1
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Pelech P, Navarro PP, Vettiger A, Chao LH, Allolio C. Stress-mediated growth determines E. coli division site morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612282. [PMID: 39314472 PMCID: PMC11419054 DOI: 10.1101/2024.09.11.612282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
In order to proliferate, bacteria must remodel their cell wall at the division site. The division process is driven by the enzymatic activity of peptidoglycan (PG) synthases and hydrolases around the constricting Z-ring. PG remodelling is reg-ulated by de-and re-crosslinking enzymes, and the directing constrictive force of the Z-ring. We introduce a model that is able to reproduce correctly the shape of the division site during the constriction and septation phase of E. coli . The model represents mechanochemical coupling within the mathematical framework of morphoelasticity. It contains only two parameters, associated with volumet-ric growth and PG remodelling, that are coupled to the mechanical stress in the bacterial wall. Different morphologies, corresponding either to mutant or wild type cells were recovered as a function of the remodeling parameter. In addition, a plausible range for the cell stiffness and turgor pressure was determined by comparing numerical simulations with bacterial cell lysis data.
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2
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Castanheira S, López-Escarpa D, Paradela A, García-Del Portillo F. In Vivo Cross-Linking Sheds Light on the Salmonella Divisome in Which PBP3 and PBP3 SAL Compete for Occupancy. Mol Microbiol 2024. [PMID: 39233506 DOI: 10.1111/mmi.15309] [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: 01/12/2024] [Revised: 07/31/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024]
Abstract
Bacterial cell division is orchestrated by proteins that assemble in dynamic complexes collectively known as the divisome. Essential monofunctional enzymes with glycosyltransferase or transpeptidase (TPase) activities, FtsW and FtsI respectively, engage in the synthesis of septal peptidoglycan (sPG). Enigmatically, Salmonella has two TPases that can promote cell division independently: FtsI (PBP3) and the pathogen-specific paralogue PBP3SAL. How Salmonella regulates the assembly of the sPG synthase complex with these two TPases, is unknown. Here, we characterized Salmonella division complexes in wild-type cells and isogenic mutants lacking PBP3 or PBP3SAL. The complexes were cross-linked in vivo and pulled down with antibodies recognizing each enzyme. Proteomics of the immunoprecipitates showed that PBP3 and PBP3SAL do not extensively cross-link in wild type cells, supporting the presence of independent complexes. More than 40 proteins cross-link in complexes in which these two TPases are present. Those identified with high scores include FtsA, FtsK, FtsQLB, FtsW, PBP1B, SPOR domain-containing proteins (FtsN, DedD, RlpA, DamX), amidase activators (FtsX, EnvC, NlpD) and Tol-Pal proteins. Other cross-linked proteins are the protease Prc, the elongasome TPase PBP2 and, D,D-endo- and D,D-carboxypeptidases. PBP3 and PBP3SAL localize at midcell and compete for occupying the division complex in response to environmental cues. Thus, a catalytic-dead PBP3SAL-S300A variant impairs cell division in a high osmolarity and acidic condition in which it is produced at levels exceeding those of PBP3. Salmonella may therefore exploit an 'adjustable' divisome to exchange TPases for ensuring cell division in distinct environments and, in this manner, expand its colonization capacities.
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Affiliation(s)
- Sónia Castanheira
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - David López-Escarpa
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Alberto Paradela
- Proteomics Facility, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
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3
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Cao L, Wang L. Biospecific Chemistry for Covalent Linking of Biomacromolecules. Chem Rev 2024; 124:8516-8549. [PMID: 38913432 PMCID: PMC11240265 DOI: 10.1021/acs.chemrev.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Interactions among biomacromolecules, predominantly noncovalent, underpin biological processes. However, recent advancements in biospecific chemistry have enabled the creation of specific covalent bonds between biomolecules, both in vitro and in vivo. This Review traces the evolution of biospecific chemistry in proteins, emphasizing the role of genetically encoded latent bioreactive amino acids. These amino acids react selectively with adjacent natural groups through proximity-enabled bioreactivity, enabling targeted covalent linkages. We explore various latent bioreactive amino acids designed to target different protein residues, ribonucleic acids, and carbohydrates. We then discuss how these novel covalent linkages can drive challenging protein properties and capture transient protein-protein and protein-RNA interactions in vivo. Additionally, we examine the application of covalent peptides as potential therapeutic agents and site-specific conjugates for native antibodies, highlighting their capacity to form stable linkages with target molecules. A significant focus is placed on proximity-enabled reactive therapeutics (PERx), a pioneering technology in covalent protein therapeutics. We detail its wide-ranging applications in immunotherapy, viral neutralization, and targeted radionuclide therapy. Finally, we present a perspective on the existing challenges within biospecific chemistry and discuss the potential avenues for future exploration and advancement in this rapidly evolving field.
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Affiliation(s)
- Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, United States
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4
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Steffen CL, Manoharan GB, Pavic K, Yeste-Vázquez A, Knuuttila M, Arora N, Zhou Y, Härmä H, Gaigneaux A, Grossmann TN, Abankwa DK. Identification of an H-Ras nanocluster disrupting peptide. Commun Biol 2024; 7:837. [PMID: 38982284 PMCID: PMC11233548 DOI: 10.1038/s42003-024-06523-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 06/28/2024] [Indexed: 07/11/2024] Open
Abstract
Hyperactive Ras signalling is found in most cancers. Ras proteins are only active in membrane nanoclusters, which are therefore potential drug targets. We previously showed that the nanocluster scaffold galectin-1 (Gal1) enhances H-Ras nanoclustering via direct interaction with the Ras binding domain (RBD) of Raf. Here, we establish that the B-Raf preference of Gal1 emerges from the divergence of the Raf RBDs at their proposed Gal1-binding interface. We then identify the L5UR peptide, which disrupts this interaction by binding with low micromolar affinity to the B- and C-Raf-RBDs. Its 23-mer core fragment is sufficient to interfere with H-Ras nanoclustering, modulate Ras-signalling and moderately reduce cell viability. These latter two phenotypic effects may also emerge from the ability of L5UR to broadly engage with several RBD- and RA-domain containing Ras interactors. The L5UR-peptide core fragment is a starting point for the development of more specific reagents against Ras-nanoclustering and -interactors.
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Affiliation(s)
- Candy Laura Steffen
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Karolina Pavic
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Matias Knuuttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Neha Arora
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, McGovern Medical School, UT Health, Houston, TX, 77030, USA
| | - Harri Härmä
- Chemistry of Drug Development, Department of Chemistry, University of Turku, 20500, Turku, Finland
| | - Anthoula Gaigneaux
- Bioinformatics Core, Department of Life Sciences and Medicine, University of Luxembourg, 4367, Esch-sur-Alzette, Luxembourg
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands
| | - Daniel Kwaku Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
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5
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Habjan E, Schouten GK, Speer A, van Ulsen P, Bitter W. Diving into drug-screening: zebrafish embryos as an in vivo platform for antimicrobial drug discovery and assessment. FEMS Microbiol Rev 2024; 48:fuae011. [PMID: 38684467 PMCID: PMC11078164 DOI: 10.1093/femsre/fuae011] [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: 11/01/2023] [Revised: 02/24/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
The rise of multidrug-resistant bacteria underlines the need for innovative treatments, yet the introduction of new drugs has stagnated despite numerous antimicrobial discoveries. A major hurdle is a poor correlation between promising in vitro data and in vivo efficacy in animal models, which is essential for clinical development. Early in vivo testing is hindered by the expense and complexity of existing animal models. Therefore, there is a pressing need for cost-effective, rapid preclinical models with high translational value. To overcome these challenges, zebrafish embryos have emerged as an attractive model for infectious disease studies, offering advantages such as ethical alignment, rapid development, ease of maintenance, and genetic manipulability. The zebrafish embryo infection model, involving microinjection or immersion of pathogens and potential antibiotic hit compounds, provides a promising solution for early-stage drug screening. It offers a cost-effective and rapid means of assessing the efficacy, toxicity and mechanism of action of compounds in a whole-organism context. This review discusses the experimental design of this model, but also its benefits and challenges. Additionally, it highlights recently identified compounds in the zebrafish embryo infection model and discusses the relevance of the model in predicting the compound's clinical potential.
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Affiliation(s)
- Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Gina K Schouten
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Peter van Ulsen
- Section Molecular Microbiology of A-LIFE, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center,De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Section Molecular Microbiology of A-LIFE, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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6
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Compain G, Monsarrat C, Blagojevic J, Brillet K, Dumas P, Hammann P, Kuhn L, Martiel I, Engilberge S, Oliéric V, Wolff P, Burnouf DY, Wagner J, Guichard G. Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp. JACS AU 2024; 4:432-440. [PMID: 38425897 PMCID: PMC10900491 DOI: 10.1021/jacsau.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 03/02/2024]
Abstract
Peptide-based covalent inhibitors targeted to nucleophilic protein residues have recently emerged as new modalities to target protein-protein interactions (PPIs) as they may provide some benefits over more classic competitive inhibitors. Covalent inhibitors are generally targeted to cysteine, the most intrinsically reactive amino acid residue, and to lysine, which is more abundant at the surface of proteins but much less frequently to histidine. Herein, we report the structure-guided design of targeted covalent inhibitors (TCIs) able to bind covalently and selectively to the bacterial sliding clamp (SC), by reacting with a well-conserved histidine residue located on the edge of the peptide-binding pocket. SC is an essential component of the bacterial DNA replication machinery, identified as a promising target for the development of new antibacterial compounds. Thermodynamic and kinetic analyses of ligands bearing different mild electrophilic warheads confirmed the higher efficiency of the chloroacetamide compared to Michael acceptors. Two high-resolution X-ray structures of covalent inhibitor-SC adducts were obtained, revealing the canonical orientation of the ligand and details of covalent bond formation with histidine. Proteomic studies were consistent with a selective SC engagement by the chloroacetamide-based TCI. Finally, the TCI of SC was substantially more active than the parent noncovalent inhibitor in an in vitro SC-dependent DNA synthesis assay, validating the potential of the approach to design covalent inhibitors of protein-protein interactions targeted to histidine.
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Affiliation(s)
- Guillaume Compain
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
| | - Clément Monsarrat
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
| | - Julie Blagojevic
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Karl Brillet
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Philippe Dumas
- Department
of Integrative Structural Biology, IGBMC, Strasbourg University, ESBS, 1 Rue Laurent Fries, 67404 Illkirch, Cedex, France
| | - Philippe Hammann
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Lauriane Kuhn
- Université
de Strasbourg, CNRS, FR1589, Plateforme Protéomique Strasbourg
Esplanade, 2 Allée K. Roentgen, 67084 Strasbourg, France
| | - Isabelle Martiel
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Sylvain Engilberge
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Vincent Oliéric
- Swiss
Light Source (SLS), Paul Scherrer Institute
(PSI), 5232 Villigen-PSI, Switzerland
| | - Philippe Wolff
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Dominique Y. Burnouf
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Jérôme Wagner
- Université
de Strasbourg, CNRS, Architecture et Réactivité de l’ARN,
UPR 9002, Institut de Biologie Moléculaire et Cellulaire du
CNRS, 2 Allée
K. Roentgen, 67084 Strasbourg, France
| | - Gilles Guichard
- Univ.
Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, F-33607 Pessac, France
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7
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Cameron TA, Margolin W. Insights into the assembly and regulation of the bacterial divisome. Nat Rev Microbiol 2024; 22:33-45. [PMID: 37524757 PMCID: PMC11102604 DOI: 10.1038/s41579-023-00942-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/02/2023]
Abstract
The ability to split one cell into two is fundamental to all life, and many bacteria can accomplish this feat several times per hour with high accuracy. Most bacteria call on an ancient homologue of tubulin, called FtsZ, to localize and organize the cell division machinery, the divisome, into a ring-like structure at the cell midpoint. The divisome includes numerous other proteins, often including an actin homologue (FtsA), that interact with each other at the cytoplasmic membrane. Once assembled, the protein complexes that comprise the dynamic divisome coordinate membrane constriction with synthesis of a division septum, but only after overcoming checkpoints mediated by specialized protein-protein interactions. In this Review, we summarize the most recent evidence showing how the divisome proteins of Escherichia coli assemble at the cell midpoint, interact with each other and regulate activation of septum synthesis. We also briefly discuss the potential of divisome proteins as novel antibiotic targets.
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Affiliation(s)
- Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, USA.
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8
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Worm D, Grabe GJ, de Castro GV, Rabinovich S, Warm I, Isherwood K, Helaine S, Barnard A. Stapled Phd Peptides Inhibit Doc Toxin Induced Growth Arrest in Salmonella. ACS Chem Biol 2023; 18:2485-2494. [PMID: 38098459 PMCID: PMC10728895 DOI: 10.1021/acschembio.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 12/18/2023]
Abstract
Bacterial toxin inhibition is a promising approach to overcoming antibiotic failure. InSalmonella, knockout of the toxin Doc has been shown to significantly reduce the formation of antibiotic-tolerant persisters. Doc is a kinase that is inhibited in nontolerant cells by its cognate antitoxin, Phd. In this work, we have developed first-in-class stapled peptide antitoxin mimetics based on the Doc inhibitory sequence of Phd. After making a series of substitutions to improve bacterial uptake, we identified a lead stapled Phd peptide that is able to counteract Doc toxicity in Salmonella. This provides an exciting starting point for the further development of therapeutic peptides capable of reducing antibiotic persistence in pathogenic bacteria.
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Affiliation(s)
- Dennis
J. Worm
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Grzegorz J. Grabe
- Department
of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Guilherme V. de Castro
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Sofya Rabinovich
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Ian Warm
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Kira Isherwood
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Sophie Helaine
- Department
of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston, Massachusetts 02115, United States
| | - Anna Barnard
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
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9
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Gabizon R, Tivon B, Reddi RN, van den Oetelaar MCM, Amartely H, Cossar PJ, Ottmann C, London N. A simple method for developing lysine targeted covalent protein reagents. Nat Commun 2023; 14:7933. [PMID: 38040731 PMCID: PMC10692228 DOI: 10.1038/s41467-023-42632-5] [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: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Peptide-based covalent probes can target shallow protein surfaces not typically addressable using small molecules, yet there is a need for versatile approaches to convert native peptide sequences into covalent binders that can target a broad range of residues. Here we report protein-based thio-methacrylate esters-electrophiles that can be installed easily on unprotected peptides and proteins via cysteine side chains, and react efficiently and selectively with cysteine and lysine side chains on the target. Methacrylate phosphopeptides derived from 14-3-3-binding proteins irreversibly label 14-3-3σ via either lysine or cysteine residues, depending on the position of the electrophile. Methacrylate peptides targeting a conserved lysine residue exhibit pan-isoform binding of 14-3-3 proteins both in lysates and in extracellular media. Finally, we apply this approach to develop protein-based covalent binders. A methacrylate-modified variant of the colicin E9 immunity protein irreversibly binds to the E9 DNAse, resulting in significantly higher thermal stability relative to the non-covalent complex. Our approach offers a simple and versatile route to convert peptides and proteins into potent covalent binders.
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Affiliation(s)
- Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Barr Tivon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maxime C M van den Oetelaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Hadar Amartely
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
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10
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Britton BM, Yovanno RA, Costa SF, McCausland J, Lau AY, Xiao J, Hensel Z. Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism. Nat Commun 2023; 14:4585. [PMID: 37524712 PMCID: PMC10390529 DOI: 10.1038/s41467-023-39921-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/04/2023] [Indexed: 08/02/2023] Open
Abstract
The bacterial divisome is a macromolecular machine composed of more than 30 proteins that controls cell wall constriction during division. Here, we present a model of the structure and dynamics of the core complex of the E. coli divisome, supported by a combination of structure prediction, molecular dynamics simulation, single-molecule imaging, and mutagenesis. We focus on the septal cell wall synthase complex formed by FtsW and FtsI, and its regulators FtsQ, FtsL, FtsB, and FtsN. The results indicate extensive interactions in four regions in the periplasmic domains of the complex. FtsQ, FtsL, and FtsB support FtsI in an extended conformation, with the FtsI transpeptidase domain lifted away from the membrane through interactions among the C-terminal domains. FtsN binds between FtsI and FtsL in a region rich in residues with superfission (activating) and dominant negative (inhibitory) mutations. Mutagenesis experiments and simulations suggest that the essential domain of FtsN links FtsI and FtsL together, potentially modulating interactions between the anchor-loop of FtsI and the putative catalytic cavity of FtsW, thus suggesting a mechanism of how FtsN activates the cell wall synthesis activities of FtsW and FtsI.
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Affiliation(s)
- Brooke M Britton
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 725 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Remy A Yovanno
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 725 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Sara F Costa
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da República, 2780-157, Oeiras, Portugal
| | - Joshua McCausland
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 725 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Albert Y Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 725 N. Wolfe St, Baltimore, MD, 21205, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, 725 N. Wolfe St, Baltimore, MD, 21205, USA.
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da República, 2780-157, Oeiras, Portugal.
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11
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Käshammer L, van den Ent F, Jeffery M, Jean NL, Hale VL, Löwe J. Cryo-EM structure of the bacterial divisome core complex and antibiotic target FtsWIQBL. Nat Microbiol 2023; 8:1149-1159. [PMID: 37127704 PMCID: PMC7614612 DOI: 10.1038/s41564-023-01368-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
In most bacteria, cell division relies on the synthesis of new cell wall material by the multiprotein divisome complex. Thus, at the core of the divisome are the transglycosylase FtsW, which synthesises peptidoglycan strands from its substrate Lipid II, and the transpeptidase FtsI that cross-links these strands to form a mesh, shaping and protecting the bacterial cell. The FtsQ-FtsB-FtsL trimeric complex interacts with the FtsWI complex and is involved in regulating its enzymatic activities; however, the structure of this pentameric complex is unknown. Here, we present the cryogenic electron microscopy structure of the FtsWIQBL complex from Pseudomonas aeruginosa at 3.7 Å resolution. Our work reveals intricate structural details, including an extended coiled coil formed by FtsL and FtsB and the periplasmic interaction site between FtsL and FtsI. Our structure explains the consequences of previously reported mutations and we postulate a possible activation mechanism involving a large conformational change in the periplasmic domain. As FtsWIQBL is central to the divisome, our structure is foundational for the design of future experiments elucidating the precise mechanism of bacterial cell division, an important antibiotic target.
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Affiliation(s)
- Lisa Käshammer
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Magnus Jeffery
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Nicolas L Jean
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Victoria L Hale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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12
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Nguyen HTV, Chen X, Parada C, Luo AC, Shih O, Jeng US, Huang CY, Shih YL, Ma C. Structure of the heterotrimeric membrane protein complex FtsB-FtsL-FtsQ of the bacterial divisome. Nat Commun 2023; 14:1903. [PMID: 37019934 PMCID: PMC10076392 DOI: 10.1038/s41467-023-37543-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
The synthesis of the cell-wall peptidoglycan during bacterial cell division is mediated by a multiprotein machine, called the divisome. The essential membrane protein complex of FtsB, FtsL and FtsQ (FtsBLQ) is at the heart of the divisome assembly cascade in Escherichia coli. This complex regulates the transglycosylation and transpeptidation activities of the FtsW-FtsI complex and PBP1b via coordination with FtsN, the trigger for the onset of constriction. Yet the underlying mechanism of FtsBLQ-mediated regulation is largely unknown. Here, we report the full-length structure of the heterotrimeric FtsBLQ complex, which reveals a V-shaped architecture in a tilted orientation. Such a conformation could be strengthened by the transmembrane and the coiled-coil domains of the FtsBL heterodimer, as well as an extended β-sheet of the C-terminal interaction site involving all three proteins. This trimeric structure may also facilitate interactions with other divisome proteins in an allosteric manner. These results lead us to propose a structure-based model that delineates the mechanism of the regulation of peptidoglycan synthases by the FtsBLQ complex.
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Affiliation(s)
- Hong Thuy Vy Nguyen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
- Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Xiaorui Chen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Claudia Parada
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - An-Chi Luo
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Orion Shih
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30044, Taiwan
| | - Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Yu-Ling Shih
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
| | - Che Ma
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
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13
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Paulussen FM, Grossmann TN. Peptide-based covalent inhibitors of protein-protein interactions. J Pept Sci 2023; 29:e3457. [PMID: 36239115 PMCID: PMC10077911 DOI: 10.1002/psc.3457] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPI) are involved in all cellular processes and many represent attractive therapeutic targets. However, the frequently rather flat and large interaction areas render the identification of small molecular PPI inhibitors very challenging. As an alternative, peptide interaction motifs derived from a PPI interface can serve as starting points for the development of inhibitors. However, certain proteins remain challenging targets when applying inhibitors with a competitive mode of action. For that reason, peptide-based ligands with an irreversible binding mode have gained attention in recent years. This review summarizes examples of covalent inhibitors that employ peptidic binders and have been tested in a biological context.
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Affiliation(s)
- Felix M Paulussen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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14
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Scoffone VC, Irudal S, AbuAlshaar A, Piazza A, Trespidi G, Barbieri G, Makarov V, Migliavacca R, De Rossi E, Buroni S. Bactericidal and Anti-Biofilm Activity of the FtsZ Inhibitor C109 against Acinetobacter baumannii. Antibiotics (Basel) 2022; 11:1571. [PMID: 36358226 PMCID: PMC9687021 DOI: 10.3390/antibiotics11111571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/03/2022] [Accepted: 11/05/2022] [Indexed: 09/29/2023] Open
Abstract
In the last few years, Acinetobacter baumannii has ranked as a number one priority due to its Multi Drug Resistant phenotype. The different metabolic states, such as the one adopted when growing as biofilm, help the bacterium to resist a wide variety of compounds, placing the discovery of new molecules able to counteract this pathogen as a topic of utmost importance. In this context, bacterial cell division machinery and the conserved protein FtsZ are considered very interesting cellular targets. The benzothiadiazole compound C109 is able to inhibit bacterial growth and to block FtsZ GTPase and polymerization activities in Burkholderia cenocepacia, Pseudomonas aeruginosa, and Staphylococcus aureus. In this work, the activity of C109 was tested against a panel of antibiotic sensitive and resistant A. baumannii strains. Its ability to inhibit biofilm formation was explored, together with its activity against the A. baumannii FtsZ purified protein. Our results indicated that C109 has good MIC values against A. baumannii clinical isolates. Moreover, its antibiofilm activity makes it an interesting alternative treatment, effective against diverse metabolic states. Finally, its activity was confirmed against A. baumannii FtsZ.
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Affiliation(s)
- Viola Camilla Scoffone
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Samuele Irudal
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Aseel AbuAlshaar
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Aurora Piazza
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Gabriele Trespidi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Giulia Barbieri
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Vadim Makarov
- Research Center of Biotechnology RAS, 119071 Moscow, Russia
| | - Roberta Migliavacca
- Unit of Microbiology and Clinical Microbiology, Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy
| | - Edda De Rossi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
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