1
|
Carbajo D, Pérez Y, Guerra-Rebollo M, Prats E, Bujons J, Alfonso I. Dynamic Combinatorial Optimization of In Vitro and In Vivo Heparin Antidotes. J Med Chem 2022; 65:4865-4877. [PMID: 35235323 PMCID: PMC8958503 DOI: 10.1021/acs.jmedchem.1c02054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Heparin-like macromolecules
are widely used in clinics as anticoagulant,
antiviral, and anticancer drugs. However, the search of heparin antidotes
based on small synthetic molecules to control blood coagulation still
remains a challenging task due to the physicochemical properties of
this anionic polysaccharide. Here, we use a dynamic combinatorial
chemistry approach to optimize heparin binders with submicromolar
affinity. The recognition of heparin by the most amplified members
of the dynamic library has been studied with different experimental
(SPR, fluorescence, NMR) and theoretical approaches, rendering a detailed
interaction model. The enzymatic assays with selected library members
confirm the correlation between the dynamic covalent screening and
the in vitro heparin inhibition. Moreover, both ex vivo and in vivo blood coagulation assays
with mice show that the optimized molecules are potent antidotes with
potential use as heparin reversal drugs. Overall, these results underscore
the power of dynamic combinatorial chemistry targeting complex and
elusive biopolymers.
Collapse
Affiliation(s)
| | | | - Marta Guerra-Rebollo
- Grup d'Enginyeria de Materials (Gemat), Institut Químic de Sarriá (IQS), Universitat Ramon Llull (URL), Via Augusta 390, 08017 Barcelona, Spain
| | - Eva Prats
- Research and Development Center (CID-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | | | | |
Collapse
|
2
|
Illa O, Ospina J, Sánchez-Aparicio JE, Pulido X, Abengozar MÁ, Gaztelumendi N, Carbajo D, Nogués C, Rivas L, Maréchal JD, Royo M, Ortuño RM. Hybrid Cyclobutane/Proline-Containing Peptidomimetics: The Conformational Constraint Influences Their Cell-Penetration Ability. Int J Mol Sci 2021; 22:ijms22105092. [PMID: 34065025 PMCID: PMC8151717 DOI: 10.3390/ijms22105092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 01/22/2023] Open
Abstract
A new family of hybrid β,γ-peptidomimetics consisting of a repetitive unit formed by a chiral cyclobutane-containing trans-β-amino acid plus a Nα-functionalized trans-γ-amino-l-proline joined in alternation were synthesized and evaluated as cell penetrating peptides (CPP). They lack toxicity on the human tumoral cell line HeLa, with an almost negligible cell uptake. The dodecapeptide showed a substantial microbicidal activity on Leishmania parasites at 50 µM but with a modest intracellular accumulation. Their previously published γ,γ-homologues, with a cyclobutane γ-amino acid, showed a well-defined secondary structure with an average inter-guanidinium distance of 8–10 Å, a higher leishmanicidal activity as well as a significant intracellular accumulation. The presence of a very rigid cyclobutane β-amino acid in the peptide backbone precludes the acquisition of a defined conformation suitable for their cell uptake ability. Our results unveiled the preorganized charge-display as a relevant parameter, additional to the separation among the charged groups as previously described. The data herein reinforce the relevance of these descriptors in the design of CPPs with improved properties.
Collapse
Affiliation(s)
- Ona Illa
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
- Correspondence: (O.I.); (M.R.); (R.M.O.)
| | - Jimena Ospina
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - José-Emilio Sánchez-Aparicio
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - Ximena Pulido
- Institut de Recerca Biomèdica, c/Baldiri Reixac 10, 08028 Barcelona, Spain;
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), c/ Jordi Girona 18–26, 08034 Barcelona, Spain
- Departamento de Química, Universidad del Tolima, Santa Helena Parte Alta, Ibagué 730006299, Tolima, Colombia
| | - María Ángeles Abengozar
- Centro de Investigaciones Biológicas Margarita Salas, c/ Ramiro de Maeztu 9, CSIC, 28040 Madrid, Spain; (M.Á.A.); (L.R.)
| | - Nerea Gaztelumendi
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.G.); (C.N.)
| | - Daniel Carbajo
- Institut de Química Avançada de Catalunya (IQAC-CSIC), c/ Jordi Girona, 18-26, 08034 Barcelona, Spain;
| | - Carme Nogués
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.G.); (C.N.)
| | - Luis Rivas
- Centro de Investigaciones Biológicas Margarita Salas, c/ Ramiro de Maeztu 9, CSIC, 28040 Madrid, Spain; (M.Á.A.); (L.R.)
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
| | - Miriam Royo
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), c/ Jordi Girona 18–26, 08034 Barcelona, Spain
- Institut de Química Avançada de Catalunya (IQAC-CSIC), c/ Jordi Girona, 18-26, 08034 Barcelona, Spain;
- Correspondence: (O.I.); (M.R.); (R.M.O.)
| | - Rosa M. Ortuño
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (J.O.); (J.-E.S.-A.); (J.-D.M.)
- Correspondence: (O.I.); (M.R.); (R.M.O.)
| |
Collapse
|
3
|
Kared H, Redd AD, Bloch EM, Bonny TS, Sumatoh H, Kairi F, Carbajo D, Abel B, Newell EW, Bettinotti MP, Benner SE, Patel EU, Littlefield K, Laeyendecker O, Shoham S, Sullivan D, Casadevall A, Pekosz A, Nardin A, Fehlings M, Tobian AA, Quinn TC. SARS-CoV-2-specific CD8+ T cell responses in convalescent COVID-19 individuals. J Clin Invest 2021; 131:145476. [PMID: 33427749 DOI: 10.1172/jci145476] [Citation(s) in RCA: 167] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022] Open
Abstract
Characterization of the T cell response in individuals who recover from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is critical to understanding its contribution to protective immunity. A multiplexed peptide-MHC tetramer approach was used to screen 408 SARS-CoV-2 candidate epitopes for CD8+ T cell recognition in a cross-sectional sample of 30 coronavirus disease 2019 convalescent individuals. T cells were evaluated using a 28-marker phenotypic panel, and findings were modelled against time from diagnosis and from humoral and inflammatory responses. There were 132 SARS-CoV-2-specific CD8+ T cell responses detected across 6 different HLAs, corresponding to 52 unique epitope reactivities. CD8+ T cell responses were detected in almost all convalescent individuals and were directed against several structural and nonstructural target epitopes from the entire SARS-CoV-2 proteome. A unique phenotype for SARS-CoV-2-specific T cells was observed that was distinct from other common virus-specific T cells detected in the same cross-sectional sample and characterized by early differentiation kinetics. Modelling demonstrated a coordinated and dynamic immune response characterized by a decrease in inflammation, increase in neutralizing antibody titer, and differentiation of a specific CD8+ T cell response. Overall, T cells exhibited distinct differentiation into stem cell and transitional memory states (subsets), which may be key to developing durable protection.
Collapse
Affiliation(s)
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tania S Bonny
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | - Evan W Newell
- ImmunoScape, Singapore, Singapore.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Maria P Bettinotti
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sarah E Benner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eshan U Patel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Epidemiology and
| | - Kirsten Littlefield
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
| | | | - David Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | | | - Aaron Ar Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Department of Medicine and
| |
Collapse
|
4
|
Carbajo D, Ruiz-Sánchez AJ, Nájera F, Pérez-Inestrosa E, Alfonso I. Spontaneous macrocyclization through multiple dynamic cyclic aminal formation. Chem Commun (Camb) 2021; 57:1190-1193. [PMID: 33448267 DOI: 10.1039/d0cc07184f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of aminals in dynamic covalent chemistry is slightly underexplored, probably due to their inherent instability. Here we report the spontaneous [2+2] macrocyclization of tetrakis(aminals). Their unexpected stability and structural modularity, the dynamic nature of the connections and their water tolerance make them appealing systems for future applications as stimulus-responsive materials.
Collapse
Affiliation(s)
- Daniel Carbajo
- Department of Biological Chemistry, Institute of Advanced Chemistry of Catalonia, IQAC-CSIC c/Jordi Girona 18-26, Barcelona, 08034, Spain.
| | - Antonio Jesús Ruiz-Sánchez
- Universidad de Málaga-IBIMA, Departamento de Química Orgánica, Campus de Teatinos s/n, Málaga-29071, Spain. and Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, Málaga-29590, Spain
| | - Francisco Nájera
- Universidad de Málaga-IBIMA, Departamento de Química Orgánica, Campus de Teatinos s/n, Málaga-29071, Spain. and Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, Málaga-29590, Spain
| | - Ezequiel Pérez-Inestrosa
- Universidad de Málaga-IBIMA, Departamento de Química Orgánica, Campus de Teatinos s/n, Málaga-29071, Spain. and Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Parque Tecnológico de Andalucía, c/Severo Ochoa, 35, Málaga-29590, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute of Advanced Chemistry of Catalonia, IQAC-CSIC c/Jordi Girona 18-26, Barcelona, 08034, Spain.
| |
Collapse
|
5
|
Kared H, Bloch E, Redd A, Nardin A, Sumatoh H, Kairi F, Carbajo D, Abel B, Newell E, Laeyendecker O, Bonny T, Benner S, Pekosz A, Tobian A, Quinn T. LB-18. Broad and Prevalent SARS-CoV-2 CD8+ T Cell Response in Recovered COVID-19 Individuals Demonstrates Kinetics of Early Differentiation. Open Forum Infect Dis 2020. [PMCID: PMC7776945 DOI: 10.1093/ofid/ofaa515.1915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Understanding the diversity, breadth, magnitude, and functional profile of the T cell response against SARS-CoV-2 in recovered COVID-19 individuals is critical to evaluate the contribution of T cells to produce a potentially protective immune response. Methods We used a multiplexed peptide-MHC tetramer approach to screen a total of 408 SARS-CoV-2 candidate peptide epitopes for CD8+ T cell recognition in a cohort of 30 individuals recovered from COVID-19. The peptides spanned the whole viral genome and were restricted to six prevalent HLA alleles; T cells were simultaneously characterized by a 28-marker phenotypic panel. The evolution of the SARS-CoV-2 T cell responses was then statistically modeled against time from diagnosis, and in relation to humoral and inflammatory response. Workflow for Study. A multiplexed peptide-MHC tetramer approach was used to screen SARS-CoV-2 candidate peptide epitopes in a cohort of 30 COVID-19 recovered patients across 6 prevalent HLA alleles, and T cells profiled with a 28-marker phenotypic panel. ![]()
Multiplex tetramer screen. One representative COVID-19 recovered patient and one healthy donor were screened for HLA- relevant SARS-CoV-2 epitopes, as well as epitopes for CMV, EBV, Influenza, Adenovirus and MART-1. Shown are the frequencies of tetramer-positive CD8 T cells from 2 technical replicates per subject. ![]()
Results Almost all individuals screened showed a T cell response against SARS-CoV-2 (29/30): 132 SARS-CoV-2-specific CD8+ T cells hits were detected, corresponding to 52 unique reactive epitopes. Twelve of the 52 unique SARS-CoV-2-specific epitopes were recognized by more than 40% of the individuals screened, indicating high prevalence in the subjects. Importantly, these CD8+ T cell responses were directed against both structural and non-structural viral proteins, with the highest magnitude against nucleocapsid derived peptides, but without any antigen-driven bias in the phenotype of specific T cells. Overall, SARS-CoV-2 T cells showed specific states of differentiation (stem-cell memory and transitional memory), which differed from those of MART-1, influenza, CMV and EBV-specific T cells. UMAP visualization revealed a phenotypic profile of SARS-CoV-2-specific CD8 T cells in COVID-19 convalescent donors that is distinct from other viral specificities, such as influenza, CMV, EBV and Adenovirus. ![]()
SARS-CoV-2 epitope screening revealed CD8+ T cell responses directed against both structural and non-structural viral proteins, with the highest magnitude response against nucleocapsid derived peptides ![]()
Conclusion The kinetics modeling demonstrates a dynamic, evolving immune response characterized by a time-dependent decrease in overall inflammation, increase in neutralizing antibody titer, and progressive differentiation of a broad SARS-CoV-2 CD8 T cell response. It could be desirable to aim at recapitulating the hallmarks of this robust CD8 T cell response in the design of protective COVID-19 vaccines. Disclosures Hassen Kared, PhD, ImmunoScape (Shareholder) Alessandra Nardin, DvM, ImmunoScape (Shareholder) Hermi Sumatoh, BSc, Dip MTech, ImmunoScape (Shareholder) Faris Kairi, BSc, ImmunoScape (Shareholder) Daniel Carbajo, PhD, ImmunoScape (Shareholder) Brian Abel, PhD, MBA, ImmunoScape (Shareholder) Evan Newell, PhD, ImmunoScape (Shareholder)
Collapse
Affiliation(s)
- Hassen Kared
- ImmunoScape, Singapore, Not Applicable, Singapore
| | - Evan Bloch
- Johns Hopkins University, Baltimore, Maryland
| | | | | | | | - Faris Kairi
- ImmunoScape, Singapore, Not Applicable, Singapore
| | | | | | | | | | - Tania Bonny
- Johns Hopkins University, Baltimore, Maryland
| | | | - Andy Pekosz
- Johns Hopkins University, Baltimore, Maryland
| | | | | |
Collapse
|
6
|
Kared H, Redd AD, Bloch EM, Bonny TS, Sumatoh H, Kairi F, Carbajo D, Abel B, Newell EW, Bettinotti MP, Benner SE, Patel EU, Littlefield K, Laeyendecker O, Shoham S, Sullivan D, Casadevall A, Pekosz A, Nardin A, Fehlings M, Tobian AAR, Quinn TC. CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entire SARS-CoV-2 proteome and show kinetics of early differentiation. bioRxiv 2020:2020.10.08.330688. [PMID: 33052343 PMCID: PMC7553170 DOI: 10.1101/2020.10.08.330688] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Characterization of the T cell response in individuals who recover from SARS-CoV-2 infection is critical to understanding its contribution to protective immunity. A multiplexed peptide-MHC tetramer approach was used to screen 408 SARS-CoV-2 candidate epitopes for CD8+ T cell recognition in a cross-sectional sample of 30 COVID-19 convalescent individuals. T cells were evaluated using a 28-marker phenotypic panel, and findings were modelled against time from diagnosis, humoral and inflammatory responses. 132 distinct SARS-CoV-2-specific CD8+ T cell epitope responses across six different HLAs were detected, corresponding to 52 unique reactivities. T cell responses were directed against several structural and non-structural virus proteins. Modelling demonstrated a coordinated and dynamic immune response characterized by a decrease in inflammation, increase in neutralizing antibody titer, and differentiation of a specific CD8+ T cell response. Overall, T cells exhibited distinct differentiation into stem-cell and transitional memory states, subsets, which may be key to developing durable protection.
Collapse
Affiliation(s)
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Evan M Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tania S. Bonny
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | | | - Evan W Newell
- ImmunoScape Pte Ltd, Singapore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Maria P. Bettinotti
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E. Benner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eshan U. Patel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kirsten Littlefield
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Oliver Laeyendecker
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shmuel Shoham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Sullivan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | - Aaron AR Tobian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
7
|
Carbajo D, Pérez Y, Bujons J, Alfonso I. Cover Picture: Live‐Cell‐Templated Dynamic Combinatorial Chemistry (Angew. Chem. Int. Ed. 39/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Carbajo
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| |
Collapse
|
8
|
Carbajo D, Pérez Y, Bujons J, Alfonso I. Titelbild: Live‐Cell‐Templated Dynamic Combinatorial Chemistry (Angew. Chem. 39/2020). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Daniel Carbajo
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| |
Collapse
|
9
|
Carbajo D, Pérez Y, Bujons J, Alfonso I. Live‐Cell‐Templated Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2020; 59:17202-17206. [DOI: 10.1002/anie.202004745] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Daniel Carbajo
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| |
Collapse
|
10
|
Affiliation(s)
- Daniel Carbajo
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry Institute of Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| |
Collapse
|
11
|
Corvaglia V, Carbajo D, Prabhakaran P, Ziach K, Mandal PK, Santos VD, Legeay C, Vogel R, Parissi V, Pourquier P, Huc I. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: artificial analogues of DNA mimic proteins. Nucleic Acids Res 2019; 47:5511-5521. [PMID: 31073604 PMCID: PMC6582331 DOI: 10.1093/nar/gkz352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
Inspired by DNA mimic proteins, we have introduced aromatic foldamers bearing phosphonate groups as synthetic mimics of the charge surface of B-DNA and competitive inhibitors of some therapeutically relevant DNA-binding enzymes: the human DNA Topoisomerase 1 (Top1) and the human HIV-1 integrase (HIV-1 IN). We now report on variants of these anionic foldamers bearing carboxylates instead of phosphonates. Several new monomers have been synthesized with protecting groups suitable for solid phase synthesis (SPS). Six hexadecaamides have been prepared using SPS. Proof of their resemblance to B-DNA was brought by the first crystal structure of one of these DNA-mimic foldamers in its polyanionic form. While some of the foldamers were found to be as active as, or even more active than, the original phosphonate oligomers, others had no activity at all or could even stimulate enzyme activity in vitro. Some foldamers were found to have differential inhibitory effects on the two enzymes. These results demonstrate a strong dependence of inhibitory activity on foldamer structure and charge distribution. They open broad avenues for the development of new classes of derivatives that could inhibit the interaction of specific proteins with their DNA target thereby influencing the cellular pathways in which they are involved.
Collapse
Affiliation(s)
- Valentina Corvaglia
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Daniel Carbajo
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Panchami Prabhakaran
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Krzysztof Ziach
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Pradeep Kumar Mandal
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | | | - Carole Legeay
- Sanofi recherche & développement, Montpellier 34184, France
| | - Rachel Vogel
- Sanofi recherche & développement, Montpellier 34184, France
| | - Vincent Parissi
- Université de Bordeaux, CNRS, Laboratoire de Microbiologie Fondamentale et Pathogénicité (UMR 5234), Bordeaux 33146, France
| | - Philippe Pourquier
- INSERM U1194, Institut de Recherche en Cancérologie de Montpellier & Université de Montpellier, Montpellier 34298, France
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| |
Collapse
|
12
|
Chakarov S, Lim HY, Tan L, Lim SY, See P, Lum J, Zhang XM, Foo S, Nakamizo S, Duan K, Kong WT, Gentek R, Balachander A, Carbajo D, Bleriot C, Malleret B, Tam JKC, Baig S, Shabeer M, Toh SAES, Schlitzer A, Larbi A, Marichal T, Malissen B, Chen J, Poidinger M, Kabashima K, Bajenoff M, Ng LG, Angeli V, Ginhoux F. Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches. Science 2019; 363:363/6432/eaau0964. [PMID: 30872492 DOI: 10.1126/science.aau0964] [Citation(s) in RCA: 524] [Impact Index Per Article: 104.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Macrophages are a heterogeneous cell population involved in tissue homeostasis, inflammation, and various pathologies. Although the major tissue-resident macrophage populations have been extensively studied, interstitial macrophages (IMs) residing within the tissue parenchyma remain poorly defined. Here we studied IMs from murine lung, fat, heart, and dermis. We identified two independent IM subpopulations that are conserved across tissues: Lyve1loMHCIIhiCX3CR1hi (Lyve1loMHCIIhi) and Lyve1hiMHCIIloCX3CR1lo (Lyve1hiMHCIIlo) monocyte-derived IMs, with distinct gene expression profiles, phenotypes, functions, and localizations. Using a new mouse model of inducible macrophage depletion (Slco2b1 flox/DTR), we found that the absence of Lyve1hiMHCIIlo IMs exacerbated experimental lung fibrosis. Thus, we demonstrate that two independent populations of IMs coexist across tissues and exhibit conserved niche-dependent functional programming.
Collapse
Affiliation(s)
- Svetoslav Chakarov
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Hwee Ying Lim
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Leonard Tan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Sheau Yng Lim
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Peter See
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Xiao-Meng Zhang
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Shihui Foo
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Satoshi Nakamizo
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Wan Ting Kong
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Rebecca Gentek
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Akhila Balachander
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Daniel Carbajo
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Camille Bleriot
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - John Kit Chung Tam
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore
| | - Sonia Baig
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore, Singapore
| | - Muhammad Shabeer
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore, Singapore
| | - Sue-Anne Ee Shiow Toh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 119228 Singapore, Singapore
| | - Andreas Schlitzer
- Myeloid Cell Biology, Life & Medical Sciences Institute, University of Bonn, 53115 Bonn, Germany
| | - Anis Larbi
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Thomas Marichal
- Laboratory of Cellular and Molecular Immunology, GIGA Research, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, Liège University, 4000 Liège, Belgium.,WELBIO, Walloon Excellence in Life Sciences and Biotechnology, 1300 Wallonia, Belgium
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS UMR, 13288 Marseille, France
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Kenji Kabashima
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore.,Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Marc Bajenoff
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Veronique Angeli
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A*STAR, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore.
| |
Collapse
|
13
|
Carbajo D, El-Faham A, Royo M, Albericio F. Optimized Stepwise Synthesis of the API Liraglutide Using BAL Resin and Pseudoprolines. ACS Omega 2019; 4:8674-8680. [PMID: 31459957 PMCID: PMC6648002 DOI: 10.1021/acsomega.9b00974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/18/2019] [Indexed: 05/15/2023]
Abstract
The number of peptide-based active pharmaceutical ingredients (APIs) has increased enormously in recent years. Furthermore, the emerging new peptide drug candidates are more complex and larger. For the industrial solid-phase synthesis of C-carboxylic acid peptides, the two main resins available, Wang and chlorotrityl chloride (CTC), have a number of drawbacks. In this context, resins that form an amide bond with the first amino acid are more robust than Wang and CTC resins. Here, we address the use of the backbone (BAL) resin for the synthesis of the peptide liraglutide. The BAL resin, in conjunction with the use of pseudoprolines to avoid aggregation, allows the stepwise solid-phase synthesis of this API in excellent purity and yield.
Collapse
Affiliation(s)
- Daniel Carbajo
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine,
Barcelona Science Park, 08028 Barcelona, Spain
- Institute
of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research
Council (CSIC), 08034 Barcelona, Spain
| | - Ayman El-Faham
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Department
of Chemistry, Faculty of Science, Alexandria
University, P.O. Box 426, Alexandria 21321, Egypt
| | - Miriam Royo
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine,
Barcelona Science Park, 08028 Barcelona, Spain
- Institute
of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research
Council (CSIC), 08034 Barcelona, Spain
| | - Fernando Albericio
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine,
Barcelona Science Park, 08028 Barcelona, Spain
- Institute
of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research
Council (CSIC), 08034 Barcelona, Spain
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Department
of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
- School of
Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
- E-mail: , . Phone: (+34) 618 089
145, (+27) 614 009 144
| |
Collapse
|
14
|
Carbajo D, Fransen P, El-Faham A, Royo M, Albericio F. Pseudo-Wang Handle for the Preparation of Fully Protected Peptides. Synthesis of Liraglutide by Fragment Condensation. Org Lett 2019; 21:2459-2463. [DOI: 10.1021/acs.orglett.9b00813] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Carbajo
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia (IQAC−CSIC), Spanish National Research Council (CSIC), 08034 Barcelona, Spain
| | - Peter Fransen
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain
| | - Ayman El-Faham
- Department of Chemistry, College of Science, King Saud University, 2455, Riyadh 11451, Saudi Arabia
- Department of Chemistry, Faculty of Science, Alexandria University, 426, Alexandria 21321, Egypt
| | - Miriam Royo
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia (IQAC−CSIC), Spanish National Research Council (CSIC), 08034 Barcelona, Spain
| | - Fernando Albericio
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, University of Barcelona, 08028 Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia (IQAC−CSIC), Spanish National Research Council (CSIC), 08034 Barcelona, Spain
- Department of Chemistry, College of Science, King Saud University, 2455, Riyadh 11451, Saudi Arabia
- Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
- School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| |
Collapse
|
15
|
Xu W, Monaco G, Wong EH, Tan WLW, Kared H, Simoni Y, Tan SW, How WZY, Tan CTY, Lee BTK, Carbajo D, K G S, Low ICH, Mok EWH, Foo S, Lum J, Tey HL, Tan WP, Poidinger M, Newell E, Ng TP, Foo R, Akbar AN, Fülöp T, Larbi A. Mapping of γ/δ T cells reveals Vδ2+ T cells resistance to senescence. EBioMedicine 2018; 39:44-58. [PMID: 30528453 PMCID: PMC6354624 DOI: 10.1016/j.ebiom.2018.11.053] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Immune adaptation with aging is a major of health outcomes. Studies in humans have mainly focus on αβ T cells while γδ T cells have been neglected despite their role in immunosurveillance. We investigated the impact of aging on γδ T cell subsets phenotypes, functions, senescence and their molecular response to stress. Methods Peripheral blood of young and old donors in Singapore have been used to assess the phenotype, functional capacity, proliferation capacity and gene expression of the various γδ T cell subsets. Peripheral blood mononuclear cells from apheresis cones and young donors have been used to characterize the telomere length, epigenetics profile and DNA damage response of the various γδ T cell subsets phenotype. Findings Our data shows that peripheral Vδ2+ phenotype, functional capacity (cytokines, cytotoxicity, proliferation) and gene expression profile are specific when compared against all other αβ and γδ T cells in aging. Hallmarks of senescence including telomere length, epigenetic profile and DNA damage response of Vδ2+ also differs against all other αβ and γδ T cells. Interpretation Our results highlight the differential impact of lifelong stress on γδ T cells subsets, and highlight possible mechanisms that enable Vδ2+ to be resistant to cellular aging. The new findings reinforce the concept that Vδ2+ have an “innate-like” behavior and are more resilient to the environment as compared to “adaptive-like” Vδ1+ T cells.
Collapse
Affiliation(s)
- Weili Xu
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Gianni Monaco
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore; Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Eleanor Huijin Wong
- Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), Genome Building, Biopolis, Singapore, Singapore
| | - Wilson Lek Wen Tan
- Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), Genome Building, Biopolis, Singapore, Singapore
| | - Hassen Kared
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Yannick Simoni
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Shu Wen Tan
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore; Immunology Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Wilson Zhi Yong How
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Crystal Tze Ying Tan
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Bernett Teck Kwong Lee
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Daniel Carbajo
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Srinivasan K G
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Ivy Chay Huang Low
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Esther Wing Hei Mok
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Shihui Foo
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | | | | | - Michael Poidinger
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Evan Newell
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore
| | - Tze Pin Ng
- Gerontology Research Programme, Department of Psychological Medicine, National University Health System, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Roger Foo
- Genome Institute of Singapore (GIS), Agency for Science Technology and Research (A*STAR), Genome Building, Biopolis, Singapore, Singapore
| | - Arne N Akbar
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Tamas Fülöp
- Research Center on Aging, Graduate Program in Immunology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Department of Microbiology, National University of Singapore, Singapore, Singapore; Department of Biology, Faculty of Science, University Tunis El Manar, Tunis, Tunisia.
| |
Collapse
|
16
|
Lim HY, Lim SY, Tan CK, Thiam CH, Goh CC, Carbajo D, Chew SHS, See P, Chakarov S, Wang XN, Lim LH, Johnson LA, Lum J, Fong CY, Bongso A, Biswas A, Goh C, Evrard M, Yeo KP, Basu R, Wang JK, Tan Y, Jain R, Tikoo S, Choong C, Weninger W, Poidinger M, Stanley ER, Collin M, Tan NS, Ng LG, Jackson DG, Ginhoux F, Angeli V. Hyaluronan Receptor LYVE-1-Expressing Macrophages Maintain Arterial Tone through Hyaluronan-Mediated Regulation of Smooth Muscle Cell Collagen. Immunity 2018; 49:1191. [PMID: 30566884 DOI: 10.1016/j.immuni.2018.12.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
17
|
Corredor M, Carbajo D, Domingo C, Pérez Y, Bujons J, Messeguer A, Alfonso I. Dynamic Covalent Identification of an Efficient Heparin Ligand. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Miriam Corredor
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Daniel Carbajo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Cecilia Domingo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility, Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Angel Messeguer
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| |
Collapse
|
18
|
Corredor M, Carbajo D, Domingo C, Pérez Y, Bujons J, Messeguer A, Alfonso I. Dynamic Covalent Identification of an Efficient Heparin Ligand. Angew Chem Int Ed Engl 2018; 57:11973-11977. [DOI: 10.1002/anie.201806770] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Miriam Corredor
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Daniel Carbajo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Cecilia Domingo
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Yolanda Pérez
- NMR Facility, Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Bujons
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Angel Messeguer
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry; Institute of Advanced Chemistry of Catalonia; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| |
Collapse
|
19
|
Lim HY, Lim SY, Tan CK, Thiam CH, Goh CC, Carbajo D, Chew SHS, See P, Chakarov S, Wang XN, Lim LH, Johnson LA, Lum J, Fong CY, Bongso A, Biswas A, Goh C, Evrard M, Yeo KP, Basu R, Wang JK, Tan Y, Jain R, Tikoo S, Choong C, Weninger W, Poidinger M, Stanley RE, Collin M, Tan NS, Ng LG, Jackson DG, Ginhoux F, Angeli V. Hyaluronan Receptor LYVE-1-Expressing Macrophages Maintain Arterial Tone through Hyaluronan-Mediated Regulation of Smooth Muscle Cell Collagen. Immunity 2018; 49:326-341.e7. [PMID: 30054204 DOI: 10.1016/j.immuni.2018.06.008] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/01/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023]
Abstract
The maintenance of appropriate arterial tone is critically important for normal physiological arterial function. However, the cellular and molecular mechanisms remain poorly defined. Here, we have shown that in the mouse aorta, resident macrophages prevented arterial stiffness and collagen deposition in the steady state. Using phenotyping, transcriptional profiling, and targeted deletion of Csf1r, we have demonstrated that these macrophages-which are a feature of blood vessels invested with smooth muscle cells (SMCs) in both mouse and human tissues-expressed the hyaluronan (HA) receptor LYVE-l. Furthermore, we have shown they possessed the unique ability to modulate collagen expression in SMCs by matrix metalloproteinase MMP-9-dependent proteolysis through engagement of LYVE-1 with the HA pericellular matrix of SMCs. Our study has unveiled a hitherto unknown homeostatic contribution of arterial LYVE-1+ macrophages through the control of collagen production by SMCs and has identified a function of LYVE-1 in leukocytes.
Collapse
Affiliation(s)
- Hwee Ying Lim
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Sheau Yng Lim
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Chek Kun Tan
- School of Biological Sciences, Nanyang Technological University, Nanyang, Singapore 637551, Singapore
| | - Chung Hwee Thiam
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Chi Ching Goh
- Singapore Immunology Network, A(∗)STAR, Singapore 138648, Singapore
| | - Daniel Carbajo
- Singapore Immunology Network, A(∗)STAR, Singapore 138648, Singapore
| | - Samantha Hui Shang Chew
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Peter See
- Singapore Immunology Network, A(∗)STAR, Singapore 138648, Singapore
| | | | - Xiao Nong Wang
- Institute of Cellular Medicine, Newcastle University, Newcastle NE2 4HH, UK
| | - Li Hui Lim
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Louise A Johnson
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliff Hospital, Oxford OX3 9DS, UK
| | - Josephine Lum
- Singapore Immunology Network, A(∗)STAR, Singapore 138648, Singapore
| | - Chui Yee Fong
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore 119074, Singapore
| | - Ariff Bongso
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore 119074, Singapore
| | - Arijit Biswas
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore 119074, Singapore
| | - Chern Goh
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | | | - Kim Pin Yeo
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Ranu Basu
- Department of Development and Molecular Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Jun Kit Wang
- School of Material Science and Engineering, Nanyang Technological University, Singapore 639977, Singapore
| | - Yingrou Tan
- Singapore Immunology Network, A(∗)STAR, Singapore 138648, Singapore
| | - Rohit Jain
- The Centenary Institute, Newtown, NSW 2050, Australia
| | - Shweta Tikoo
- The Centenary Institute, Newtown, NSW 2050, Australia
| | - Cleo Choong
- School of Material Science and Engineering, Nanyang Technological University, Singapore 639977, Singapore
| | | | | | - Richard E Stanley
- Department of Development and Molecular Biology, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Matthew Collin
- Institute of Cellular Medicine, Newcastle University, Newcastle NE2 4HH, UK
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, Nanyang, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore; KK Women's and Children Hospital, Singapore 229899, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network, A(∗)STAR, Singapore 138648, Singapore
| | - David G Jackson
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliff Hospital, Oxford OX3 9DS, UK
| | - Florent Ginhoux
- Singapore Immunology Network, A(∗)STAR, Singapore 138648, Singapore
| | - Véronique Angeli
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| |
Collapse
|
20
|
He JS, Subramaniam S, Narang V, Srinivasan K, Saunders SP, Carbajo D, Wen-Shan T, Hidayah Hamadee N, Lum J, Lee A, Chen J, Poidinger M, Zolezzi F, Lafaille JJ, Curotto de Lafaille MA. IgG1 memory B cells keep the memory of IgE responses. Nat Commun 2017; 8:641. [PMID: 28935935 PMCID: PMC5608722 DOI: 10.1038/s41467-017-00723-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 07/23/2017] [Indexed: 02/03/2023] Open
Abstract
The unique differentiation of IgE cells suggests unconventional mechanisms of IgE memory. IgE germinal centre cells are transient, most IgE cells are plasma cells, and high affinity IgE is produced by the switching of IgG1 cells to IgE. Here we investigate the function of subsets of IgG1 memory B cells in IgE production and find that two subsets of IgG1 memory B cells, CD80+CD73+ and CD80-CD73-, contribute distinctively to the repertoires of high affinity pathogenic IgE and low affinity non-pathogenic IgE. Furthermore, repertoire analysis indicates that high affinity IgE and IgG1 plasma cells differentiate from rare CD80+CD73+ high affinity memory clones without undergoing further mutagenesis. By identifying the cellular origin of high affinity IgE and the clonal selection of high affinity memory B cells into the plasma cell fate, our findings provide fundamental insights into the pathogenesis of allergies, and on the mechanisms of antibody production in memory B cell responses.IgE is an important mediator of protective immunity as well as allergic reaction, but how high affinity IgE antibodies are produced in memory responses is not clear. Here the authors show that IgE can be generated via class-switch recombination in IgG1 memory B cells without additional somatic hypermutation.
Collapse
Affiliation(s)
- Jin-Shu He
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Sharrada Subramaniam
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Vipin Narang
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | | | - Sean P Saunders
- Division of Pulmonary, Critical Care and Sleep Medicine, Departments of Medicine and Cell Biology, New York University School of Medicine, 550 First Ave, New York, 10016, USA
| | - Daniel Carbajo
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Tsao Wen-Shan
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Nur Hidayah Hamadee
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Andrea Lee
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Francesca Zolezzi
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore
- Galderma R&D, Les Templiers, 2400 route des Colles, Sophia Antipolis, 06410, Biot, France
| | - Juan J Lafaille
- Skirball Institute and Department of Pathology, New York University School of Medicine, 540 First Ave, New York, 10016, USA
| | - Maria A Curotto de Lafaille
- Singapore Immunology Network (SIgN), 8A Biomedical Grove, Singapore, 138648, Singapore.
- Division of Pulmonary, Critical Care and Sleep Medicine, Departments of Medicine and Cell Biology, New York University School of Medicine, 550 First Ave, New York, 10016, USA.
| |
Collapse
|
21
|
Appanna R, Kg S, Xu MH, Toh YX, Velumani S, Carbajo D, Lee CY, Zuest R, Balakrishnan T, Xu W, Lee B, Poidinger M, Zolezzi F, Leo YS, Thein TL, Wang CI, Fink K. Plasmablasts During Acute Dengue Infection Represent a Small Subset of a Broader Virus-specific Memory B Cell Pool. EBioMedicine 2016; 12:178-188. [PMID: 27628668 PMCID: PMC5078588 DOI: 10.1016/j.ebiom.2016.09.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 01/12/2023] Open
Abstract
Dengue is endemic in tropical countries worldwide and the four dengue virus serotypes often co-circulate. Infection with one serotype results in high titers of cross-reactive antibodies produced by plasmablasts, protecting temporarily against all serotypes, but impairing protective immunity in subsequent infections. To understand the development of these plasmablasts, we analyzed virus-specific B cell properties in patients during acute disease and at convalescence. Plasmablasts were unrelated to classical memory cells expanding in the blood during early recovery. We propose that only a small subset of memory B cells is activated as plasmablasts during repeat infection and that plasmablast responses are not representative of the memory B cell repertoire after dengue infection. Antibody sequences and functions were analyzed in longitudinal acute and convalescent samples from dengue patients Plasmablast antibodies were virus glycoprotein-specific whereas memory B cell-derived antibodies bound to more viral proteins plasmablasts seem to be activated from only a small subset of memory B cells
Antibody-mediated immune memory is orchestrated by various B cell types that are relevant during different phases after an infection. Antibody-secreting cells or so-called plasmablasts are generated from activated specific memory B cell a few days after re-infection. However, little in known whether the antibodies produced by these plasmablasts are relevant for protection in humans and whether the parent memory B cells are further maintained in the memory pool, possibly as affinity-matured versions of the original clones. This is important in the context of vaccination since the repertoires of individual B cell subsets could represent biomarkers to assess efficacy and long-term protection. In addition, the generation of “protective” B cell subsets could potentially be influenced by vaccine design and by the use of adjuvants. We studied the relationship of plasmablasts and memory B cells in longitudinal blood samples from dengue patients. Dengue virus (DENV) has four serotypes and pre-existing antibodies can be cross-protective or can enhance disease after a heterologous infection via Fc-gamma-receptor-mediated uptake of virus-antibody complexes. B cell memory can therefore be both beneficial and detrimental. Here we studied plasmablasts and DENV-specific memory B cells and their relationship and protective potential by assessing antibody sequences and monoclonal antibodies. We found that both populations produced largely serotype cross-neutralizing antibodies, whereas more plasmablast antibodies were neutralizing. Few plasmablast clones could be found in the memory pool, suggesting that only a subset of memory B cells is activated during acute disease and that a separate repertoire of cells is retained as longer-term memory. In this study we started to dissect the complexity of B cell immune memory to dengue infection and the finding can inform further investigations into which immune cell subsets are disease-enhancing after a heterologous infection.
Collapse
Affiliation(s)
| | | | - Mei Hui Xu
- Singapore Immunology Network, A*STAR, Singapore
| | | | | | | | | | | | | | - Weili Xu
- Singapore Immunology Network, A*STAR, Singapore
| | - Bernett Lee
- Singapore Immunology Network, A*STAR, Singapore
| | | | | | - Yee Sin Leo
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tun Linn Thein
- Communicable Disease Centre, Institute of Infectious Disease and Epidemiology, Tan Tock Seng Hospital, Singapore
| | | | - Katja Fink
- Singapore Immunology Network, A*STAR, Singapore.
| |
Collapse
|
22
|
Carbajo D, Magi S, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest ARR, Carninci P, Hayashizaki Y, Daub CO, Okada-Hatakeyama M, Mar JC. Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PLoS One 2015; 10:e0144176. [PMID: 26658111 PMCID: PMC4682858 DOI: 10.1371/journal.pone.0144176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 11/13/2015] [Indexed: 01/05/2023] Open
Abstract
Understanding how cells use complex transcriptional programs to alter their fate in response to specific stimuli is an important question in biology. For the MCF-7 human breast cancer cell line, we applied gene expression trajectory models to identify the genes involved in driving cell fate transitions. We modified trajectory models to account for the scenario where cells were exposed to different stimuli, in this case epidermal growth factor and heregulin, to arrive at different cell fates, i.e. proliferation and differentiation respectively. Using genome-wide CAGE time series data collected from the FANTOM5 consortium, we identified the sets of promoters that were involved in the transition of MCF-7 cells to their specific fates versus those with expression changes that were generic to both stimuli. Of the 1,552 promoters identified, 1,091 had stimulus-specific expression while 461 promoters had generic expression profiles over the time course surveyed. Many of these stimulus-specific promoters mapped to key regulators of the ERK (extracellular signal-regulated kinases) signaling pathway such as FHL2 (four and a half LIM domains 2). We observed that in general, generic promoters peaked in their expression early on in the time course, while stimulus-specific promoters tended to show activation of their expression at a later stage. The genes that mapped to stimulus-specific promoters were enriched for pathways that control focal adhesion, p53 signaling and MAPK signaling while generic promoters were enriched for cell death, transcription and the cell cycle. We identified 162 genes that were controlled by an alternative promoter during the time course where a subset of 37 genes had separate promoters that were classified as stimulus-specific and generic. The results of our study highlighted the degree of complexity involved in regulating a cell fate transition where multiple promoters mapping to the same gene can demonstrate quite divergent expression profiles.
Collapse
Affiliation(s)
- Daniel Carbajo
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Shigeyuki Magi
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Japan
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Tsurumi-ku, Yokohama, Japan
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako-shi, Japan
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Tsurumi-ku, Yokohama, Japan
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako-shi, Japan
| | - Timo Lassmann
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Tsurumi-ku, Yokohama, Japan
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
- Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia, Australia
| | - Erik Arner
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Tsurumi-ku, Yokohama, Japan
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
- Department of Medicine, Karolinska Institutet and Center for Metabolism and Endocrinology, Karolinska University Hospital, Stockholm, Sweden
| | - Alistair R. R. Forrest
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Tsurumi-ku, Yokohama, Japan
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Piero Carninci
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Tsurumi-ku, Yokohama, Japan
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako-shi, Japan
| | - Carsten O. Daub
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Tsurumi-ku, Yokohama, Japan
- RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
- Department of Biosciences and Nutrition and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | | | - Mariko Okada-Hatakeyama
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Japan
- * E-mail: (MO); (JCM)
| | - Jessica C. Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
- * E-mail: (MO); (JCM)
| |
Collapse
|
23
|
Egusquiaguirre SP, Manguán-García C, Pintado-Berninches L, Iarriccio L, Carbajo D, Albericio F, Royo M, Pedraz JL, Hernández RM, Perona R, Igartua M. Development of surface modified biodegradable polymeric nanoparticles to deliver GSE24.2 peptide to cells: A promising approach for the treatment of defective telomerase disorders. Eur J Pharm Biopharm 2015; 91:91-102. [DOI: 10.1016/j.ejpb.2015.01.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 12/20/2022]
|
24
|
Abstract
Background Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. Results This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. Conclusions The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. Implementation, availability and requirements Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php. Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.
Collapse
Affiliation(s)
- Daniel Carbajo
- Department of Physics, Sapienza University of Rome, P,le A, Moro, 5, 00185 Rome, Italy
| | | |
Collapse
|
25
|
Rosés C, Carbajo D, Sanclimens G, Farrera-Sinfreu J, Blancafort A, Oliveras G, Cirac AD, Bardají E, Puig T, Planas M, Feliu L, Albericio F, Royo M. Cell-penetrating γ-peptide/antimicrobial undecapeptide conjugates with anticancer activity. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
|
26
|
Cavalli S, Carbajo D, Acosta M, Lope-Piedrafita S, Candiota AP, Arús C, Royo M, Albericio F. Efficient γ-amino-proline-derived cell penetrating peptide-superparamagnetic iron oxide nanoparticle conjugates via aniline-catalyzed oxime chemistry as bimodal imaging nanoagents. Chem Commun (Camb) 2012; 48:5322-4. [PMID: 22516929 DOI: 10.1039/c2cc17937g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aniline-catalyzed oxime chemistry was employed to conjugate a γ-amino-proline-derived cell penetrating peptide to superparamagnetic iron oxide nanoparticles (SPIONs). Internalization of the novel nanoconjugate into HeLa cells was found to be remarkably higher compared to the analogous TAT-SPION conjugate.
Collapse
Affiliation(s)
- Silvia Cavalli
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials, and Nanomedicine, 08028 Barcelona, Spain.
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Gorrea E, Carbajo D, Gutiérrez-Abad R, Illa O, Branchadell V, Royo M, Ortuño RM. Searching for new cell-penetrating agents: hybrid cyclobutane-proline γ,γ-peptides. Org Biomol Chem 2012; 10:4050-7. [PMID: 22514076 DOI: 10.1039/c2ob25220a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Two generations of hybrid γ,γ-peptides containing cyclobutane amino acids and cis-γ-amino-L-proline joined in alternation have been synthesized and their capacity to cross the eukaryotic cell membrane has been evaluated. The first generation consists of di-, tetra- and hexapeptides, and their properties have been analyzed as well as the influence of peptide length and chirality of the cyclobutane residues. Results have shown that the absolute configuration of the cyclobutane amino acid does not have a relevant influence. The second generation consists of hybrid γ,γ-hexapeptides with a common backbone and distinct side chains introduced with different linkage types through the α-amino group (N(α)) of the proline monomers. These peptides have been shown to be non-toxic towards HeLa cells and to internalize them effectively, the best results being obtained for the peptides with a spacer of five carbons between the N(α) atom and the guanidinium group. The introduction of cyclobutane residues inside the sequence affords a good balance between charge and hydrophobicity, reducing the number of positive charges. This results in lower toxicity and similar cell-uptake properties when compared to previously described peptide agents.
Collapse
Affiliation(s)
- Esther Gorrea
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | | | | | | | | | | |
Collapse
|
28
|
Gutiérrez-Abad R, Carbajo D, Nolis P, Acosta-Silva C, Cobos JA, Illa O, Royo M, Ortuño RM. Synthesis and structural study of highly constrained hybrid cyclobutane-proline γ,γ-peptides. Amino Acids 2011; 41:673-86. [PMID: 21541681 DOI: 10.1007/s00726-011-0912-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 04/02/2011] [Indexed: 11/24/2022]
Abstract
Two diastereomeric series of hybrid γ,γ-peptides derived from conveniently protected derivatives of (1R,2S)- and (1S,2R)-3-amino-2,2-dimethylcyclobutane-1-carboxylic acid and cis-4-amino-L: -proline joined in alternation have efficiently been prepared through convergent synthesis. High-resolution NMR experiments show that these compounds present defined conformations in solution affording very compact structures as the result of intra and inter residue hydrogen-bonded ring formation. (R,S)-cyclobutane containing peptides adopt more twisted conformations than (S,R) diastereomers. In addition, all these γ-peptides have high tendency to aggregation providing vesicles of nanometric size, which were stable when allowed to stand for several days, as verified by transmission electron microscopy.
Collapse
Affiliation(s)
- Raquel Gutiérrez-Abad
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A. Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res 2010; 39:D268-71. [PMID: 20965970 PMCID: PMC3013787 DOI: 10.1093/nar/gkq936] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Phospho3D is a database of three-dimensional (3D) structures of phosphorylation sites (P-sites) derived from the Phospho.ELM database, which also collects information on the residues surrounding the P-site in space (3D zones). The database also provides the results of a large-scale structural comparison of the 3D zones versus a representative dataset of structures, thus associating to each P-site a number of structurally similar sites. The new version of Phospho3D presents an 11-fold increase in the number of 3D sites and incorporates several additional features, including new structural descriptors, the possibility of selecting non-redundant sets of 3D structures and the availability for download of non-redundant sets of structurally annotated P-sites. Moreover, it features P3Dscan, a new functionality that allows the user to submit a protein structure and scan it against the 3D zones collected in the Phospho3D database. Phospho3D version 2.0 is available at: http://www.phospho3d.org/.
Collapse
Affiliation(s)
- Andreas Zanzoni
- Institute for Research in Biomedicine, Joint IRB-BSC program in Computational Biology, 08028 Barcelona, Spain.
| | | | | | | | | | | | | |
Collapse
|