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Ramos da Silva Grillo VT, Bertanha M, da Silva Rodrigues L, de Lima MA, Mellucci Filho PL, Rahal Guaragna Machado R, Durigon EL, Dias Sertorio N, de Assis Golim M, Moroz A, Marques Braz AM, de Moraes LN, Leite MA, Bonciani Nader H, de Campos GC, Rodrigues Guzzo Carvalho C, Florença Cardoso F, Magro AJ, Caputo Nunes H, Tommasini Grotto RM, de Cássia Alvarado R, de Moura Campos Pardini MI, Lima Sobreira M, da Costa EAPN, Naime Barbosa A, Fortaleza CMCB. Nebulized enriched heparin improves respiratory parameters in patients with COVID-19: a phase I/II randomized and triple-blind clinical trial. Sci Rep 2024; 14:19902. [PMID: 39191809 PMCID: PMC11350104 DOI: 10.1038/s41598-024-70064-8] [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: 03/23/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
To evaluate the safety and the potential antiviral treatment of inhaled enriched heparin in patients with COVID-19. The specific objectives were to investigate the anticoagulation profile, antiviral and anti-inflammatory effects, and respiratory evolution of inhaled enriched heparin. We conducted a randomized, triple-blind, placebo-controlled Phase I/II clinical trial in hospitalized adults with COVID-19 receiving inhalation of enriched heparin or saline (placebo) every 4 h for 7 days. Among the 27 patients who completed the study, no changes in blood coagulation parameters were observed, indicating the safety of inhaled enriched heparin. The group receiving enriched heparin showed a significant reduction in the need for supplemental oxygen and improvement in respiratory parameters, such as the PaO2/FiO2 ratio. Inhalation of enriched heparin is shown to be safe and has also demonstrated potential therapeutic benefits for patients with COVID-19. These promising results justify the continuation of the study to the next phase, Phase II/III, to further evaluate the therapeutic efficacy of inhaled enriched heparin in the treatment of COVID-19-associated viral pneumonia.Trial registration: ClinicalTrials.gov. 08/02/2021. Identifier: NCT04743011.
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Affiliation(s)
- Vinicius Tadeu Ramos da Silva Grillo
- Department of Surgery and Orthopedics, Botucatu Medical School, São Paulo State University - UNESP, Clinical Hospital, Professor Montenegro Avenue, Botucatu, SP, 18618687, Brazil
| | - Matheus Bertanha
- Department of Surgery and Orthopedics, Botucatu Medical School, São Paulo State University - UNESP, Clinical Hospital, Professor Montenegro Avenue, Botucatu, SP, 18618687, Brazil.
- Applied Biotechnology Laboratory, Research Nucleus of Clinical Hospital, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil.
| | - Lenize da Silva Rodrigues
- Department of Surgery and Orthopedics, Botucatu Medical School, São Paulo State University - UNESP, Clinical Hospital, Professor Montenegro Avenue, Botucatu, SP, 18618687, Brazil
- Applied Biotechnology Laboratory, Research Nucleus of Clinical Hospital, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Marcelo Andrade de Lima
- Centre for Glycoscience, School of Life Sciences, Keele University, Newcastle-Under-Lyme, Staffordshire, UK
| | - Pedro Luciano Mellucci Filho
- Department of Surgery and Orthopedics, Botucatu Medical School, São Paulo State University - UNESP, Clinical Hospital, Professor Montenegro Avenue, Botucatu, SP, 18618687, Brazil
| | | | - Edson Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, - USP, São Paulo, Brazil
- Scientific Platform Pasteur USP (SPPU), University of São Paulo, São Paulo, Brazil
| | - Nathália Dias Sertorio
- Department of Surgery and Orthopedics, Botucatu Medical School, São Paulo State University - UNESP, Clinical Hospital, Professor Montenegro Avenue, Botucatu, SP, 18618687, Brazil
| | - Marjorie de Assis Golim
- Applied Biotechnology Laboratory, Research Nucleus of Clinical Hospital, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Andrei Moroz
- Department of Bioprocess and Biotechnology, School of Pharmaceutical Sciences, São Paulo State University - UNESP, Araraquara, SP, Brazil
| | - Aline Márcia Marques Braz
- Applied Biotechnology Laboratory, Research Nucleus of Clinical Hospital, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Leonardo Nazário de Moraes
- Applied Biotechnology Laboratory, Research Nucleus of Clinical Hospital, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Marco Antonio Leite
- Clinical Hospital of the Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Helena Bonciani Nader
- Department of Biochemistry, Federal University of São Paulo - UNIFESP, São Paulo, SP, Brazil
| | - Gustavo Constantino de Campos
- Department of Orthopedics and Traumatology, School of Medical Sciences, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | | | - Fábio Florença Cardoso
- Department of Biophysics and Pharmacology, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Angelo José Magro
- Department of Biophysics and Pharmacology, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Helga Caputo Nunes
- Teaching and Research Center of the Albert Einstein Hospital, São Paulo, SP, Brazil
| | - Rejane Maria Tommasini Grotto
- Applied Biotechnology Laboratory, Research Nucleus of Clinical Hospital, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
- Bioprocessing and Biotechnology Department, School of Agriculture, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Rita de Cássia Alvarado
- Applied Biotechnology Laboratory, Research Nucleus of Clinical Hospital, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | | | - Marcone Lima Sobreira
- Department of Surgery and Orthopedics, Botucatu Medical School, São Paulo State University - UNESP, Clinical Hospital, Professor Montenegro Avenue, Botucatu, SP, 18618687, Brazil
| | | | - Alexandre Naime Barbosa
- Department of Infectious Diseases, Botucatu Medical School, São Paulo State University - UNESP, Botucatu, SP, Brazil
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Elste J, Saini A, Mejia-Alvarez R, Mejía A, Millán-Pacheco C, Swanson-Mungerson M, Tiwari V. Significance of Artificial Intelligence in the Study of Virus-Host Cell Interactions. Biomolecules 2024; 14:911. [PMID: 39199298 PMCID: PMC11352483 DOI: 10.3390/biom14080911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 09/01/2024] Open
Abstract
A highly critical event in a virus's life cycle is successfully entering a given host. This process begins when a viral glycoprotein interacts with a target cell receptor, which provides the molecular basis for target virus-host cell interactions for novel drug discovery. Over the years, extensive research has been carried out in the field of virus-host cell interaction, generating a massive number of genetic and molecular data sources. These datasets are an asset for predicting virus-host interactions at the molecular level using machine learning (ML), a subset of artificial intelligence (AI). In this direction, ML tools are now being applied to recognize patterns in these massive datasets to predict critical interactions between virus and host cells at the protein-protein and protein-sugar levels, as well as to perform transcriptional and translational analysis. On the other end, deep learning (DL) algorithms-a subfield of ML-can extract high-level features from very large datasets to recognize the hidden patterns within genomic sequences and images to develop models for rapid drug discovery predictions that address pathogenic viruses displaying heightened affinity for receptor docking and enhanced cell entry. ML and DL are pivotal forces, driving innovation with their ability to perform analysis of enormous datasets in a highly efficient, cost-effective, accurate, and high-throughput manner. This review focuses on the complexity of virus-host cell interactions at the molecular level in light of the current advances of ML and AI in viral pathogenesis to improve new treatments and prevention strategies.
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Affiliation(s)
- James Elste
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
| | - Akash Saini
- Hinsdale Central High School, 5500 S Grant St, Hinsdale, IL 60521, USA;
| | - Rafael Mejia-Alvarez
- Department of Physiology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA;
| | - Armando Mejía
- Departamento de Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico 09340, Mexico;
| | - Cesar Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Col Chamilpa, Cuernavaca 62209, Mexico;
| | - Michelle Swanson-Mungerson
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
| | - Vaibhav Tiwari
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
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3
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Chhabra M, Shanthamurthy CD, Kumar NV, Mardhekar S, Vishweshwara SS, Wimmer N, Modhiran N, Watterson D, Amarilla AA, Cha JS, Beckett JR, De Voss JJ, Kayal Y, Vlodavsky I, Dorsett LR, Smith RAA, Gandhi NS, Kikkeri R, Ferro V. Amphiphilic Heparinoids as Potent Antiviral Agents against SARS-CoV-2. J Med Chem 2024; 67:11885-11916. [PMID: 38995734 DOI: 10.1021/acs.jmedchem.4c00487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Herein, we report the synthesis and biological evaluation of a novel series of heparinoid amphiphiles as inhibitors of heparanase and SARS-CoV-2. By employing a tailor-made synthetic strategy, a library of highly sulfated homo-oligosaccharides bearing d-glucose or a C5-epimer (i.e., l-idose or l-iduronic acid) conjugated with various lipophilic groups was synthesized and investigated for antiviral activity. Sulfated higher oligosaccharides of d-glucose or l-idose with lipophilic aglycones displayed potent anti-SARS-CoV-2 and antiheparanse activity, similar to or better than pixatimod (PG545), and were more potent than their isosteric l-iduronic acid congeners. Lipophilic groups such as cholestanol and C18-aliphatic substitution are more advantageous than functional group appended lipophilic moieties. These findings confirm that fine-tuning of higher oligosaccharides, degree of sulfation, and lipophilic groups can yield compounds with potent anti-SARS-CoV-2 activity.
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Affiliation(s)
- Mohit Chhabra
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Chethan D Shanthamurthy
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | | | - Sandhya Mardhekar
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sharath S Vishweshwara
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Norbert Wimmer
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Alberto A Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jonathan S Cha
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - James R Beckett
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yasmin Kayal
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion─Israel Institute of Technology, Haifa 31096, Israel
| | - Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion─Israel Institute of Technology, Haifa 31096, Israel
| | - Lauren R Dorsett
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
| | - Raymond A A Smith
- School of Chemical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Neha S Gandhi
- Centre for Genomics and Personalised Health, School of Chemistry and Physics, Queensland University of Technology, 2 George Street, Brisbane, Queensland 4000, Australia
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raghavendra Kikkeri
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
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Khodadadi Yazdi M, Seidi F, Hejna A, Zarrintaj P, Rabiee N, Kucinska-Lipka J, Saeb MR, Bencherif SA. Tailor-Made Polysaccharides for Biomedical Applications. ACS APPLIED BIO MATERIALS 2024; 7:4193-4230. [PMID: 38958361 PMCID: PMC11253104 DOI: 10.1021/acsabm.3c01199] [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: 12/17/2023] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
Abstract
Polysaccharides (PSAs) are carbohydrate-based macromolecules widely used in the biomedical field, either in their pure form or in blends/nanocomposites with other materials. The relationship between structure, properties, and functions has inspired scientists to design multifunctional PSAs for various biomedical applications by incorporating unique molecular structures and targeted bulk properties. Multiple strategies, such as conjugation, grafting, cross-linking, and functionalization, have been explored to control their mechanical properties, electrical conductivity, hydrophilicity, degradability, rheological features, and stimuli-responsiveness. For instance, custom-made PSAs are known for their worldwide biomedical applications in tissue engineering, drug/gene delivery, and regenerative medicine. Furthermore, the remarkable advancements in supramolecular engineering and chemistry have paved the way for mission-oriented biomaterial synthesis and the fabrication of customized biomaterials. These materials can synergistically combine the benefits of biology and chemistry to tackle important biomedical questions. Herein, we categorize and summarize PSAs based on their synthesis methods, and explore the main strategies used to customize their chemical structures. We then highlight various properties of PSAs using practical examples. Lastly, we thoroughly describe the biomedical applications of tailor-made PSAs, along with their current existing challenges and potential future directions.
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Affiliation(s)
- Mohsen Khodadadi Yazdi
- Division
of Electrochemistry and Surface Physical Chemistry, Faculty of Applied
Physics and Mathematics, Gdańsk University
of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
- Advanced
Materials Center, Gdańsk University
of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
| | - Farzad Seidi
- Jiangsu
Co−Innovation Center for Efficient Processing and Utilization
of Forest Resources and International Innovation Center for Forest
Chemicals and Materials, Nanjing Forestry
University, Nanjing 210037, China
| | - Aleksander Hejna
- Institute
of Materials Technology, Poznan University
of Technology, PL-61-138 Poznań, Poland
| | - Payam Zarrintaj
- School
of Chemical Engineering, Oklahoma State
University, 420 Engineering
North, Stillwater, Oklahoma 74078, United States
| | - Navid Rabiee
- Department
of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai 600077, India
| | - Justyna Kucinska-Lipka
- Department
of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, 80-233 Gdańsk, Poland
| | - Mohammad Reza Saeb
- Department
of Pharmaceutical Chemistry, Medical University
of Gdańsk, J.
Hallera 107, 80-416 Gdańsk, Poland
| | - Sidi A. Bencherif
- Chemical
Engineering Department, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Harvard
John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
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Ives CM, Nguyen L, Fogarty CA, Harbison AM, Durocher Y, Klassen J, Fadda E. Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. eLife 2024; 13:RP95708. [PMID: 38864493 PMCID: PMC11168744 DOI: 10.7554/elife.95708] [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] [Indexed: 06/13/2024] Open
Abstract
Glycosylation of the SARS-CoV-2 spike (S) protein represents a key target for viral evolution because it affects both viral evasion and fitness. Successful variations in the glycan shield are difficult to achieve though, as protein glycosylation is also critical to folding and structural stability. Within this framework, the identification of glycosylation sites that are structurally dispensable can provide insight into the evolutionary mechanisms of the shield and inform immune surveillance. In this work, we show through over 45 μs of cumulative sampling from conventional and enhanced molecular dynamics (MD) simulations, how the structure of the immunodominant S receptor binding domain (RBD) is regulated by N-glycosylation at N343 and how this glycan's structural role changes from WHu-1, alpha (B.1.1.7), and beta (B.1.351), to the delta (B.1.617.2), and omicron (BA.1 and BA.2.86) variants. More specifically, we find that the amphipathic nature of the N-glycan is instrumental to preserve the structural integrity of the RBD hydrophobic core and that loss of glycosylation at N343 triggers a specific and consistent conformational change. We show how this change allosterically regulates the conformation of the receptor binding motif (RBM) in the WHu-1, alpha, and beta RBDs, but not in the delta and omicron variants, due to mutations that reinforce the RBD architecture. In support of these findings, we show that the binding of the RBD to monosialylated ganglioside co-receptors is highly dependent on N343 glycosylation in the WHu-1, but not in the delta RBD, and that affinity changes significantly across VoCs. Ultimately, the molecular and functional insight we provide in this work reinforces our understanding of the role of glycosylation in protein structure and function and it also allows us to identify the structural constraints within which the glycosylation site at N343 can become a hotspot for mutations in the SARS-CoV-2 S glycan shield.
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Affiliation(s)
- Callum M Ives
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | - Linh Nguyen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Carl A Fogarty
- Department of Chemistry, Maynooth UniversityMaynoothIreland
| | | | - Yves Durocher
- Human Health Therapeutics Research Centre, Life Sciences Division, National Research Council CanadaQuébecCanada
- Département de Biochimie et Médecine Moléculaire, Université de MontréalQuébecCanada
| | - John Klassen
- Department of Chemistry, University of AlbertaEdmontonCanada
| | - Elisa Fadda
- School of Biological Sciences, University of SouthamptonSouthamptonUnited Kingdom
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Fu L, Bridges CA, Kim HN, Ding C, Bao Hou NC, Yeow J, Fok S, Macmillan A, Sterling JD, Baker SM, Lord MS. Cationic Polysaccharides Bind to the Endothelial Cell Surface Extracellular Matrix Involving Heparan Sulfate. Biomacromolecules 2024; 25:3850-3862. [PMID: 38775104 DOI: 10.1021/acs.biomac.4c00477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Cationic polysaccharides have been extensively studied for drug delivery via the bloodstream, yet few have progressed to clinical use. Endothelial cells lining the blood vessel wall are coated in an anionic extracellular matrix called the glycocalyx. However, we do not fully comprehend the charged polysaccharide interactions with the glycocalyx. We reveal that the cationic polysaccharide poly(acetyl, arginyl) glucosamine (PAAG) exhibits the highest association with the endothelial glycocalyx, followed by dextran (neutral) and hyaluronan (anionic). Furthermore, we demonstrate that PAAG binds heparan sulfate (HS) within the glycocalyx, leading to intracellular accumulation. Using an in vitro glycocalyx model, we demonstrate a charge-based extent of association of polysaccharides with HS. Mechanistically, we observe that PAAG binding to HS occurs via a condensation reaction and functionally protects HS from degradation. Together, this study reveals the interplay between polysaccharide charge properties and interactions with the endothelial cell glycocalyx toward improved delivery system design and application.
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Affiliation(s)
- Lu Fu
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Claire A Bridges
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ha Na Kim
- Molecular Surface Interaction Laboratory, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Catherine Ding
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Nicole Chiwei Bao Hou
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jonathan Yeow
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sandra Fok
- Katherina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Alexander Macmillan
- Katherina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - James D Sterling
- Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, California 91711, United States
| | - Shenda M Baker
- Synedgen Inc, Claremont, California 91711, United States
| | - Megan S Lord
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
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Ertan-Bolelli T, Bolelli K, Elçi SD, Belen-Apak FB. Promising Drug Fondaparinux for the Treatment of COVID-19: an In Silico Analysis of Low Molecular Weight Heparin, Direct Oral Anticoagulant, and Antiplatelet Drug Interactions with Host Protease Furin. Cardiovasc Drugs Ther 2024; 38:425-432. [PMID: 36401727 PMCID: PMC9676724 DOI: 10.1007/s10557-022-07406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 11/21/2022]
Abstract
PURPOSE As of July 2022, the COVID-19 pandemic has affected over 555 million worldwide confirmed cases and caused more than 6.3 million deaths. The studies showed that the D-dimer levels were increased in non-survivors compared to survivors and heparin treatment has begun to be administered to the patients in severe clinics. As we knew that the entrance of SARS-CoV-2 to the host cell needs to be facilitated by host proteases; we published our hypothesis that heparin as a serine protease inhibitor may block the interaction between spike protein receptor-binding domain and host proteases. In our study, we aimed to investigate the interactions between not only heparins but also other antiplatelet and anticoagulant drugs including fondaparinux. METHODS In this study, docking studies were carried out to evaluate the interactions between low molecular weight heparins (LMWHs) (enoxaparin, dalteparin, tinzaparin), direct oral anticoagulant, and antiplatelet drugs with host proteases. Molecular docking studies were performed by using Schrödinger molecular modeling software. 3D structures of the ligands were obtained from the 2D structures by assigning the OPLS-2005 force field using the Maestro 12.7. The 3D crystal structure of the furin complexed with an inhibitor, 2,5-dideoksistreptamin derivative, was extracted from the Protein Data Bank (PDB ID: 5MIM). Docking studies were carried out using the Grid-based Ligand Docking with Energetics module of the Schrödinger Software. RESULTS The docking studies revealed that fondaparinux was the most relevant molecule to interact with furin with a docking score of - 12.74. It showed better interaction than the natural ligand of furin with an increased score compared to the docking score of - 8.155 of the natural ligand. AnaGA*IsA structure representing LMWH structure has shown a docking score of - 11.562 which was also better than the score of the natural ligand of furin. CONCLUSION Our findings have shown that LMWHs and fondaparinux can be used for their possible antiviral effects in COVID-19 patients. Our results have shown that in accordance with heparin and LMWH, fondaparinux can also be a candidate for "drug repurposing" in COVID-19 therapy, not only because of their anticoagulant but also possible antiviral effects.
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Affiliation(s)
- Tugba Ertan-Bolelli
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06560 Ankara, Turkey
- Bolelli Lab LLC, Stone Mountain, GA 30083 USA
| | - Kayhan Bolelli
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06560 Ankara, Turkey
- Bolelli Lab LLC, Stone Mountain, GA 30083 USA
- LumiLabs, Ulus, Ankara, 06610 Turkey
| | | | - F. Burcu Belen-Apak
- Department of Pediatric Hematology and Oncology, Medical Faculty, Baskent University, Sehit Temel Kuguluoglu Street No 24, 06490 Bahcelievler/Ankara, Turkey
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8
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Nahain AA, Li J, Modhiran N, Watterson D, Li JP, Ignjatovic V, Monagle P, Tsanaktsidis J, Vamvounis G, Ferro V. Antiviral Activities of Heparan Sulfate Mimetic RAFT Polymers Against Mosquito-borne Viruses. ACS APPLIED BIO MATERIALS 2024; 7:2862-2871. [PMID: 38699864 DOI: 10.1021/acsabm.3c01223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Mosquito-borne viruses are a major worldwide health problem associated with high morbidity and mortality rates and significant impacts on national healthcare budgets. The development of antiviral drugs for both the treatment and prophylaxis of these diseases is thus of considerable importance. To address the need for therapeutics with antiviral activity, a library of heparan sulfate mimetic polymers was screened against dengue virus (DENV), Yellow fever virus (YFV), Zika virus (ZIKV), and Ross River virus (RRV). The polymers were prepared by RAFT polymerization of various acidic monomers with a target MW of 20 kDa (average Mn ∼ 27 kDa by GPC). Among the polymers, poly(SS), a homopolymer of sodium styrenesulfonate, was identified as a broad spectrum antiviral with activity against all the tested viruses and particularly potent inhibition of YFV (IC50 = 310 pM). Our results further uncovered that poly(SS) exhibited a robust inhibition of ZIKV infection in both mosquito and human cell lines, which points out the potential functions of poly(SS) in preventing mosquito-borne viruses associated diseases by blocking viral transmission in their mosquito vectors and mitigating viral infection in patients.
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Affiliation(s)
- Abdullah Al Nahain
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jinlin Li
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, University of Uppsala, 75123 Uppsala, Sweden
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jin-Ping Li
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, University of Uppsala, 75123 Uppsala, Sweden
| | - Vera Ignjatovic
- Haematology Research, Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Paul Monagle
- Haematology Research, Murdoch Children's Research Institute, Parkville, Victoria 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3052, Australia
- Department of Clinical Haematology, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - John Tsanaktsidis
- CSIRO Manufacturing, Research Way, Clayton, Victoria 3168, Australia
| | - George Vamvounis
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
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9
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Tay EA, Vijayakumar V, Morales RF, Lee ES, Teo A. Protecting the endothelial glycocalyx in COVID-19. PLoS Pathog 2024; 20:e1012203. [PMID: 38753622 PMCID: PMC11098429 DOI: 10.1371/journal.ppat.1012203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Affiliation(s)
- Emira Adam Tay
- School of Applied Science, Republic Polytechnic, Singapore, Singapore
| | | | | | - Ee Soo Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Pharmacy, University of Nottingham Malaysia, Selangor, Malaysia
| | - Andrew Teo
- National Centre for Infectious Diseases, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Medicine, The Doherty Institute, University of Melbourne, Melbourne, Australia
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10
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Loffredo LF, Surpur A, Ringham OR, Li F, de Los Santos-Alexis K, Arpaia N. Heparan sulfate regulates amphiregulin signaling towards reparative lung mesenchymal cells during influenza A infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591175. [PMID: 38712053 PMCID: PMC11071614 DOI: 10.1101/2024.04.25.591175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Amphiregulin (Areg), a growth factor produced by regulatory T (Treg) cells to facilitate tissue repair/regeneration, contains a heparan sulfate (HS) binding domain. How HS, a highly sulfated glycan subtype that alters growth factor signaling, influences Areg repair/regeneration functions is unclear. Here we report that inhibition of HS in various cell lines and primary lung mesenchymal cells (LMC) qualitatively alters downstream signaling and highlights the existence of HS-dependent vs. -independent Areg transcriptional signatures. Utilizing a panel of cell lines with targeted deletions in HS synthesis-related genes, we found that the presence of the glypican family of heparan sulfate proteoglycans is critical for Areg signaling and confirmed this dependency in primary LMC by siRNA-mediated knockdown. Furthermore, in the context of influenza A (IAV) infection in vivo , we found that an Areg-responsive subset of reparative LMC upregulate glypican-4 and HS. Conditional deletion of HS primarily within this LMC subset resulted in reduced blood oxygen saturation following infection with IAV, with no changes in viral load. Finally, we found that co-culture of HS-knockout LMC with IAV-induced Treg cells results in reduced LMC responses. Collectively, this study reveals the essentiality of HS on a specific lung mesenchymal population as a mediator of Treg cell-derived Areg reparative signaling during IAV infection.
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11
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Alotaibi FS, Alsadun MMR, Alsaiari SA, Ramakrishnan K, Yates EA, Fernig DG. Interactions of proteins with heparan sulfate. Essays Biochem 2024:EBC20230093. [PMID: 38646914 DOI: 10.1042/ebc20230093] [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: 02/06/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Heparan sulfate (HS) is a glycosaminoglycan, polysaccharides that are considered to have arisen in the last common unicellular ancestor of multicellular animals. In this light, the large interactome of HS and its myriad functions in relation to the regulation of cell communication are not surprising. The binding of proteins to HS determines their localisation and diffusion, essential for embryonic development and homeostasis. Following the biosynthesis of the initial heparosan polymer, the subsequent modifications comprise an established canonical pathway and a minor pathway. The more frequent former starts with N-deacetylation and N-sulfation of GlcNAc residues, the latter with C-5 epimerisation of a GlcA residue adjacent to a GlcNAc. The binding of proteins to HS is driven by ionic interactions. The multivalent effect arising from the many individual ionic bonds between a single protein and a polysaccharide chain results in a far stronger interaction than would be expected from an ion-exchange process. In many instances, upon binding, both parties undergo substantial conformational change, the resulting hydrogen and van der Waal bonds contributing significant free energy to the binding reaction. Nevertheless, ionic bonds dominate the protein-polysaccharide interaction kinetically. Together with the multivalent effect, this provides an explanation for the observed trapping of HS-binding proteins in extracellular matrix. Importantly, individual ionic bonds have been observed to be dynamic; breaking and reforming, while the protein remains bound to the polysaccharide. These considerations lead to a model for 1D diffusion of proteins in extracellular matrix on HS, involving mechanisms such as sliding, chain switching and rolling.
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Affiliation(s)
- Faizah S Alotaibi
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Marim M R Alsadun
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Biology, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Sarah A Alsaiari
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Krithika Ramakrishnan
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Edwin A Yates
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - David G Fernig
- Department of Biochemistry, Systems and Cell Biology, Institute of Molecular, Integrative and Systems Biology, University of Liverpool, Liverpool L69 7ZB, U.K
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12
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Zhang Q, Pavlinov I, Ye Y, Zheng W. Therapeutic development targeting host heparan sulfate proteoglycan in SARS-CoV-2 infection. Front Med (Lausanne) 2024; 11:1364657. [PMID: 38618194 PMCID: PMC11014733 DOI: 10.3389/fmed.2024.1364657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 04/16/2024] Open
Abstract
The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an urgent need for effective therapeutic options. SARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic that has resulted in significant morbidity and mortality worldwide. The virus is known to enter host cells by binding to the angiotensin-converting enzyme 2 (ACE2) receptor, and emerging evidence suggests that heparan sulfate proteoglycans (HSPGs) play a crucial role in facilitating this process. HSPGs are abundant cell surface proteoglycan present in many tissues, including the lung, and have been shown to interact directly with the spike protein of SARS-CoV-2. This review aims to summarize the current understanding of the role of HSPGs in SARS-CoV-2 infection and the potential of developing new therapies targeting HSPGs.
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Affiliation(s)
- Qi Zhang
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Ivan Pavlinov
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Wei Zheng
- Therapeutic Development Branch, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
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13
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Golzari-Sorkheh M, Liyanage I, Reed MA, Weaver DF. Alzheimer's Disease and COVID-19 Pathogenic Overlap: Implications for Drug Repurposing. Can J Neurol Sci 2024; 51:161-172. [PMID: 36991574 DOI: 10.1017/cjn.2023.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
As COVID-19 continues, a safe, cost-effective treatment strategy demands continued inquiry. Chronic neuroinflammatory disorders may appear to be of little relevance in this regard; often indolent and progressive disorders characterized by neuroinflammation (such as Alzheimer's disease (AD)) are fundamentally dissimilar in etiology and symptomology to COVID-19's rapid infectivity and pathology. However, the two disorders share extensive pathognomonic features, including at membrane, cytoplasmic, and extracellular levels, culminating in analogous immunogenic destruction of their respective organ parenchyma. We hypothesize that these mechanistic similarities may extent to therapeutic targets, namely that it is conceivable an agent against AD's immunopathy may have efficacy against COVID-19 and vice versa. It is notable that while extensively investigated, no agent has yet demonstrated significant therapeutic efficacy against AD's cognitive and memory declines. Yet this very failure has driven the development of numerous agents with strong mechanistic potential and clinical characteristics. Having already approved for clinical trials, these agents may be an expedient starting point in the urgent search for an effective COVID-19 therapy. Herein, we review the overlapping Alzheimer's/ COVID-19 targets and theorize several initial platforms.
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Affiliation(s)
| | - Imindu Liyanage
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Mark A Reed
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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14
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Rabinowitz ZM, Wang Z, Liu J, Zhang Y, Ybargollin AJ, Saketkhou M, Cui L. A Fluorogenic Green Merocyanine-Based Probe to Detect Heparanase-1 Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581963. [PMID: 38464176 PMCID: PMC10925095 DOI: 10.1101/2024.02.25.581963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Heparanase-1 (HPSE-1), an endo-β-D-glucuronidase, is an extracellular matrix (ECM) remodeling enzyme that degrades heparan sulfate (HS) chains of heparan sulfate proteoglycans (HSPGs). HPSE-1 functions to remodel the ECM and thereby disseminate cells, liberate HS-bound bioactive molecules, and release biologically active HS fragments. Being the only known enzyme for the cleavage of HS, HPSE-1 regulates a number of fundamental cellular processes including cell migration, cytokine regulation, angiogenesis, and wound healing. Overexpression of HPSE-1 has been discovered in most cancers, inflammatory diseases, viral infections, among others. As an emerging therapeutic target, the biological role of HPSE-1 remains to be explored but is hampered by a lack of research tools. To expand the chemical tool-kit of fluorogenic probes to interrogate HPSE-1 activity, we design and synthesized a fluorogenic green disaccharide-based HPSE-1 probe using our design strategy of tuning the electronic effect of the aryl aglycon. The novel probe exhibits a highly sensitive 278-fold fluorescence turn-on response in the presence of recombinant human HPSE-1, while emitting green light at 560 nm, enabling the fluorescence imaging of HPSE-1 activity in cells.
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15
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Xiao LX, Zhu DL, Chen J, Lv J, Liu MJ, Dai X, Wang DX, Deng W. Exploring the therapeutic role of early heparin administration in ARDS management: a MIMIC-IV database analysis. J Intensive Care 2024; 12:9. [PMID: 38409068 PMCID: PMC10895755 DOI: 10.1186/s40560-024-00723-5] [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: 11/29/2023] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a severe respiratory condition characterized by a high mortality rate, the management of which relies on supportive care and a profound understanding of its pathophysiology. Heparin, with its anticoagulant and potential anti-inflammatory properties, offers a new therapeutic opportunity for the treatment of ARDS. METHODS In this retrospective cohort study, we examined the MIMIC-IV database for ARDS patients who received prophylactic heparin within the first 72 h of ICU admission. Employing propensity score matching and inverse probability weighting (IPW) analysis, we evaluated the impact of early heparin use on patient outcomes, focusing on mortality rates. RESULTS Patients who received prophylactic heparin had a significantly lower in-hospital mortality rate compared to those who did not (13.55% vs 17.93%, HR = 0.71, 95% CI: 0.54-0.93, P = 0.012). This result remained significant after propensity score matching (12.75% vs 17.93%, HR = 0.65, 95% CI 0.47-0.90, P = 0.010). Analysis using five different statistical models indicated that early use of heparin significantly reduced the in-hospital mortality rate, with HR = 0.669 (95% CI 0.487-0.919, P = 0.013) in the doubly robust model without balanced covariates; HR = 0.705 (95% CI 0.515-0.965, P = 0.029) with all covariates considered; HR = 0.660 (95% CI 0.491-0.888, P = 0.006) in the propensity score (IPW) model; HR = 0.650 (95% CI 0.470-0.900, P = 0.010) in the propensity score matching model; and HR = 0.706 (95% CI 0.536-0.930, P = 0.013) in the multivariate Cox regression model. Secondary outcomes indicated that heparin use was also associated with reduced mortality rates at 60 days, and 90 days. CONCLUSION This research highlights that early prophylactic administration of heparin may substantially lower mortality in ARDS patients. These findings underscore the potential of heparin as a key component in the management of ARDS, offering a new perspective and novel strategies for clinical treatment.
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Affiliation(s)
- Ling-Xi Xiao
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, 400010, China
| | - De Liang Zhu
- Department of Gastrointestinal Surgery, China-Japan Union Hospital of Jilin University, No. 126, Xiantai Street, Changchun, 130033, China
| | - Juan Chen
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, 400010, China
| | - Jing Lv
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, 400010, China
| | - Mei-Jun Liu
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, 400010, China
| | - Xue Dai
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, 400010, China
| | - Dao-Xin Wang
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, 400010, China
| | - Wang Deng
- Department of Pulmonary and Critical Care Medicine, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong District, Chongqing, 400010, China.
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16
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Maity S, Acharya A. Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding. ACS APPLIED BIO MATERIALS 2024; 7:646-656. [PMID: 36947738 PMCID: PMC10880061 DOI: 10.1021/acsabm.2c01064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023]
Abstract
Glycosylation is one of the post-translational modifications with more than 50% of human proteins being glycosylated. The exact nature and chemical composition of glycans are inaccessible to X-ray or cryo-electron microscopy imaging techniques. Therefore, computational modeling studies and molecular dynamics must be used as a "computational microscope". The spike (S) protein of SARS-CoV-2 is heavily glycosylated, and a few glycans play a more functional role "beyond shielding". In this mini-review, we discuss computational investigations of the roles of specific S-protein and ACE2 glycans in the overall ACE2-S protein binding. We highlight different functions of specific glycans demonstrated in myriad computational models and simulations in the context of the SARS-CoV-2 virus binding to the receptor. We also discuss interactions between glycocalyx and the S protein, which may be utilized to design prophylactic polysaccharide-based therapeutics targeting the S protein. In addition, we underline the recent emergence of coronavirus variants and their impact on the S protein and its glycans.
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Affiliation(s)
- Suman Maity
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Atanu Acharya
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse University, Syracuse, New York 13244, United States
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17
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Pongener I, Sletten ET, Danglad-Flores J, Seeberger PH, Miller GJ. Synthesis of a heparan sulfate tetrasaccharide using automated glycan assembly. Org Biomol Chem 2024; 22:1395-1399. [PMID: 38291974 PMCID: PMC10865181 DOI: 10.1039/d3ob01909h] [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: 11/23/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Herein we utilise automated glycan assembly to complete solid-phase synthesis of defined heparan sulfate oligosaccharides, employing challenging D-glucuronate disaccharide donors. Using an orthogonally protected D-GlcN-α-D-GlcA donor, milligram-scale synthesis of a heparan sulfate tetrasaccharide is completed in 18% yield over five steps. Furthermore, orthogonal protecting groups enabled regiospecific on-resin 6-O-sulfation. This methodology provides an important benchmark for the rapid assembly of biologically relevant heparan sulfate sequences.
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Affiliation(s)
- Imlirenla Pongener
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
| | - Eric T Sletten
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - José Danglad-Flores
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Gavin J Miller
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, UK.
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18
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Bhattacharyya S, Tobacman JK. SARS-CoV-2 spike protein-ACE2 interaction increases carbohydrate sulfotransferases and reduces N-acetylgalactosamine-4-sulfatase by p38 MAPK. Signal Transduct Target Ther 2024; 9:39. [PMID: 38355690 PMCID: PMC10866996 DOI: 10.1038/s41392-024-01741-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/04/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024] Open
Abstract
Immunostaining in lungs of patients who died with COVID-19 infection showed increased intensity and distribution of chondroitin sulfate and decline in N-acetylgalactostamine-4-sulfatase (Arylsulfatase B; ARSB). To explain these findings, human small airway epithelial cells were exposed to the SARS-CoV-2 spike protein receptor binding domain (SPRBD) and transcriptional mechanisms were investigated. Phospho-p38 MAPK and phospho-SMAD3 increased following exposure to the SPRBD, and their inhibition suppressed the promoter activation of the carbohydrate sulfotransferases CHST15 and CHST11, which contributed to chondroitin sulfate biosynthesis. Decline in ARSB was mediated by phospho-38 MAPK-induced N-terminal Rb phosphorylation and an associated increase in Rb-E2F1 binding and decline in E2F1 binding to the ARSB promoter. The increases in chondroitin sulfotransferases were inhibited when treated with phospho-p38-MAPK inhibitors, SMAD3 (SIS3) inhibitors, as well as antihistamine desloratadine and antibiotic monensin. In the mouse model of carrageenan-induced systemic inflammation, increases in phospho-p38 MAPK and expression of CHST15 and CHST11 and declines in DNA-E2F binding and ARSB expression occurred in the lung, similar to the observed effects in this SPRBD model of COVID-19 infection. Since accumulation of chondroitin sulfates is associated with fibrotic lung conditions and diffuse alveolar damage, increased attention to p38-MAPK inhibition may be beneficial in ameliorating Covid-19 infections.
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Affiliation(s)
- Sumit Bhattacharyya
- Jesse Brown VA Medical Center and University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Joanne K Tobacman
- Jesse Brown VA Medical Center and University of Illinois at Chicago, Chicago, IL, 60612, USA.
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19
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Mycroft-West CJ, Abdelkarim S, Duyvesteyn HME, Gandhi NS, Skidmore MA, Owens RJ, Wu L. Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1. Nat Commun 2024; 15:1326. [PMID: 38351061 PMCID: PMC10864358 DOI: 10.1038/s41467-024-45419-4] [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: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo.
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Affiliation(s)
| | - Sahar Abdelkarim
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Neha S Gandhi
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- School of Chemistry and Physics, Queensland University of Technology, QLD 4000, Brisbane, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Mark A Skidmore
- Centre for Glycoscience Research and Training, Keele University, ST5 5BG, Newcastle-Under-Lyme, UK
| | - Raymond J Owens
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Liang Wu
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK.
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20
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Zhu J, Lu H, Lin Q, Zhang T, Chen G, Zhou Y, Sui G. Fucoidan-based antibody-free magnetic nanoparticle for on-site detection of waterborne SARS-CoV-2. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168619. [PMID: 37977397 DOI: 10.1016/j.scitotenv.2023.168619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
The portable and sensitive point-of-care-test (POCT) method is in urgent need to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for ensuring public health and safety. However, detection of trace number of pathogens in real water sample from the environment still faces challenges, because complex environment disruptors can rapidly degrade targets. Herein, magnetic beads coated with fucoidan and polydopamine (Fuc-PDA-MBs) were introduced as the capture carrier for pretreatment of samples. Fucoidan, a sulfated polysaccharide, can recognize the SARS-CoV-2 spike (S1) protein receptor-binding domain (S1 RBD) and was chosen for replacement of antibody in enrichment. Environmental water seeded with SARS-CoV-2 spike pseudovirus was applied to test performance of Fuc-PDA-MBs method. Under optimal conditions, the use of Fuc-PDA-MBs showed average 76 % capture efficiency at SARS-CoV-2 spike pseudovirus concentration ranging from 107.62 to 104.34 gene copies (gc)/L. Compared with Electronegative filtration (ENF), Fuc-PDA-MBs showed better virion sorption effectiveness. Fuc-PDA-MBs also validated by raw contaminated urban wastewater and showed high recovery results for SARS-CoV-2 variants. To rapidly detect virus in POCT, nucleic acid extraction-free Loop-Mediated Isothermal Amplification (LAMP) was used for simplifying experimental process. The Fuc-PDA-MBs-LAMP assay showed the quantitation limit of sample (LOQ) was 105.49 gc/L. The whole procedure could be completed within 90 min, including 30 min for virus pre-enrichment, 10 min nucleic acid release and 45 min LAMP analysis. Compared with regular antibody-based immunodetection, this integrated system provides broad-spectrum, economic way to detect SARS-CoV-2 mutants in complex environments and also adaptable for high throughput test, which might be used for on-site early warning of SARS-CoV-2 outbreaks in developing area.
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Affiliation(s)
- Jinhui Zhu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Huijun Lu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Tong Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China
| | - Guang Chen
- Shanghai Chengtou Wastewater Treatment Co., LtD., Shanghai 201203, China
| | - Yang Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, China
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science & Engineering, Fudan University, Shanghai 200438, China; Shanghai Institute of Infectious Disease and Biosecurity, Shanghai 200032, China.
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21
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Monti M, Milanetti E, Frans MT, Miotto M, Di Rienzo L, Baranov MV, Gosti G, Somavarapu AK, Nagaraj M, Golbek TW, Rossing E, Moons SJ, Boltje TJ, van den Bogaart G, Weidner T, Otzen DE, Tartaglia GG, Ruocco G, Roeters SJ. Two Receptor Binding Strategy of SARS-CoV-2 Is Mediated by Both the N-Terminal and Receptor-Binding Spike Domain. J Phys Chem B 2024; 128:451-464. [PMID: 38190651 PMCID: PMC10801686 DOI: 10.1021/acs.jpcb.3c06258] [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: 09/18/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024]
Abstract
It is not well understood why severe acute respiratory syndrome (SARS)-CoV-2 spreads much faster than other β-coronaviruses such as SARS-CoV and Middle East respiratory syndrome (MERS)-CoV. In a previous publication, we predicted the binding of the N-terminal domain (NTD) of SARS-CoV-2 spike to sialic acids (SAs). Here, we experimentally validate this interaction and present simulations that reveal a second possible interaction between SAs and the spike protein via a binding site located in the receptor-binding domain (RBD). The predictions from molecular-dynamics simulations and the previously-published 2D-Zernike binding-site recognition approach were validated through flow-induced dispersion analysis (FIDA)─which reveals the capability of the SARS-CoV-2 spike to bind to SA-containing (glyco)lipid vesicles, and flow-cytometry measurements─which show that spike binding is strongly decreased upon inhibition of SA expression on the membranes of angiotensin converting enzyme-2 (ACE2)-expressing HEK cells. Our analyses reveal that the SA binding of the NTD and RBD strongly enhances the infection-inducing ACE2 binding. Altogether, our work provides in silico, in vitro, and cellular evidence that the SARS-CoV-2 virus utilizes a two-receptor (SA and ACE2) strategy. This allows the SARS-CoV-2 spike to use SA moieties on the cell membrane as a binding anchor, which increases the residence time of the virus on the cell surface and aids in the binding of the main receptor, ACE2, via 2D diffusion.
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Affiliation(s)
- Michele Monti
- RNA
Systems Biology, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152 Genova, Italy
- Center
for Life Nanoscience, Istituto Italiano
di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Edoardo Milanetti
- Center
for Life Nanoscience, Istituto Italiano
di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department
of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Myrthe T. Frans
- Molecular
Immunology—Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Mattia Miotto
- Center
for Life Nanoscience, Istituto Italiano
di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Lorenzo Di Rienzo
- Center
for Life Nanoscience, Istituto Italiano
di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Maksim V. Baranov
- Molecular
Immunology—Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Giorgio Gosti
- Center
for Life Nanoscience, Istituto Italiano
di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- DHILab,
Istituto di Scienze del Patrimonio Culturale, Sede di Roma, Consiglio Nazionale delle Ricerche, Via Salaria km, 29300, 00010 Rome, Italy
| | - Arun Kumar Somavarapu
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Madhu Nagaraj
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Thaddeus W. Golbek
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Emiel Rossing
- Synthetic
Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Sam J. Moons
- Synthetic
Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas J. Boltje
- Synthetic
Organic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Molecular
Immunology—Groningen Biomolecular Sciences and Biotechnology, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Tobias Weidner
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology, Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152 Genova, Italy
- Center
for Life Nanoscience, Istituto Italiano
di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Giancarlo Ruocco
- Center
for Life Nanoscience, Istituto Italiano
di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department
of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Steven J. Roeters
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Amsterdam
UMC, Vrije Universiteit, Department of Anatomy
and Neurosciences, De
Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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22
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Wu A, Shi K, Wang J, Zhang R, Wang Y. Targeting SARS-CoV-2 entry processes: The promising potential and future of host-targeted small-molecule inhibitors. Eur J Med Chem 2024; 263:115923. [PMID: 37981443 DOI: 10.1016/j.ejmech.2023.115923] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/21/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has had a huge impact on global health. To respond to rapidly mutating viruses and to prepare for the next pandemic, there is an urgent need to develop small molecule therapies that target critical stages of the SARS-CoV-2 life cycle. Inhibiting the entry process of the virus can effectively control viral infection and play a role in prevention and treatment. Host factors involved in this process, such as ACE2, TMPRSS2, ADAM17, furin, PIKfyve, TPC2, CTSL, AAK1, V-ATPase, HSPG, and NRP1, have been found to be potentially good targets with stability. Through further exploration of the cell entry process of SARS-CoV-2, small-molecule drugs targeting these host factors have been developed. This review focuses on the structural functions of potential host cell targets during the entry of SARS-CoV-2 into host cells. The research progress, chemical structure, structure-activity relationship, and clinical value of small-molecule inhibitors against COVID-19 are reviewed to provide a reference for the development of small-molecule drugs against COVID-19.
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Affiliation(s)
- Aijia Wu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Kunyu Shi
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Ruofei Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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23
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Petitjean SJL, Eeckhout S, Delguste M, Zhang Q, Durlet K, Alsteens D. Heparin-Induced Allosteric Changes in SARS-CoV-2 Spike Protein Facilitate ACE2 Binding and Viral Entry. NANO LETTERS 2023; 23:11678-11684. [PMID: 38055954 DOI: 10.1021/acs.nanolett.3c03550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Understanding the entry of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) into host cells is crucial in the battle against COVID-19. Using atomic force microscopy (AFM), we probed the interaction between the virus's spike protein and heparan sulfate (HS) as a potential attachment factor. Our AFM studies revealed a moderate-affinity interaction between the spike protein and HS on both model surfaces and living cells, highlighting HS's role in early viral attachment. Remarkably, we observed an interplay between HS and the host cell receptor angiotensin-converting enzyme 2 (ACE2), with HS engagement resulting in enhanced ACE2 binding and subsequent viral entry. Our research furthers our understanding of SARS-CoV-2 infection mechanisms and reveals potential interventions targeting viral entry. These insights are valuable as we navigate the evolving landscape of viral threats and seek effective strategies to combat emerging infectious diseases.
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Affiliation(s)
- Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Savannah Eeckhout
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Kimberley Durlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Walloon Brabant 1300, Belgium
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24
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Parsons RJ, Acharya P. Evolution of the SARS-CoV-2 Omicron spike. Cell Rep 2023; 42:113444. [PMID: 37979169 PMCID: PMC10782855 DOI: 10.1016/j.celrep.2023.113444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/21/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern, first identified in November 2021, rapidly spread worldwide and diversified into several subvariants. The Omicron spike (S) protein accumulated an unprecedented number of sequence changes relative to previous variants. In this review, we discuss how Omicron S protein structural features modulate host cell receptor binding, virus entry, and immune evasion and highlight how these structural features differentiate Omicron from previous variants. We also examine how key structural properties track across the still-evolving Omicron subvariants and the importance of continuing surveillance of the S protein sequence evolution over time.
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Affiliation(s)
- Ruth J Parsons
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA.
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Duke University, Department of Biochemistry, Durham, NC 27710, USA; Duke University, Department of Surgery, Durham, NC 27710, USA.
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25
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Córneo ES, Veras FP, Gomes GF, Schneider AH, Manuella B, Almeida CJLR, Silva CM, Martins RB, Batah SS, Simon CS, Prestes GDS, Alves-Filho JC, Arruda E, Louzada-Junior P, de Oliveira RDR, Fabro AT, Cunha TM, Cunha FQ, Dal-Pizzol F. Enoxaparin improves COVID-19 by reducing Neutrophils Extracellular Traps (NETs) production. Clin Immunol 2023; 257:109836. [PMID: 37951516 DOI: 10.1016/j.clim.2023.109836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND COVID-19 causes consequences such as imbalance of the immune system and thrombotic events. During the infection process, NETs in excess induce a pro-inflammatory response and disseminated intravascular coagulation. We evaluated the role of enoxaparin as a potential inhibitor of NETs. METHODS K18-hACE2 animals infected with the SARS-CoV-2 virus and a group of 23 individuals admitted to the hospital with COVID-19 treated with enoxaparin or without treatment and controls without the disease were included. RESULTS Enoxaparin decreased the levels of NETs, reduced the signs of the disease and mitigated lung damage in the animals infected with SARS-CoV-2. These effects were partially associated with prevention of SARS-CoV-2 entry and NETs synthesis. Clinical data revealed that treatment with enoxaparin decreased the levels of inflammatory markers, the levels of NETs in isolated neutrophils and the organ dysfunction. CONCLUSION This study provides evidence for the beneficial effects of enoxaparin in COVID-19 in addition to its anticoagulant role.
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Affiliation(s)
- Emily S Córneo
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil.
| | - Flavio Protasio Veras
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center; Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Giovanni F Gomes
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | - Ayda H Schneider
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | - Bruna Manuella
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | - Cicero J L R Almeida
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | - Camila M Silva
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | | | - Sabrina S Batah
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Carla S Simon
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - Gabriele da S Prestes
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - José Carlos Alves-Filho
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | | | - Paulo Louzada-Junior
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Internal Medicine, Division of Clinical Immunology and Division of Infectious Diseases
| | - Renê D R de Oliveira
- Internal Medicine, Division of Clinical Immunology and Division of Infectious Diseases
| | - Alexandre T Fabro
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thiago M Cunha
- Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | - Fernando Queiroz Cunha
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil; Center of Research in Inflammatory Diseases (CRID), Ribeirão Preto Medical School, Ribeirão Preto, Brazil; Departments of Pharmacology Research Center
| | - Felipe Dal-Pizzol
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, Health Sciences Unit, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
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26
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Bamberger C, Pankow S, Martínez-Bartolomé S, Diedrich JK, Park RSK, Yates JR. Analysis of the Tropism of SARS-CoV-2 Based on the Host Interactome of the Spike Protein. J Proteome Res 2023; 22:3742-3753. [PMID: 37939376 DOI: 10.1021/acs.jproteome.3c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The β-coronavirus SARS-CoV-2 causes severe acute respiratory syndrome (COVID-19) in humans. It enters and infects epithelial airway cells upon binding of the receptor binding domain (RBD) of the virus entry protein spike to the host receptor protein Angiotensin Converting Enzyme 2 (ACE2). Here, we used coimmunoprecipitation coupled with bottom-up mass spectrometry to identify host proteins that engaged with the spike protein in human bronchial epithelial cells (16HBEo-). We found that the spike protein bound to extracellular laminin and thrombospondin and endoplasmatic reticulum (ER)-resident DJB11 and FBX2 proteins. The ER-resident proteins UGGT1, CALX, HSP7A, and GRP78/BiP bound preferentially to the original Wuhan D614 over the mutated G614 spike protein in the more rapidly spreading Alpha SARS-CoV-2 strain. The increase in protein binding to the D614 spike might be explained by higher accessibility of cryptic sites in "RDB open" and "S2 only" D614 spike protein conformations and may enable SARS-CoV-2 to infect additional, ACE2-negative cell types. Moreover, a novel proteome-based cell type set enrichment analysis (pCtSEA) found that host factors like laminin might render additional cell types such as macrophages and epithelial cells in the nephron permissive to SARS-CoV-2 infection.
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Affiliation(s)
- Casimir Bamberger
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sandra Pankow
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Salvador Martínez-Bartolomé
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Robin S K Park
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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27
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Xie C, Schaefer L, Iozzo RV. Global impact of proteoglycan science on human diseases. iScience 2023; 26:108095. [PMID: 37867945 PMCID: PMC10589900 DOI: 10.1016/j.isci.2023.108095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023] Open
Abstract
In this comprehensive review, we will dissect the impact of research on proteoglycans focusing on recent developments involved in their synthesis, degradation, and interactions, while critically assessing their usefulness in various biological processes. The emerging roles of proteoglycans in global infections, specifically the SARS-CoV-2 pandemic, and their rising functions in regenerative medicine and biomaterial science have significantly affected our current view of proteoglycans and related compounds. The roles of proteoglycans in cancer biology and their potential use as a next-generation protein-based adjuvant therapy to combat cancer is also emerging as a constructive and potentially beneficial therapeutic strategy. We will discuss the role of proteoglycans in selected and emerging areas of proteoglycan science, such as neurodegenerative diseases, autophagy, angiogenesis, cancer, infections and their impact on mammalian diseases.
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Affiliation(s)
- Christopher Xie
- Department of Pathology and Genomic Medicine, the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt, Germany
| | - Renato V. Iozzo
- Department of Pathology and Genomic Medicine, the Translational Cellular Oncology Program, Sidney Kimmel Cancer Center, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
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28
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Abdelouahed M, Yateem D, Fredericks S. Fc γRIIa - dependent platelet activation identified in COVID-19 vaccine-induced immune thrombotic thrombocytopenia-, heparin-induced thrombocytopenia, streptokinase- and anisoylated plasminogen-streptokinase activator complex-induced platelet activation. Front Cardiovasc Med 2023; 10:1282637. [PMID: 38034388 PMCID: PMC10684751 DOI: 10.3389/fcvm.2023.1282637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which was caused by the coronavirus - severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was globally responsible for remarkable morbidity and mortality. Several highly effective vaccines for COVID-19 were developed and disseminated worldwide within an unprecedented timescale. Rare but dangerous clotting and thrombocytopenia events, and subsequent coagulation abnormalities, have been reported after massive vaccination against SARS-CoV-2. Soon after their global rollout, reports of a morbid clinical syndrome following vaccination with adenovirus-DNA-based vaccines appeared. In the spring of 2021, reports of a novel, rare and morbid clinical syndrome, with clinically devastating and fatal complication after vaccination with adenovirus-based coronavirus vaccines (Janssen/Johnson & Johnson and Astra-Zeneca vaccines) led to a brief suspension of their use by several countries. Those complications were associated with unusual cerebral and splanchnic venous thrombosis, and circulating autoantibodies directed against anti-platelet factor 4 (PF4), a protein secreted from platelets, leading to the designation: Vaccine-Induced Immune Thrombotic Thrombocytopenia (VITT). The reported VITT incidence remains very low and does not affect the overall benefit of immunization, however, if left untreated, VITT can be debilitating or even fatal. VITT resembled specific adverse drugs' reactions that also involved the production of autoantibodies and subsequent abnormal platelet activation through platelet FcγRIIa. These unusual but well-documented drug reactions were heparin-induced thrombocytopenia (HIT), streptokinase- (SK), and anisoylated plasminogen-streptokinase activator complex- (APSAC) associated with platelet-activating antibodies. There was considerable overlapping of clinical features between VITT, COVID-19 and these adverse drugs' reactions. We review the phenomenon of VITT against the backdrop of shared and common mechanisms that underlie HIT-, SK-, and APSAC-platelet FcγRIIa-dependent platelet activation. An understanding of VITT's pathogenesis may be achieved by comparing and contrasting VITT-, HIT-, SK- and APSAC-induced platelet activation mechanisms, their respective physiopathology and similarities. Discussing these conditions in parallel provides insight into complex immunological disorders and diseases associated with abnormal hemostasis and thrombosis in particular.
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Affiliation(s)
- Mustapha Abdelouahed
- Department of Medical Sciences and Education, Boston University School of Medicine, Boston, MA, United States
| | - Dana Yateem
- School of Medicine, The Royal College of Surgeons in Ireland, Medical University of Bahrain, Al Sayh, Muharraq Governorate, Bahrain
| | - Salim Fredericks
- School of Medicine, The Royal College of Surgeons in Ireland, Medical University of Bahrain, Al Sayh, Muharraq Governorate, Bahrain
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29
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Li B, Zhang T, Cao H, Ferro V, Li J, Yu M. Identification of a Pentasaccharide Lead Compound with High Affinity to the SARS-CoV-2 Spike Protein via In Silico Screening. Int J Mol Sci 2023; 24:16115. [PMID: 38003304 PMCID: PMC10671481 DOI: 10.3390/ijms242216115] [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: 09/27/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The spike (S) protein on the surface of the SARS-CoV-2 virus is critical to mediate fusion with the host cell membrane through interaction with angiotensin-converting enzyme 2 (ACE2). Additionally, heparan sulfate (HS) on the host cell surface acts as an attachment factor to facilitate the binding of the S receptor binding domain (RBD) to the ACE2 receptor. Aiming at interfering with the HS-RBD interaction to protect against SARS-CoV-2 infection, we have established a pentasaccharide library composed of 14,112 compounds covering the possible sulfate substitutions on the three sugar units (GlcA, IdoA, and GlcN) of HS. The library was used for virtual screening against RBD domains of SARS-CoV-2. Molecular modeling was carried out to evaluate the potential antiviral properties of the top-hit pentasaccharide focusing on the interactive regions around the interface of RBD-HS-ACE2. The lead pentasaccharide with the highest affinity for RBD was analyzed via drug-likeness calculations, showing better predicted druggable profiles than those currently reported for RBD-binding HS mimetics. The results provide significant information for the development of HS-mimetics as anti-SARS-CoV-2 agents.
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Affiliation(s)
- Binjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China;
| | - Tianji Zhang
- Division of Chemistry and Analytical Science, National Institute of Metrology, Beijing 100029, China;
| | - Hui Cao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China;
| | - Vito Ferro
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia;
| | - Jinping Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China;
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mingjia Yu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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30
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Xu P, Cai X, Guan X, Xie W. Sulfoconjugation of protein peptides and glycoproteins in physiology and diseases. Pharmacol Ther 2023; 251:108540. [PMID: 37777160 PMCID: PMC10842354 DOI: 10.1016/j.pharmthera.2023.108540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Protein sulfoconjugation, or sulfation, represents a critical post-translational modification (PTM) process that involves the attachment of sulfate groups to various positions of substrates within the protein peptides or glycoproteins. This process plays a dynamic and complex role in many physiological and pathological processes. Here, we summarize the importance of sulfation in the fields of oncology, virology, drug-induced liver injury (DILI), inflammatory bowel disease (IBD), and atherosclerosis. In oncology, sulfation is involved in tumor initiation, progression, and migration. In virology, sulfation influences viral entry, replication, and host immune response. In DILI, sulfation is associated with the incidence of DILI, where altered sulfation affects drug metabolism and toxicity. In IBD, dysregulation of sulfation compromises mucosal barrier and immune response. In atherosclerosis, sulfation influences the development of atherosclerosis by modulating the accumulation of lipoprotein, and the inflammation, proliferation, and migration of smooth muscle cells. The current review underscores the importance of further research to unravel the underlying mechanisms and therapeutic potential of targeting sulfoconjugation in various diseases. A better understanding of sulfation could facilitate the emergence of innovative diagnostic or therapeutic strategies.
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Affiliation(s)
- Pengfei Xu
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China
| | - Xinran Cai
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xiuchen Guan
- Department of Orthodontics, School of Stomatology, Capital Medical University, Beijing 100069, China
| | - Wen Xie
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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31
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Mishra S, Sharma M, Singh MK, Pati S, Dehury B. Dissecting the Molecular Basis of Host Leucine-Rich Repeat Containing 15 Mediated Interaction with Receptor Binding Domain of SARS-CoV-2 Spike Protein: A Computational Approach. J Phys Chem Lett 2023; 14:8994-9001. [PMID: 37781985 DOI: 10.1021/acs.jpclett.3c01443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The detection of leucine-rich repeat containing 15 (LRRC15) as a connecting link with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the possibility of its involvement in differential restriction activity of SARS-CoV-2 pathways. However, the structure-function mechanism of LRRC15 involving the receptor binding domain (RBD) of the SARS-CoV-2 spike protein and their mode of interaction is largely unknown. Using state-of-the-art AlphaFold2 and all-atom molecular dynamics simulations, our findings provide evidences of alternative binding modes of RBD with LRR units of LRRC15 having varied affinities. Contribution of both the receptor binding regions in RBD, including receptor binding motif in accommodating the LRR domain, towards the C-terminal region, emphasizes its differential role in modulating host cell receptiveness for SARS-CoV-2, the innate immune system, as well as antiviral tone. However, further experimental validations are necessary for unravelling the unknown mechanism and distinctive features of this host receptor in the COVID-19 pandemic, involving both the transmembrane as well as cytoplasmic domain.
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Affiliation(s)
- Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Mansi Sharma
- KIIT School of Biotechnology, Sikharchandi Vihar, Bhubaneswar 751024, Odisha, India
| | - Mahendra Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana 122052, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
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32
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Abdulsalam H, Li J, Loka RS, Sletten ET, Nguyen HM. Heparan Sulfate-Mimicking Glycopolymers Bind SARS-CoV-2 Spike Protein in a Length- and Sulfation Pattern-Dependent Manner. ACS Med Chem Lett 2023; 14:1411-1418. [PMID: 37849547 PMCID: PMC10577887 DOI: 10.1021/acsmedchemlett.3c00319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
Heparan sulfate-mimicking glycopolymers, composed of glucosamine (GlcN)-glucuronic acid (GlcA) repeating units, bind to the receptor-binding subunit (S1) and spike glycoprotein (S) domains of the SARS-CoV-2 spike protein in a length- and sulfation pattern-dependent fashion. A glycopolymer composed of 12 repeating GlcNS6S-GlcA units exhibits a much higher affinity to the S1 protein (IC50 = 13 ± 1.1 nM) compared with the receptor-binding domain (RBD). This glycopolymer does not interfere in angiotensin-converting enzyme 2 binding of the RBD. Although this compound binds strongly to the S1/membrane-fusion subunit (S2) junction (KD = 29.7 ± 4.18 nM), it does not shield the S1/S2 site from cleavage by furin-a behavior contrary to natural heparin. This glycopolymer lacks iduronic acid, which accounts for 70% of heparin. Further, this compound, unlike natural heparin, is well defined in both sulfation pattern and length, which results in fewer off-target interactions with heparin-binding proteins. The results highlight the potential of using polymeric heparan sulfate (HS) mimetics for the therapeutic agent development.
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Affiliation(s)
- Hawau Abdulsalam
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Jiayi Li
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Ravi S. Loka
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Eric T. Sletten
- Department
of Biomolecular Systems, Max Planck Institute
of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Hien M. Nguyen
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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33
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Ruocco V, Vavra U, König-Beihammer J, Bolaños−Martínez OC, Kallolimath S, Maresch D, Grünwald-Gruber C, Strasser R. Impact of mutations on the plant-based production of recombinant SARS-CoV-2 RBDs. FRONTIERS IN PLANT SCIENCE 2023; 14:1275228. [PMID: 37868317 PMCID: PMC10588190 DOI: 10.3389/fpls.2023.1275228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/24/2023]
Abstract
Subunit vaccines based on recombinant viral antigens are valuable interventions to fight existing and evolving viruses and can be produced at large-scale in plant-based expression systems. The recombinant viral antigens are often derived from glycosylated envelope proteins of the virus and glycosylation plays an important role for the immunogenicity by shielding protein epitopes. The receptor-binding domain (RBD) of the SARS-CoV-2 spike is a principal target for vaccine development and has been produced in plants, but the yields of recombinant RBD variants were low and the role of the N-glycosylation in RBD from different SARS-CoV-2 variants of concern is less studied. Here, we investigated the expression and glycosylation of six different RBD variants transiently expressed in leaves of Nicotiana benthamiana. All of the purified RBD variants were functional in terms of receptor binding and displayed almost full N-glycan occupancy at both glycosylation sites with predominately complex N-glycans. Despite the high structural sequence conservation of the RBD variants, we detected a variation in yield which can be attributed to lower expression and differences in unintentional proteolytic processing of the C-terminal polyhistidine tag used for purification. Glycoengineering towards a human-type complex N-glycan profile with core α1,6-fucose, showed that the reactivity of the neutralizing antibody S309 differs depending on the N-glycan profile and the RBD variant.
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Affiliation(s)
- Valentina Ruocco
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ulrike Vavra
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Julia König-Beihammer
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Omayra C. Bolaños−Martínez
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Somanath Kallolimath
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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34
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Pagani I, Ottoboni L, Panina-Bordignon P, Martino G, Poli G, Taylor S, Turnbull JE, Yates E, Vicenzi E. Heparin Precursors with Reduced Anticoagulant Properties Retain Antiviral and Protective Effects That Potentiate the Efficacy of Sofosbuvir against Zika Virus Infection in Human Neural Progenitor Cells. Pharmaceuticals (Basel) 2023; 16:1385. [PMID: 37895856 PMCID: PMC10609960 DOI: 10.3390/ph16101385] [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: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/29/2023] Open
Abstract
Zika virus (ZIKV) infection during pregnancy can result in severe birth defects, such as microcephaly, as well as a range of other related health complications. Heparin, a clinical-grade anticoagulant, is shown to protect neural progenitor cells from death following ZIKV infection. Although heparin can be safely used during pregnancy, it retains off-target anticoagulant effects if directly employed against ZIKV infection. In this study, we investigated the effects of chemically modified heparin derivatives with reduced anticoagulant activities. These derivatives were used as experimental probes to explore the structure-activity relationships. Precursor fractions of porcine heparin, obtained during the manufacture of conventional pharmaceutical heparin with decreased anticoagulant activities, were also explored. Interestingly, these modified heparin derivatives and precursor fractions not only prevented cell death but also inhibited the ZIKV replication of infected neural progenitor cells grown as neurospheres. These effects were observed regardless of the specific sulfation position or overall charge. Furthermore, the combination of heparin with Sofosbuvir, an antiviral licensed for the treatment of hepatitis C (HCV) that also belongs to the same Flaviviridae family as ZIKV, showed a synergistic effect. This suggested that a combination therapy approach involving heparin precursors and Sofosbuvir could be a potential strategy for the prevention or treatment of ZIKV infections.
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Affiliation(s)
- Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Linda Ottoboni
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Paola Panina-Bordignon
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Gianvito Martino
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Guido Poli
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
- Human Immuno-Virology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sarah Taylor
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy E Turnbull
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Edwin Yates
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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35
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Danielsson A, Samsonov SA, Liwo A, Sieradzan AK. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. J Chem Theory Comput 2023; 19:6023-6036. [PMID: 37587433 PMCID: PMC10500997 DOI: 10.1021/acs.jctc.3c00511] [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: 05/17/2023] [Indexed: 08/18/2023]
Abstract
Heparin is an unbranched periodic polysaccharide composed of negatively charged monomers and involved in key biological processes, including anticoagulation, angiogenesis, and inflammation. Its structure and dynamics have been studied extensively using experimental as well as theoretical approaches. The conventional approach of computational chemistry applied to the analysis of biomolecules is all-atom molecular dynamics, which captures the interactions of individual atoms by solving Newton's equation of motion. An alternative is molecular dynamics simulations using coarse-grained models of biomacromolecules, which offer a reduction of the representation and consequently enable us to extend the time and size scale of simulations by orders of magnitude. In this work, we extend the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules developed in our laboratory to heparin. We carried out extensive tests to estimate the optimal weights of energy terms of the effective energy function as well as the optimal Debye-Hückel screening factor for electrostatic interactions. We applied the model to study unbound heparin molecules of polymerization degree ranging from 6 to 68 residues. We compare the obtained coarse-grained heparin conformations with models obtained from X-ray diffraction studies of heparin. The SUGRES-1P force field was able to accurately predict the general shape and global characteristics of heparin molecules.
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Affiliation(s)
- Annemarie Danielsson
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A. Samsonov
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam Liwo
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Adam K. Sieradzan
- Faculty of Chemistry, University
of Gdansk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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36
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Samanta P, Mishra SK, Pomin VH, Doerksen RJ. Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein. Molecules 2023; 28:6413. [PMID: 37687244 PMCID: PMC10490367 DOI: 10.3390/molecules28176413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The entry of SARS-CoV-2 into the host cell is mediated by its S-glycoprotein (SGP). Sulfated glycans bind to the SGP receptor-binding domain (RBD), which forms a ternary complex with its receptor angiotensin converting enzyme 2. Here, we have conducted a thorough and systematic computational study of the binding of four oligosaccharide building blocks from novel marine sulfated glycans (isolated from Pentacta pygmaea and Isostichopus badionotus) to the non-glycosylated and glycosylated RBD. Blind docking studies using three docking programs identified five potential cryptic binding sites. Extensive site-targeted docking and molecular dynamics simulations using two force fields confirmed only two binding sites (Sites 1 and 5) for these novel, highly charged sulfated glycans, which were also confirmed by previously published reports. This work showed the structural features and key interactions driving ligand binding. A previous study predicted Site 2 to be a potential binding site, which was not observed here. The use of several molecular modeling approaches gave a comprehensive assessment. The detailed comparative study utilizing multiple modeling approaches is the first of its kind for novel glycan-SGP interaction characterization. This study provided insights into the key structural features of these novel glycans as they are considered for development as potential therapeutics.
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Affiliation(s)
- Priyanka Samanta
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677-1848, USA; (P.S.); (S.K.M.); (V.H.P.)
| | - Sushil K. Mishra
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677-1848, USA; (P.S.); (S.K.M.); (V.H.P.)
| | - Vitor H. Pomin
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677-1848, USA; (P.S.); (S.K.M.); (V.H.P.)
- Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, MS 38677-1848, USA
| | - Robert J. Doerksen
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS 38677-1848, USA; (P.S.); (S.K.M.); (V.H.P.)
- Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, MS 38677-1848, USA
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37
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Vanderlinden E, Boonen A, Noppen S, Schoofs G, Imbrechts M, Geukens N, Snoeck R, Stevaert A, Naesens L, Andrei G, Schols D. PRO-2000 exhibits SARS-CoV-2 antiviral activity by interfering with spike-heparin binding. Antiviral Res 2023; 217:105700. [PMID: 37562608 DOI: 10.1016/j.antiviral.2023.105700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/29/2023] [Accepted: 08/06/2023] [Indexed: 08/12/2023]
Abstract
Here, we report on the anti-SARS-CoV-2 activity of PRO-2000, a sulfonated polyanionic compound. In Vero cells infected with the Wuhan, alpha, beta, delta or omicron variant, PRO-2000 displayed EC50 values of 1.1 μM, 2.4 μM, 1.3 μM, 2.1 μM and 0.11 μM, respectively, and an average selectivity index (i.e. ratio of cytotoxic versus antiviral concentration) of 172. Its anti-SARS-CoV-2 activity was confirmed by virus yield assays in Vero cells, Caco2 cells and A549 cells overexpressing ACE2 and TMPRSS2 (A549-AT). Using pseudoviruses bearing the SARS-CoV-2 spike (S), PRO-2000 was shown to block the S-mediated pseudovirus entry in Vero cells and A549-AT cells, with EC50 values of 0.091 μM and 1.6 μM, respectively. This entry process is initiated by interaction of the S glycoprotein with angiotensin-converting enzyme 2 (ACE2) and heparan sulfate proteoglycans. Surface Plasmon Resonance (SPR) studies showed that PRO-2000 binds to the receptor-binding domain (RBD) of S with a KD of 1.6 nM. Similar KD values (range: 1.2 nM-2.1 nM) were obtained with the RBDs of the alpha, beta, delta and omicron variants. In an SPR neutralization assay, PRO-2000 had no effect on the interaction between the RBD and ACE2. Instead, PRO-2000 was proven to inhibit binding of the RBD to a heparin-coated sensor chip, yielding an IC50 of 1.1 nM. To conclude, PRO-2000 has the potential to inhibit a broad range of SARS-CoV-2 variants by blocking the heparin-binding site on the S protein.
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Affiliation(s)
- Evelien Vanderlinden
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium.
| | - Arnaud Boonen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Sam Noppen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Geert Schoofs
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Maya Imbrechts
- PharmAbs, The KU Leuven Antibody Center, Herestraat 49 box 820, 3000, Leuven, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, Herestraat 49 box 820, 3000, Leuven, Belgium
| | - Robert Snoeck
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Annelies Stevaert
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Lieve Naesens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Graciela Andrei
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
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38
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Kalk A, Sturmberg J, Van Damme W, Brown GW, Ridde V, Zizi M, Paul E. Surfing Corona waves - instead of breaking them: Rethinking the role of natural immunity in COVID-19 policy. F1000Res 2023; 11:337. [PMID: 37576385 PMCID: PMC10412939 DOI: 10.12688/f1000research.110593.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 08/15/2023] Open
Abstract
In the first two years of the pandemic, COVID-19 response policies have aimed to break Corona waves through non-pharmaceutical interventions and mass vaccination. However, for long-term strategies to be effective and efficient, and to avoid massive disruption and social harms, it is crucial to introduce the role of natural immunity in our thinking about COVID-19 (or future "Disease-X") control and prevention. We argue that any Corona or similar virus control policy must appropriately balance five key elements simultaneously: balancing the various fundamental interests of the nation, as well as the various interventions within the health sector; tailoring the prevention measures and treatments to individual needs; limiting social interaction restrictions; and balancing the role of vaccinations against the role of naturally induced immunity. Given the high infectivity of SARS-CoV-2 and its differential impact on population segments, we examine this last element in more detail and argue that an important aspect of 'living with the virus' will be to better understand the role of naturally induced immunity in our overall COVID-19 policy response. In our eyes, a policy approach that factors natural immunity should be considered for persons without major comorbidities and those having 'encountered' the antigen in the past.
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Affiliation(s)
- Andreas Kalk
- Kinshasa Country Office, Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ), Kinshasa, Democratic Republic of the Congo
| | - Joachim Sturmberg
- Foundation President – International Society for Systems and Complexity Sciences for Health, Australia, Callaghan, Australia
- A/Prof of General Practice, College of Health, Medicine and Wellbeing, University of Newcastle, Australia, Callaghan, Australia
| | - Wim Van Damme
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Antwerp, Belgium
| | | | - Valéry Ridde
- CEPED, IRD-Université de Paris, ERL INSERM SAGESUD, Institute for Research on Sustainable Development (IRD), Paris, France
| | - Martin Zizi
- Aerendir Mobile Inc., Mountain View, California, USA
| | - Elisabeth Paul
- School of Public Health, Université libre de Bruxelles, Brussels, 1070, Belgium
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39
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Pongener I, Miller GJ. d-Glucuronate and d-Glucuronate Glycal Acceptors for the Scalable Synthesis of d-GlcN-α-1,4-d-GlcA Disaccharides and Modular Assembly of Heparan Sulfate. J Org Chem 2023; 88:11130-11139. [PMID: 37458063 PMCID: PMC10407932 DOI: 10.1021/acs.joc.3c01108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 07/18/2023]
Abstract
Reported herein is a scalable chemical synthesis of disaccharide building blocks for heparan sulfate (HS) oligosaccharide assembly. The use of d-glucuronate-based acceptors for dehydrative glycosylation with d-glucosamine partners is explored, enabling diastereoselective synthesis of appropriately protected HS disaccharide building blocks (d-GlcN-α-1,4-d-GlcA) on a multigram scale. Isolation and characterization of key donor (1,2 glycal)- and acceptor (ortho-ester, anhydro)-derived side products ensure methodology improvements to reduce their formation; protecting the d-glucuronate acceptor at the anomeric position with a para-methoxyphenyl unit proves optimal. We also introduce glycal uronate acceptors, showing them to be comparative in reactivity to their pyranuronate counterparts. Taken together, this gram-scale access offers the capability to explore the iterative assembly of defined HS sequences containing the d-GlcN-α-1,4-d-GlcA repeat, highlighted by completing this for two tetrasaccharide syntheses.
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Affiliation(s)
- Imlirenla Pongener
- School of Chemical and Physical Sciences
& Centre for Glycoscience, Keele University, Keele, Staffordshire ST5 5BG, U.K.
| | - Gavin J. Miller
- School of Chemical and Physical Sciences
& Centre for Glycoscience, Keele University, Keele, Staffordshire ST5 5BG, U.K.
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40
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Patel L, Stenzel A, Van Hove C, Sidebottom A, Kethireddy R, Ha N, Beddow D, Manunga J, Qadri G, Kirven J, Skeik N. Outcomes in patients discharged with extended venous thromboembolism prophylaxis after hospitalization with COVID-19. Vasc Med 2023; 28:331-339. [PMID: 37259526 PMCID: PMC10235916 DOI: 10.1177/1358863x231159945] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
BACKGROUND Venous thromboembolism (VTE) is a known complication of coronavirus disease (COVID-19) in patients requiring hospitalization and intensive care. We examined the association between extended pharmacological VTE prophylaxis and outcomes among patients hospitalized with COVID-19. METHODS This was a retrospective cohort study of patients with an index positive SARS-CoV-2 polymerase chain reaction (PCR) test at the time of, or during hospitalization. Patients who were prescribed extended pharmacological VTE prophylaxis were compared against patients who were not. Multivariable logistic regression was used to produce odds ratio (OR) estimates and Cox proportional hazard models for hazard ratios (HR) with 95% CI to examine the association between pharmacological VTE prophylaxis and outcomes of interest. Primary outcomes were 30- and 90-day VTE events. Secondary outcomes included 30- and 90-day mortality, 30-day superficial venous thrombosis (SVT), acute myocardial infarction (MI), acute ischemic stroke, critical limb ischemia, clinically significant bleeding, and inpatient readmissions. RESULTS A total of 1936 patients were included in the study. Among them, 731 (38%) were discharged on extended pharmacological VTE prophylaxis. No significant difference was found in 30- and 90-day VTE events among groups. Patients discharged on extended VTE prophylaxis showed improved survival at 30 (HR: 0.35; 95% CI: 0.21-0.59) and 90 days (HR: 0.36; 95% CI: 0.23-0.55) and reduced inpatient readmission at 30 days (OR: 0.12; 95% CI: 0.04-0.33) when compared to those without. CONCLUSION Patients discharged on extended VTE prophylaxis after hospitalization due to COVID-19 had similar thrombotic events on follow-up. However, use of extended VTE prophylaxis was associated with improved 30- and 90-day survival and reduced risk of 30-day inpatient readmission.
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Affiliation(s)
- Love Patel
- Department of Internal Medicine, Abbott
Northwestern Hospital, Minneapolis, MN, USA
| | - Ashley Stenzel
- Care Delivery Research, Allina Health,
Minneapolis, MN, USA
| | | | | | - Rajesh Kethireddy
- Department of Internal Medicine, Abbott
Northwestern Hospital, Minneapolis, MN, USA
| | - Ngoc Ha
- Care Delivery Research, Allina Health,
Minneapolis, MN, USA
| | - David Beddow
- Department of Internal Medicine, Mercy
Hospital, Coon Rapids, MN, USA
| | - Jesse Manunga
- Department of Vascular Surgery, Allina
Health Minneapolis Heart Institute, Minneapolis, MN, USA
| | - Ghaziuddin Qadri
- Department of Internal Medicine, Abbott
Northwestern Hospital, Minneapolis, MN, USA
| | - Justin Kirven
- Department of Internal Medicine, Abbott
Northwestern Hospital, Minneapolis, MN, USA
| | - Nedaa Skeik
- Department of Vascular Medicine, Allina
Health Minneapolis Heart Institute, Minneapolis, MN, USA
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41
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Dos Santos AF, Martins MO, Lameira J, de Oliveira Araújo J, Frizzo MS, Davidson CB, de Souza DV, Machado AK, Mortari SR, Druzian DM, Tonel MZ, da Silva IZ, Fagan SB. Evaluation interaction of graphene oxide with heparin for antiviral blockade: a study of ab initio simulations, molecular docking, and experimental analysis. J Mol Model 2023; 29:235. [PMID: 37418181 DOI: 10.1007/s00894-023-05645-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023]
Abstract
CONTEXT Heparin, one of the drugs reused in studies with antiviral activity, was chosen to investigate a possible blockade of the SARS-CoV-2 spike protein for viral entry through computational simulations and experimental analysis. Heparin was associated to graphene oxide to increase in the binding affinity in biological system. First, the electronic and chemical interaction between the molecules was analyzed through ab initio simulations. Later, we evaluate the biological compatibility of the nanosystems, in the target of the spike protein, through molecular docking. The results show that graphene oxide interacts with the heparin with an increase in the affinity energy with the spike protein, indicating a possible increment in the antiviral activity. Experimental analysis of synthesis and morphology of the nanostructures were carried out, indicating heparin absorption by graphene oxide, confirming the results of the first principle simulations. Experimental tests were conducted on the structure and surface of the nanomaterial, confirming the heparin aggregation on the synthesis with a size between the GO layers of 7.44 Å, indicating a C-O type bond, and exhibiting a hydrophilic surface characteristic (36.2°). METHODS Computational simulations of the ab initio with SIESTA code, LDA approximations, and an energy shift of 0.05 eV. Molecular docking simulations were performed in the AutoDock Vina software integrated with the AMDock Tools Software using the AMBER force field. GO, GO@2.5Heparin, and GO@5Heparin were synthesized by Hummers and impregnation methods, respectively, and characterized by X-ray diffraction and surface contact angle.
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Affiliation(s)
- André Flores Dos Santos
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil.
| | - Mirkos Ortiz Martins
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará-UFPA, Belém, PA, Brazil
| | | | - Marcela Sagrilo Frizzo
- Postgraduate Program in Chemical Engineering-PosENQ, Federal University of Santa Catarina-UFSC, Florianopolis, SC, Brazil
| | - Carolina Bordin Davidson
- Postgraduate Program in Nanosciences: Laboratory of Cell Culture and Bioactive Effects, Franciscan University-UFN, Santa Maria, RS, Brazil
| | - Diulie Valente de Souza
- Postgraduate Program in Nanosciences: Laboratory of Cell Culture and Bioactive Effects, Franciscan University-UFN, Santa Maria, RS, Brazil
| | - Alencar Kolinski Machado
- Postgraduate Program in Nanosciences: Laboratory of Cell Culture and Bioactive Effects, Franciscan University-UFN, Santa Maria, RS, Brazil
| | - Sérgio Roberto Mortari
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Daniel Moro Druzian
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Mariana Zancan Tonel
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Ivana Zanella da Silva
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
| | - Solange Binotto Fagan
- Postgraduate Program in Nanoscience: Laboratory of Simulation and Modeling of Nanomaterials-LASIMON, Franciscan University-UFN, Andradas Street, 1614, Santa Maria, RS, 97010-030, Brazil
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Lauster D, Osterrieder K, Haag R, Ballauff M, Herrmann A. Respiratory viruses interacting with cells: the importance of electrostatics. Front Microbiol 2023; 14:1169547. [PMID: 37440888 PMCID: PMC10333706 DOI: 10.3389/fmicb.2023.1169547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
The COVID-19 pandemic has rekindled interest in the molecular mechanisms involved in the early steps of infection of cells by viruses. Compared to SARS-CoV-1 which only caused a relatively small albeit deadly outbreak, SARS-CoV-2 has led to fulminant spread and a full-scale pandemic characterized by efficient virus transmission worldwide within a very short time. Moreover, the mutations the virus acquired over the many months of virus transmission, particularly those seen in the Omicron variant, have turned out to result in an even more transmissible virus. Here, we focus on the early events of virus infection of cells. We review evidence that the first decisive step in this process is the electrostatic interaction of the spike protein with heparan sulfate chains present on the surface of target cells: Patches of cationic amino acids located on the surface of the spike protein can interact intimately with the negatively charged heparan sulfate chains, which results in the binding of the virion to the cell surface. In a second step, the specific interaction of the receptor binding domain (RBD) within the spike with the angiotensin-converting enzyme 2 (ACE2) receptor leads to the uptake of bound virions into the cell. We show that these events can be expressed as a semi-quantitative model by calculating the surface potential of different spike proteins using the Adaptive Poison-Boltzmann-Solver (APBS). This software allows visualization of the positive surface potential caused by the cationic patches, which increased markedly from the original Wuhan strain of SARS-CoV-2 to the Omicron variant. The surface potential thus enhanced leads to a much stronger binding of the Omicron variant as compared to the original wild-type virus. At the same time, data taken from the literature demonstrate that the interaction of the RBD of the spike protein with the ACE2 receptor remains constant within the limits of error. Finally, we briefly digress to other viruses and show the usefulness of these electrostatic processes and calculations for cell-virus interactions more generally.
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Affiliation(s)
- Daniel Lauster
- Institut für Pharmazie, Biopharmazeutika, Freie Universität Berlin, Berlin, Germany
| | | | - Rainer Haag
- Institut für Chemie und Biochemie, SupraFAB, Freie Universität Berlin, Berlin, Germany
| | - Matthias Ballauff
- Institut für Chemie und Biochemie, SupraFAB, Freie Universität Berlin, Berlin, Germany
| | - Andreas Herrmann
- Institut für Chemie und Biochemie, SupraFAB, Freie Universität Berlin, Berlin, Germany
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43
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Giroux E, Oake A, Lewis T, Martic S. Aptamer-, heparin- or cocktail-based inhibition of S1-ACE2 protein complexes. Anal Biochem 2023:115223. [PMID: 37385465 PMCID: PMC10299842 DOI: 10.1016/j.ab.2023.115223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
The Spike protein (S1) from the Severe acute respiratory syndrome 2 virus binds to angiotensin converting enzyme 2 (ACE2) receptor to initiate infection. Hence, antiviral therapeutic targeting the S1-ACE2 interface is of interest. Herein, we compare the inhibition efficacy of an aptamer to heparin or their cocktail, against wild-type (WT), Omicron, Delta, and Lambda S1-ACE2 complexes. The aptamer-protein complexes had the dissociation constant KD values in the 2-13 nM range. The aptamer half-maximal inhibitory concentration against WT S1-ACE was 17 nM, with the % inhibition in the 12-35% range. Several aptamer-S1 protein complexes were also stable at low pH with 60% inhibition. Despite the similarity in S1 sequences, the extent of inhibition (2-27%) with heparin was highly dependent on the type of S1 protein. More importantly, heparin did not inhibit the WT S1-ACE2 complex but was effective with mutants. The aptamer-heparin cocktail was less effective compared to aptamer or heparin, individually. Modelling data show that either a direct or proximal binding to RBD sites by aptamer or heparin prevents the ACE2 binding. Overall, heparin was as an effective inhibitor as aptamer against certain variants, and represents the more cost-effective neutralizing agent against emerging coronaviruses.
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Affiliation(s)
- E Giroux
- Department of Forensic Science, Trent University, Peterborough, Canada
| | - A Oake
- Flemming College, Peterborough, Canada
| | - T Lewis
- Environmental and Life Science Program, Trent University, Peterborough, Canada
| | - S Martic
- Department of Forensic Science, Trent University, Peterborough, Canada; Environmental and Life Science Program, Trent University, Peterborough, Canada.
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Pavan M, Fanti CD, Lucia AD, Canato E, Acquasaliente L, Sonvico F, Delgado J, Hicks A, Torrelles JB, Kulkarni V, Dwivedi V, Zanellato AM, Galesso D, Pasut G, Buttini F, Martinez-Sobrido L, Guarise C. AEROSOLIZED SULFATED HYALURONAN DERIVATIVES PROLONG THE SURVIVAL OF K18 ACE2 MICE INFECTED WITH A LETHAL DOSE OF SARS-COV-2. Eur J Pharm Sci 2023:106489. [PMID: 37311533 DOI: 10.1016/j.ejps.2023.106489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/19/2023] [Accepted: 06/06/2023] [Indexed: 06/15/2023]
Abstract
Despite several vaccines that are currently approved for human use to control the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent medical need for therapeutic and prophylactic options. SARS-CoV-2 binding and entry in human cells involves interactions of its spike (S) protein with several host cell surface factors, including heparan sulfate proteoglycans (HSPGs), transmembrane protease serine 2 (TMPRSS2), and angiotensin-converting enzyme 2 (ACE2). In this paper we investigated the potential of sulphated Hyaluronic Acid (sHA), a HSPG mimicking polymer, to inhibit the binding of SARS-CoV-2 S protein to human ACE2 receptor. After the assessment of different sulfation degree of sHA backbone, a series of sHA functionalized with different hydrophobic side chains were synthesized and screened. The compound showing the highest binding affinity to the viral S protein was further characterized by surface plasmon resonance (SPR) towards ACE2 and viral S protein binding domain. Selected compounds were formulated as solutions for nebulization and, after being characterized in terms of aerosolization performance and droplet size distribution, their efficacy was assessed in vivo using the K18 human (h)ACE2 transgenic mouse model of SARS-CoV-2 infection.
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Affiliation(s)
- Mauro Pavan
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy.
| | - Chiara D Fanti
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Alba Di Lucia
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Elena Canato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Fabio Sonvico
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27a, 43124 Parma, Italy
| | - Jennifer Delgado
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Amberlee Hicks
- Population Health and Host-Pathogens Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Jordi B Torrelles
- Population Health and Host-Pathogens Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Varun Dwivedi
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Anna M Zanellato
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Devis Galesso
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
| | - Gianfranco Pasut
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Francesca Buttini
- Food and Drug Department, University of Parma, Parco Area delle Scienze 27a, 43124 Parma, Italy
| | - Luis Martinez-Sobrido
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Cristian Guarise
- Fidia Farmaceutici SpA, via Ponte della Fabbrica 3/A, 35031 Abano Terme, Italy
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45
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Moro-Pérez L, Boggiano-Ayo T, Lozada-Chang SL, Fernández-Saiz OL, de la Luz KR, Gómez-Pérez JA. Conformational characterization of the mammalian-expressed SARS-CoV-2 recombinant receptor binding domain, a COVID-19 vaccine. Biol Res 2023; 56:22. [PMID: 37150832 PMCID: PMC10164616 DOI: 10.1186/s40659-023-00434-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 04/20/2023] [Indexed: 05/09/2023] Open
Abstract
The COVID-19 pandemic has caused a large number of diseases worldwide. There are few vaccines to constrain this disease and the value of them is high. In this sense, the antigens of the vaccine platform Soberana, the receptor binding domain from SARS-CoV-2 Spike protein, both the monomeric (mRBD) and dimeric (dRBD) forms, have been developed. This study encompassed several analyses by different techniques like circular dichroism (CD), fluorescence spectroscopy (FS) and Gel Filtration- High Performance Liquid ChLC of mRBD and dRBD. Monomer and dimer exhibited similar far-UV CD spectral characteristics with 54% of β-sheet content. Similar conformational features according to near-UV CD and FS studies were observed in both RBD. Stress stability studies by far-UV CD, FS, biological activity and GF-HPLC at 37 °C showed that mRBD is very stable. On the other hand, dRBD fluorescent emission showed a shift towards higher wavelengths as the incubation time increases, suggesting exposition of tryptophan residues, unlike what happens with mRBD. Biological activity outcome confirms these results. GF-HPLC profiles showed that in mRBD, the product of molecular stress are dimers and does not increase over time. However, dRBD showed dimer fragmentation as the main degradation species. This study reveals the usefulness of CD techniques for the analysis of degradation of RBD molecules as well as showed the difference in stability of both RBD molecules. Besides, our work provides useful insights into the production of a key protein used in diagnosis and therapeutics to fight COVID-19 pandemia.
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Affiliation(s)
- Leina Moro-Pérez
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba.
| | - Tammy Boggiano-Ayo
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba.
| | - Sum Lai Lozada-Chang
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
| | - Olga Lidia Fernández-Saiz
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
| | - Kathya Rashida de la Luz
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
| | - Jose Alberto Gómez-Pérez
- Bioprocess R&D Department, Center of Molecular Immunology, 216 Street and 15 Avenue, Atabey, Playa, P.O. Box 16040, 11600, Havana, Cuba
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46
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Barbosa JR, de Fátima Henriques Lourenço L. Sulfated polysaccharides act as baits to interfere with the binding of the spike protein (SARS-CoV-2) to the ACE2 receptor and can be administered through food. J Funct Foods 2023; 104:105532. [PMID: 37035109 PMCID: PMC10073580 DOI: 10.1016/j.jff.2023.105532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
Human civilization is experiencing a global crisis involving an unprecedented viral pandemic, with a high mortality rate, uncontrolled spread, and few effective drugs for treatment. Here, we critically evaluate how sulfated polysaccharides can be applied via foods to reduce the infectious process and increase the chances of an adequate immune response. The approach is directed to the infectious process by SARS-CoV-2 and protein S as a therapeutic focus. We discuss the antiviral activities of certain natural and specific sulfated polysaccharides that bind tightly to protein S. Finally, we identified that sulfated polysaccharides act as baits to interfere with the binding of the spike protein (SARS-CoV-2) to the ACE2 receptor and can be administered through food.
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Affiliation(s)
- Jhonatas Rodrigues Barbosa
- Institute of Technology (ITEC), Food Science and Technology Department, Federal University of Pará (UFPA), Rua Augusto Corrêa S/N, Guamá 66075-900, Belém, PA, Brazil
| | - Lúcia de Fátima Henriques Lourenço
- Institute of Technology (ITEC), Food Science and Technology Department, Federal University of Pará (UFPA), Rua Augusto Corrêa S/N, Guamá 66075-900, Belém, PA, Brazil
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47
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Sun L, Chopra P, Tomris I, van der Woude R, Liu L, de Vries RP, Boons GJ. Well-Defined Heparin Mimetics Can Inhibit Binding of the Trimeric Spike of SARS-CoV-2 in a Length-Dependent Manner. JACS AU 2023; 3:1185-1195. [PMID: 37101566 PMCID: PMC10089289 DOI: 10.1021/jacsau.3c00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
The emergence of new SARS-CoV-2 variants and the dangers of long-covid necessitate the development of broad-acting therapeutics that can reduce viral burden. SARS-CoV-2 employs heparan sulfate (HS) as an initial cellular attachment factor, and therefore, there is interest in developing heparin as a therapeutic for SARS-CoV-2. Its use is, however, complicated by structural heterogeneity and the risk of causing bleeding and thrombocytopenia. Here, we describe the preparation of well-defined heparin mimetics by a controlled head-to-tail assembly of HS oligosaccharides having an alkyne or azide moiety by copper-catalyzed azide-alkyne cycloaddition (CuAAC). Alkyne- and azide-containing sulfated oligosaccharides were prepared from a common precursor by modifying an anomeric linker with 4-pentynoic acid and by enzymatic extension with an N-acetyl-glucosamine having an azide moiety at C-6 (GlcNAc6N3), respectively, followed by CuAAC. The process of enzymatic extension with GlcNAc6N3 followed by CuAAC with the desired alkyne-containing oligosaccharides could be repeated to give compounds composed of 20 and 27 monosaccharides, respectively. The heparin mimetics could inhibit the binding of the SARS-CoV-2 spike or RBD to immobilized heparin or to Vero E6 cells. The inhibitory potency increased with increasing chain length, and a compound composed of four sulfated hexasaccharides linked by triazoles had a similar potency as unfractionated heparin. Sequence analysis and HS microarray binding studies with a wide range of RBDs of variants of concern indicate that they have maintained HS-binding capabilities and selectivities. The heparin mimetics exhibit no or reduced binding to antithrombin-III and platelet factor 4, respectively, which are associated with side effects.
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Affiliation(s)
- Lifeng Sun
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Pradeep Chopra
- Complex
Carbohydrate Research Center, The University
of Georgia, Athens, Georgia 30602, United States
| | - Ilhan Tomris
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Roosmarijn van der Woude
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Lin Liu
- Complex
Carbohydrate Research Center, The University
of Georgia, Athens, Georgia 30602, United States
| | - Robert P. de Vries
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department
of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
- Complex
Carbohydrate Research Center, The University
of Georgia, Athens, Georgia 30602, United States
- Bijvoet
Center for Biomolecular Research, Utrecht
University, 3584 CG Utrecht, The Netherlands
- Chemistry
Department, The University of Georgia, Athens, Georgia 30602, United States
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48
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Kim SH, Kearns FL, Rosenfeld MA, Votapka L, Casalino L, Papanikolas M, Amaro RE, Freeman R. SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101346. [PMID: 37077408 PMCID: PMC10080732 DOI: 10.1016/j.xcrp.2023.101346] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/07/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023]
Abstract
Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods for detection and mechanisms of action. Here, we investigate the effect of an evolving spike positive charge in SARS-CoV-2 variants and subsequent interactions with heparan sulfate and the angiotensin converting enzyme 2 (ACE2) in the glycocalyx. We show that the positively charged Omicron variant evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discover that while the Omicron spike-ACE2 affinity is comparable to that of the Delta variant, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-heparan sulfate-ACE2 with a large proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. This discovery enables us to engineer a second-generation lateral-flow test strip that harnesses both heparin and ACE2 to reliably detect all variants of concern, including Omicron.
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Affiliation(s)
- Sang Hoon Kim
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lane Votapka
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 4238 Urey Hall, MC-0340, La Jolla, CA 92093-0340, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina - Chapel Hill, 1112 Murray Hall, CB#3050, Chapel Hill, NC 27599-2100, USA
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Goonewardena SN, Grushko OG, Wells J, Herty L, Rosenson RS, Haus JM, Hummel SL. Immune-Mediated Glycocalyx Remodeling in Hospitalized COVID-19 Patients. Cardiovasc Drugs Ther 2023; 37:307-313. [PMID: 34792686 PMCID: PMC8600103 DOI: 10.1007/s10557-021-07288-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 01/08/2023]
Abstract
PURPOSE Vascular and immune dysfunction are hallmarks of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections and coronavirus disease 2019 (COVID-19). Although our understanding of the pathogenesis of COVID-19 has rapidly evolved, much of the focus has been on the immune mechanisms underlying COVID-19. In addition to immune dysfunction, vascular injury is also associated with COVID-19 and is a major driver of clinical deterioration in SARS-CoV-2 infections. The glycocalyx (GAC), a sugar-based shell that surrounds all mammalian cells, is an important regulator of vascular and immune responses. In sepsis, vascular dysfunction contributes to acute respiratory distress syndrome (ARDS) by altering vessel integrity, promoting thrombosis, and accelerating inflammation, all of which are also present in COVID-19. Observational studies in sepsis have found an association between levels of circulating GAC degradation products with both organ dysfunction and mortality. Although vascular dysfunction is a hallmark of COVID-19, it remains unclear whether GAC disruption occurs in COVID-19 and if GAC disruption contributes to the clinical progression of COVID-19. METHODS In this prospective cohort study, we measured the GAC components syndecan-1 (SDC1) and hyaluronan (Hyal) along with inflammatory cytokines in 12 hospitalized COVID-19 patients and 8 healthy controls (HC). RESULTS In agreement with other studies, we found that inflammatory cytokines are elevated in hospitalized COVID-19 patients compared with HC [median (IQR), all units picograms per milliliter: IL-6 4.65 (3.32-9.16) vs 0.69 (0.55-0.89), p < 0.001; TNFα 4.49 (1.87-8.03) vs 0.04 (0.04-0.84), p < 0.001]. Additionally, we found that the GAC components SDC1 and Hyal are also elevated in COVID-19 patients [median (IQR), all units picograms per milliliter: SDC1: 247.37 (101.43-458.26) vs 84.8 (52.88-123.59), p = 0.036; Hyal: 26.41 (16.4-35.1) vs 3.01 (1.66-4.61), p < 0.001]. CONCLUSION We propose that GAC markers offer insights into the pathobiology of COVID-19, potentially guide therapeutic approaches, and could aid in early risk stratification that is particularly beneficial in phasic diseases such as COVID-19.
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Affiliation(s)
- Sascha N Goonewardena
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
- Ann Arbor Veterans Affairs Health System, Ann Arbor, MI, USA.
- University of Michigan Frankel Cardiovascular Center, 1500 East Medical Center Drive, SPC 5853, Ann Arbor, MI, 48109-5853, USA.
| | - Olga G Grushko
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Joanna Wells
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lauren Herty
- Ann Arbor Veterans Affairs Health System, Ann Arbor, MI, USA
| | - Robert S Rosenson
- Metabolism and Lipids Unit, Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacob M Haus
- School of Kinesiology, University of Michigan, Ann Arbor, MI, USA
| | - Scott L Hummel
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
- Ann Arbor Veterans Affairs Health System, Ann Arbor, MI, USA.
- University of Michigan Frankel Cardiovascular Center, 1500 East Medical Center Drive, SPC 5853, Ann Arbor, MI, 48109-5853, USA.
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Barsanti L, Gualtieri P. Glucans, Paramylon and Other Algae Bioactive Molecules. Int J Mol Sci 2023; 24:ijms24065844. [PMID: 36982916 PMCID: PMC10059136 DOI: 10.3390/ijms24065844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Algae (macro- and micro-algae) can be defined as light-driven cell factories that synthesize bioactive compounds consisting of primary metabolites (i [...].
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Affiliation(s)
- Laura Barsanti
- Istituto di Biofisica, Area della Ricerca CNR, via Moruzzi 1, 56124 Pisa, Italy
| | - Paolo Gualtieri
- Istituto di Biofisica, Area della Ricerca CNR, via Moruzzi 1, 56124 Pisa, Italy
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