiana A Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
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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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Silale A, Lea SM, Berks BC. The DNA transporter ComEC has metal-dependent nuclease activity that is important for natural transformation. Mol Microbiol 2021; 116:416-426. [PMID: 33772889 PMCID: PMC8579336 DOI: 10.1111/mmi.14720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/25/2022]
Abstract
In the process of natural transformation bacteria import extracellular DNA molecules for integration into their genome. One strand of the incoming DNA molecule is degraded, whereas the remaining strand is transported across the cytoplasmic membrane. The DNA transport channel is provided by the protein ComEC. Many ComEC proteins have an extracellular C-terminal domain (CTD) with homology to the metallo-β-lactamase fold. Here we show that this CTD binds Mn2+ ions and exhibits Mn2+ -dependent phosphodiesterase and nuclease activities. Inactivation of the enzymatic activity of the CTD severely inhibits natural transformation in Bacillus subtilis. These data suggest that the ComEC CTD is a nuclease responsible for degrading the nontransforming DNA strand during natural transformation and that this process is important for efficient DNA import.
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Affiliation(s)
- Augustinas Silale
- Department of Biochemistry, University of Oxford, Oxford, UK.,Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK
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35
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Pfleiderer MM, Galej WP. Structure of the catalytic core of the Integrator complex. Mol Cell 2021; 81:1246-1259.e8. [PMID: 33548203 PMCID: PMC7980224 DOI: 10.1016/j.molcel.2021.01.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/29/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022]
Abstract
The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.
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Affiliation(s)
- Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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36
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Yang F, Yan Z, Nie W, Cheng X, Liu Z, Wang W, Shao C, Fu G, Yu Y. LACTB induced apoptosis of oxaliplatin-resistant gastric cancer through regulating autophagy-mediated mitochondrial apoptosis pathway. Am J Transl Res 2021; 13:601-616. [PMID: 33594312 PMCID: PMC7868839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Oxaliplatin (OXA), as a third-generation platinum anticancer drug, is a treatment drug for gastric cancer (GC). However, OXA resistance has become the main reason for OXA treatment failure. Serine beta-lactamase-like protein (LACTB), acts as a mitochondrial protein, can affect multiple cancer processes. Here, we aimed to investigate the function and mechanism of LACTB in OXA-resistant GC. After LACTB overexpression or autophagy activator (RAPA) treatment, cell proliferation, reactive oxygen species (ROS), apoptosis, mitochondrial dysfunction were evaluated through CCK-8 assay, Edu staining, flow cytometry and immunofluorescence assay. Moreover, DNA double-stranded damage and autophagy-related proteins were examined via western blot. We revealed that LACTB was downregulated in OXA-resistant MGC-803 cells, and overexpression of LACTB reduced the resistance of GC cells to OXA. Besides, our results uncovered that overexpression of LACTB induced apoptosis, reduced the mitochondrial membrane potential (MMP) and accelerated ROS accumulation in OXA-resistant MGC-803 (MGC-803/OXA) cells. Meanwhile, we verified that overexpression of LACTB decreased glucose uptake and ATP synthesis, induced mitochondria and DNA damages, and inhibited autophagy of MGC-803/OXA cells. Furthermore, our results certified that RAPA could weaken the function of LACTB on apoptosis and mitochondrial morphology and function in OXA-resistant MGC-803 cells with OXA treatment. Therefore, we demonstrated that LACTB could attenuate the resistance of MGC-803/OXA cells to OXA through autophagy-mediated mitochondrial morphological changes, mitochondrial dysfunction, and apoptosis, suggesting that LACTB, functions as a suppressor, is conducive to the therapy of OXA-resistant GC.
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Affiliation(s)
- Fang Yang
- Department of Pathology, Guizhou Medical UniversityGuiyang, Guizhou, China
- College of Basic Medical Science, Guizhou Medical UniversityGuiyang, Guizhou, China
- Department of Laboratory Medicine, Guizhou Cancer HospitalGuiyang, Guizhou, China
- School of Clinical Laboratory Science, Guizhou Medical UniversityGuiyang, Guizhou, China
| | - Zhiqiang Yan
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guizhou Medical UniversityGuiyang, Guizhou, China
| | - Wei Nie
- Department of Laboratory Medicine, Guizhou Cancer HospitalGuiyang, Guizhou, China
- School of Clinical Laboratory Science, Guizhou Medical UniversityGuiyang, Guizhou, China
| | - Xingzhen Cheng
- Department of Gastrointestinal Surgery, Affiliated Hospital of Guizhou Medical UniversityGuiyang, Guizhou, China
| | - Zeying Liu
- Department of Laboratory Medicine, Guizhou Cancer HospitalGuiyang, Guizhou, China
- School of Clinical Laboratory Science, Guizhou Medical UniversityGuiyang, Guizhou, China
| | - Wei Wang
- Department of Laboratory Medicine, Guizhou Cancer HospitalGuiyang, Guizhou, China
| | - Chunyan Shao
- Department of Laboratory Medicine, Guizhou Cancer HospitalGuiyang, Guizhou, China
| | - Gui Fu
- Department of Laboratory Medicine, Guizhou Cancer HospitalGuiyang, Guizhou, China
| | - Yanni Yu
- Department of Pathology, Guizhou Medical UniversityGuiyang, Guizhou, China
- College of Basic Medical Science, Guizhou Medical UniversityGuiyang, Guizhou, China
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Dalhoff A. Selective toxicity of antibacterial agents-still a valid concept or do we miss chances and ignore risks? Infection 2021; 49:29-56. [PMID: 33367978 PMCID: PMC7851017 DOI: 10.1007/s15010-020-01536-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Selective toxicity antibacteribiotics is considered to be due to interactions with targets either being unique to bacteria or being characterized by a dichotomy between pro- and eukaryotic pathways with high affinities of agents to bacterial- rather than eukaryotic targets. However, the theory of selective toxicity oversimplifies the complex modes of action of antibiotics in pro- and eukaryotes. METHODS AND OBJECTIVE This review summarizes data describing multiple modes of action of antibiotics in eukaryotes. RESULTS Aminoglycosides, macrolides, oxazolidinones, chloramphenicol, clindamycin, tetracyclines, glycylcyclines, fluoroquinolones, rifampicin, bedaquillin, ß-lactams inhibited mitochondrial translation either due to binding to mitosomes, inhibition of mitochondrial RNA-polymerase-, topoisomerase 2ß-, ATP-synthesis, transporter activities. Oxazolidinones, tetracyclines, vancomycin, ß-lactams, bacitracin, isoniazid, nitroxoline inhibited matrix-metalloproteinases (MMP) due to chelation with zinc and calcium, whereas fluoroquinols fluoroquinolones and chloramphenicol chelated with these cations, too, but increased MMP activities. MMP-inhibition supported clinical efficacies of ß-lactams and daptomycin in skin-infections, and of macrolides, tetracyclines in respiratory-diseases. Chelation may have contributed to neuroprotection by ß-lactams and fluoroquinolones. Aminoglycosides, macrolides, chloramphenicol, oxazolidins oxazolidinones, tetracyclines caused read-through of premature stop codons. Several additional targets for antibiotics in human cells have been identified like interaction of fluoroquinolones with DNA damage repair in eukaryotes, or inhibition of mucin overproduction by oxazolidinones. CONCLUSION The effects of antibiotics on eukaryotes are due to identical mechanisms as their antibacterial activities because of structural and functional homologies of pro- and eukaryotic targets, so that the effects of antibiotics on mammals are integral parts of their overall mechanisms of action.
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Affiliation(s)
- Axel Dalhoff
- Christian-Albrechts-University of Kiel, Institue for Infection Medicine, Brunswiker Str. 4, D-24105, Kiel, Germany.
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Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A. Molecules 2021; 26:molecules26020320. [PMID: 33435514 PMCID: PMC7827217 DOI: 10.3390/molecules26020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5'-position or 3'-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5'-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors.
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Malgapo MIP, Safadi JM, Linder ME. Metallo-β-lactamase domain-containing protein 2 is S-palmitoylated and exhibits acyl-CoA hydrolase activity. J Biol Chem 2021; 296:100106. [PMID: 33219126 PMCID: PMC7949124 DOI: 10.1074/jbc.ra120.015701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 11/24/2022] Open
Abstract
Members of the metallo-β-lactamase (MBL) superfamily of enzymes harbor a highly conserved αββα MBL-fold domain and were first described as inactivators of common β-lactam antibiotics. In humans, these enzymes have been shown to exhibit diverse functions, including hydrolase activity toward amides, esters, and thioesters. An uncharacterized member of the human MBL family, MBLAC2, was detected in multiple palmitoylproteomes, identified as a zDHHC20 S-acyltransferase interactor, and annotated as a potential thioesterase. In this study, we confirmed that MBLAC2 is palmitoylated and identified the likely S-palmitoylation site as Cys254. S-palmitoylation of MBLAC2 is increased in cells when expressed with zDHHC20, and MBLAC2 is a substrate for purified zDHHC20 in vitro. To determine its biochemical function, we tested the ability of MBLAC2 to hydrolyze a variety of small molecules and acylprotein substrates. MBLAC2 has acyl-CoA thioesterase activity with kinetic parameters and acyl-CoA selectivity comparable with acyl-CoA thioesterase 1 (ACOT1). Two predicted zinc-binding residues, Asp87 and His88, are required for MBLAC2 hydrolase activity. Consistent with a role in fatty acid metabolism in cells, MBLAC2 was cross-linked to a photoactivatable fatty acid in a manner that was independent of its S-fatty acylation at Cys254. Our study adds to previous investigations demonstrating the versatility of the MBL-fold domain in supporting a variety of enzymatic reactions.
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Affiliation(s)
- Martin Ian P Malgapo
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jenelle M Safadi
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Maurine E Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.
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Kasamatsu S. Persulfide-Dependent Regulation of Electrophilic Redox Signaling in Neural Cells. Antioxid Redox Signal 2020; 33:1320-1331. [PMID: 32536194 DOI: 10.1089/ars.2020.8130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significance: Redox homeostasis is precisely modulated by intricate systems that regulate production, elimination, and metabolism of electrophilic substances (electrophiles) in the nervous system. Since the first report of the endogenous production of reactive persulfide species in cells, such as cysteine persulfides (CysSSH), these reactive species have been a topic of extreme interest in the field of redox biology; persulfides/polysulfides possess unique chemical properties and are involved in multiple cellular functions. Recent Advances: Electrophilic signaling is mainly regulated by endogenous electrophiles that are generated from reactive oxygen species, nitric oxide, and their derivatives during stress responses, as well as by exogenous electrophiles, including compounds in foods and environmental pollutants, such as methylmercury (MeHg). Among diverse electrophiles that are endogenously generated, 8-nitroguanosine 3',5'-cyclic monophosphate (8-nitro-cGMP) possesses unique redox properties, of which the biosynthetic pathway, signaling mechanism, and metabolism in cells have been elucidated. Critical Issues: Persulfides, such as CysSSH, that are endogenously produced are critically involved in 8-nitro-cGMP metabolism. Exposure of neurons to the exogenous neurotoxicant, MeHg, causes severe neurodegeneration via disruption of persulfide-dependent 8-nitro-cGMP metabolism. Future Directions: Accumulating evidence indicates that persulfides are involved in various cellular functions under physiological and pathological conditions. These new aspects of redox biology related to persulfides may be frontiers of cell research, medical and clinical investigations of neurodegenerative diseases, as well as other fields. 8-Nitro-cGMP-mediated signaling and its persulfide-dependent metabolism in cells could, therefore, be potential targets for drug development, which may lead to the discovery of new therapeutic agents for many diseases, including neurodegenerative diseases.
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Affiliation(s)
- Shingo Kasamatsu
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Osaka, Japan
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Diene SM, Pinault L, Armstrong N, Azza S, Keshri V, Khelaifia S, Chabrière E, Caetano-Anolles G, Rolain JM, Pontarotti P, Raoult D. Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea. Life (Basel) 2020; 10:life10110280. [PMID: 33202677 PMCID: PMC7697635 DOI: 10.3390/life10110280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/11/2023] Open
Abstract
β-lactam antibiotics have a well-known activity which disturbs the bacterial cell wall biosynthesis and may be cleaved by β-lactamases. However, these drugs are not active on archaea microorganisms, which are naturally resistant because of the lack of β-lactam target in their cell wall. Here, we describe that annotation of genes as β-lactamases in Archaea on the basis of homologous genes is a remnant of identification of the original activities of this group of enzymes, which in fact have multiple functions, including nuclease, ribonuclease, β-lactamase, or glyoxalase, which may specialized over time. We expressed class B β-lactamase enzyme from Methanosarcina barkeri that digest penicillin G. Moreover, while weak glyoxalase activity was detected, a significant ribonuclease activity on bacterial and synthetic RNAs was demonstrated. The β-lactamase activity was inhibited by β-lactamase inhibitor (sulbactam), but its RNAse activity was not. This gene appears to have been transferred to the Flavobacteriaceae group especially the Elizabethkingia genus, in which the expressed gene shows a more specialized activity on thienamycin, but no glyoxalase activity. The expressed class C-like β-lactamase gene, from Methanosarcina sp., also shows hydrolysis activity on nitrocefin and is more closely related to DD-peptidase enzymes. Our findings highlight the need to redefine the nomenclature of β-lactamase enzymes and the specification of multipotent enzymes in different ways in Archaea and bacteria over time.
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Affiliation(s)
- Seydina M. Diene
- MEPHI, IHU-Mediterranee Infection, Aix Marseille University, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.M.D.); (V.K.); (E.C.); (J.-M.R.)
| | - Lucile Pinault
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France; (L.P.); (N.A.); (S.A.)
| | - Nicholas Armstrong
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France; (L.P.); (N.A.); (S.A.)
| | - Said Azza
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France; (L.P.); (N.A.); (S.A.)
| | - Vivek Keshri
- MEPHI, IHU-Mediterranee Infection, Aix Marseille University, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.M.D.); (V.K.); (E.C.); (J.-M.R.)
| | | | - Eric Chabrière
- MEPHI, IHU-Mediterranee Infection, Aix Marseille University, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.M.D.); (V.K.); (E.C.); (J.-M.R.)
| | - Gustavo Caetano-Anolles
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Jean-Marc Rolain
- MEPHI, IHU-Mediterranee Infection, Aix Marseille University, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.M.D.); (V.K.); (E.C.); (J.-M.R.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France; (L.P.); (N.A.); (S.A.)
| | - Pierre Pontarotti
- MEPHI, IHU-Mediterranee Infection, Aix Marseille University, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.M.D.); (V.K.); (E.C.); (J.-M.R.)
- CNRS, 13005 Marseille, France;
| | - Didier Raoult
- MEPHI, IHU-Mediterranee Infection, Aix Marseille University, 19-21 Bd Jean Moulin, 13005 Marseille, France; (S.M.D.); (V.K.); (E.C.); (J.-M.R.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France; (L.P.); (N.A.); (S.A.)
- IHU-Méditerranée Infection, 13005 Marseille, France;
- Correspondence: ; Tel.: +33-4-1373-2401
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Isolation and genomic characterization of a pathogenic Providencia rettgeri strain G0519 in turtle Trachemys scripta. Antonie van Leeuwenhoek 2020; 113:1633-1662. [PMID: 32951105 DOI: 10.1007/s10482-020-01469-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
Providencia rettgeri infection has occurred occasionally in aquaculture, but is rare in turtles. Here, a pathogenic P. rettgeri strain G0519 was isolated from a diseased slider turtle (Trachemys scripta) in China, and qPCR assay was established for the RTX toxin (rtxD) gene. Histopathological examination showed that many inflammatory cells were infiltrated into heart, liver and intestine, as well as the necrosis of liver, kidney and spleen. The genome consisted of one circular chromosome (4.493 Mb) and one plasmid (18.8 kb), and predicted to contain 4170 and 19 protein-coding genes, respectively. Multiple pathogenic and virulence factors (e.g., fimbria, adhesion, invasion, toxin, hemolysin, chemotaxis, secretion system), multidrug-resistant genes (e.g., ampC, per-1, oxa-1, sul1, tetR) and a novel genomic resistance island PRI519 were identified. Comparative genome analysis revealed the closest relationship was with P. rettgeri, and with P. heimbachae closer than with other Providencia spp. To our knowledge, this was first report on genomic characterization of multidrug-resistant pathogenic P. rettgeri in cultured turtles.
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Selleck C, Pedroso MM, Wilson L, Krco S, Knaven EG, Miraula M, Mitić N, Larrabee JA, Brück T, Clark A, Guddat LW, Schenk G. Structure and mechanism of potent bifunctional β-lactam- and homoserine lactone-degrading enzymes from marine microorganisms. Sci Rep 2020; 10:12882. [PMID: 32732933 PMCID: PMC7392888 DOI: 10.1038/s41598-020-68612-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/26/2020] [Indexed: 11/11/2022] Open
Abstract
Genes that confer antibiotic resistance can rapidly be disseminated from one microorganism to another by mobile genetic elements, thus transferring resistance to previously susceptible bacterial strains. The misuse of antibiotics in health care and agriculture has provided a powerful evolutionary pressure to accelerate the spread of resistance genes, including those encoding β-lactamases. These are enzymes that are highly efficient in inactivating most of the commonly used β-lactam antibiotics. However, genes that confer antibiotic resistance are not only associated with pathogenic microorganisms, but are also found in non-pathogenic (i.e. environmental) microorganisms. Two recent examples are metal-dependent β-lactamases (MBLs) from the marine organisms Novosphingobium pentaromativorans and Simiduia agarivorans. Previous studies have demonstrated that their β-lactamase activity is comparable to those of well-known MBLs from pathogenic sources (e.g. NDM-1, AIM-1) but that they also possess efficient lactonase activity, an activity associated with quorum sensing. Here, we probed the structure and mechanism of these two enzymes using crystallographic, spectroscopic and fast kinetics techniques. Despite highly conserved active sites both enzymes demonstrate significant variations in their reaction mechanisms, highlighting both the extraordinary ability of MBLs to adapt to changing environmental conditions and the rather promiscuous acceptance of diverse substrates by these enzymes.
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Affiliation(s)
- Christopher Selleck
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Marcelo Monteiro Pedroso
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Liam Wilson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Stefan Krco
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Esmée Gianna Knaven
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Manfredi Miraula
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.,Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - Nataša Mitić
- Department of Chemistry, Maynooth University, Maynooth, County Kildare, Ireland
| | - James A Larrabee
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenberg Str. 4, 85748, Garching, Germany
| | - Alice Clark
- Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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44
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Aggarwal G, Zarrow JE, Mashhadi Z, Flynn CR, Vinson P, Weaver CD, Davies SS. Symmetrically substituted dichlorophenes inhibit N-acyl-phosphatidylethanolamine phospholipase D. J Biol Chem 2020; 295:7289-7300. [PMID: 32284327 PMCID: PMC7247316 DOI: 10.1074/jbc.ra120.013362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/06/2020] [Indexed: 01/09/2023] Open
Abstract
N-Acyl-phosphatidylethanolamine phospholipase D (NAPE-PLD) (EC 3.1.4.4) catalyzes the final step in the biosynthesis of N-acyl-ethanolamides. Reduced NAPE-PLD expression and activity may contribute to obesity and inflammation, but a lack of effective NAPE-PLD inhibitors has been a major obstacle to elucidating the role of NAPE-PLD and N-acyl-ethanolamide biosynthesis in these processes. The endogenous bile acid lithocholic acid (LCA) inhibits NAPE-PLD activity (with an IC50 of 68 μm), but LCA is also a highly potent ligand for TGR5 (EC50 0.52 μm). Recently, the first selective small-molecule inhibitor of NAPE-PLD, ARN19874, has been reported (having an IC50 of 34 μm). To identify more potent inhibitors of NAPE-PLD, here we used a quenched fluorescent NAPE analog, PED-A1, as a substrate for recombinant mouse Nape-pld to screen a panel of bile acids and a library of experimental compounds (the Spectrum Collection). Muricholic acids and several other bile acids inhibited Nape-pld with potency similar to that of LCA. We identified 14 potent Nape-pld inhibitors in the Spectrum Collection, with the two most potent (IC50 = ∼2 μm) being symmetrically substituted dichlorophenes, i.e. hexachlorophene and bithionol. Structure-activity relationship assays using additional substituted dichlorophenes identified key moieties needed for Nape-pld inhibition. Both hexachlorophene and bithionol exhibited significant selectivity for Nape-pld compared with nontarget lipase activities such as Streptomyces chromofuscus PLD or serum lipase. Both also effectively inhibited NAPE-PLD activity in cultured HEK293 cells. We conclude that symmetrically substituted dichlorophenes potently inhibit NAPE-PLD in cultured cells and have significant selectivity for NAPE-PLD versus other tissue-associated lipases.
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Affiliation(s)
- Geetika Aggarwal
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - Jonah E Zarrow
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - Zahra Mashhadi
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - C Robb Flynn
- Division of Surgery, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Paige Vinson
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232; Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee 37232
| | - C David Weaver
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Sean S Davies
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232; Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
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45
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ZN148 Is a Modular Synthetic Metallo-β-Lactamase Inhibitor That Reverses Carbapenem Resistance in Gram-Negative Pathogens In Vivo. Antimicrob Agents Chemother 2020; 64:AAC.02415-19. [PMID: 32179522 PMCID: PMC7269481 DOI: 10.1128/aac.02415-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/05/2020] [Indexed: 12/24/2022] Open
Abstract
Carbapenem-resistant Gram-negative pathogens are a critical public health threat and there is an urgent need for new treatments. Carbapenemases (β-lactamases able to inactivate carbapenems) have been identified in both serine β-lactamase (SBL) and metallo-β-lactamase (MBL) families. The recent introduction of SBL carbapenemase inhibitors has provided alternative therapeutic options. Unfortunately, there are no approved inhibitors of MBL-mediated carbapenem-resistance and treatment options for infections caused by MBL-producing Gram-negatives are limited. Carbapenem-resistant Gram-negative pathogens are a critical public health threat and there is an urgent need for new treatments. Carbapenemases (β-lactamases able to inactivate carbapenems) have been identified in both serine β-lactamase (SBL) and metallo-β-lactamase (MBL) families. The recent introduction of SBL carbapenemase inhibitors has provided alternative therapeutic options. Unfortunately, there are no approved inhibitors of MBL-mediated carbapenem-resistance and treatment options for infections caused by MBL-producing Gram-negatives are limited. Here, we present ZN148, a zinc-chelating MBL-inhibitor capable of restoring the bactericidal effect of meropenem and in vitro clinical susceptibility to carbapenems in >98% of a large international collection of MBL-producing clinical Enterobacterales strains (n = 234). Moreover, ZN148 was able to potentiate the effect of meropenem against NDM-1-producing Klebsiella pneumoniae in a murine neutropenic peritonitis model. ZN148 showed no inhibition of the human zinc-containing enzyme glyoxylase II at 500 μM, and no acute toxicity was observed in an in vivo mouse model with cumulative dosages up to 128 mg/kg. Biochemical analysis showed a time-dependent inhibition of MBLs by ZN148 and removal of zinc ions from the active site. Addition of exogenous zinc after ZN148 exposure only restored MBL activity by ∼30%, suggesting an irreversible mechanism of inhibition. Mass-spectrometry and molecular modeling indicated potential oxidation of the active site Cys221 residue. Overall, these results demonstrate the therapeutic potential of a ZN148-carbapenem combination against MBL-producing Gram-negative pathogens and that ZN148 is a highly promising MBL inhibitor that is capable of operating in a functional space not presently filled by any clinically approved compound.
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Khedher MB, Baron SA, Riziki T, Ruimy R, Raoult D, Diene SM, Rolain JM. Massive analysis of 64,628 bacterial genomes to decipher water reservoir and origin of mobile colistin resistance genes: is there another role for these enzymes? Sci Rep 2020; 10:5970. [PMID: 32249837 PMCID: PMC7136264 DOI: 10.1038/s41598-020-63167-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/12/2020] [Indexed: 11/09/2022] Open
Abstract
Since 2015, new worrying colistin resistance mechanism, mediated by mcr-1 gene has been reported worldwide along with eight newly described variants but their source(s) and reservoir(s) remain largely unexplored. Here, we conducted a massive bioinformatic analysis of bacterial genomes to investigate the reservoir and origin of mcr variants. We identified 13'658 MCR-1 homologous sequences in 494 bacterial genera. Moreover, analysis of 64'628 bacterial genomes (60 bacterial genera and 1'047 species) allows identifying a total of 6'651 significant positive hits (coverage >90% and similarity >50%) with the nine MCR variants from 39 bacterial genera and more than 1'050 species. A high number of MCR-1 was identified in Escherichia coli (n = 862). Interestingly, while almost all variants were identified in bacteria from different sources (i.e. human, animal, and environment), the last variant, MCR-9, was exclusively detected in bacteria from human. Although these variants could be identified in bacteria from human and animal sources, we found plenty MCR variants in unsuspected bacteria from environmental origin, especially from water sources. The ubiquitous presence of mcr variants in bacteria from water likely suggests another role in the biosphere of these enzymes as an unknown defense system against natural antimicrobial peptides and/or bacteriophage predation.
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Affiliation(s)
- Mariem Ben Khedher
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU-Mediterranee Infection, Marseille, France
| | - Sophie Alexandra Baron
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU-Mediterranee Infection, Marseille, France
- IHU-Mediterranee Infection, Marseille, France
| | - Toilhata Riziki
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU-Mediterranee Infection, Marseille, France
| | - Raymond Ruimy
- Centre Hospitalier Universitaire de Nice, Laboratoire de bactériologie, Nice, France
| | - Didier Raoult
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU-Mediterranee Infection, Marseille, France
- IHU-Mediterranee Infection, Marseille, France
| | - Seydina M Diene
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU-Mediterranee Infection, Marseille, France.
- IHU-Mediterranee Infection, Marseille, France.
| | - Jean-Marc Rolain
- Aix Marseille Univ., IRD, APHM, MEPHI, IHU-Mediterranee Infection, Marseille, France.
- IHU-Mediterranee Infection, Marseille, France.
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47
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Yan Y, Li G, Li G. Principles and current strategies targeting metallo‐β‐lactamase mediated antibacterial resistance. Med Res Rev 2020; 40:1558-1592. [PMID: 32100311 DOI: 10.1002/med.21665] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Yu‐Hang Yan
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Gen Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
| | - Guo‐Bo Li
- Key Laboratory of Drug‐Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant‐Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of PharmacySichuan UniversityChengdu Sichuan China
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48
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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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Lee JH, Takahashi M, Jeon JH, Kang LW, Seki M, Park KS, Hong MK, Park YS, Kim TY, Karim AM, Lee JH, Nashimoto M, Lee SH. Dual activity of PNGM-1 pinpoints the evolutionary origin of subclass B3 metallo- β-lactamases: a molecular and evolutionary study. Emerg Microbes Infect 2019; 8:1688-1700. [PMID: 31749408 PMCID: PMC6882493 DOI: 10.1080/22221751.2019.1692638] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Resistance to β-lactams is one of the most serious problems associated with Gram-negative infections. β-Lactamases are able to hydrolyze β-lactams such as cephalosporins and/or carbapenems. Evolutionary origin of metallo-β-lactamases (MBLs), conferring critical antibiotic resistance threats, remains unknown. We discovered PNGM-1, the novel subclass B3 MBL, in deep-sea sediments that predate the antibiotic era. Here, our phylogenetic analysis suggests that PNGM-1 yields insights into the evolutionary origin of subclass B3 MBLs. We reveal the structural similarities between tRNase Zs and PNGM-1, and demonstrate that PNGM-1 has both MBL and tRNase Z activities, suggesting that PNGM-1 is thought to have evolved from a tRNase Z. We also show kinetic and structural comparisons between PNGM-1 and other proteins including subclass B3 MBLs and tRNase Zs. These comparisons revealed that the B3 MBL activity of PNGM-1 is a promiscuous activity and subclass B3 MBLs are thought to have evolved through PNGM-1 activity.
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Affiliation(s)
- Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Masayuki Takahashi
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Jeong Ho Jeon
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Myoung-Ki Hong
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Yoon Sik Park
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Tae Yeong Kim
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Asad Mustafa Karim
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, Republic of Korea
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 440] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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