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Bangaru S, Jackson AM, Copps J, Fernández-Quintero ML, Torres JL, Richey ST, Nogal B, Sewall LM, de la Peña AT, Rehman A, Guebre-Xabier M, Girard B, Das R, Corbett-Helaire KS, Seder RA, Graham BS, Edwards DK, Patel N, Smith G, Ward AB. Structural serology of polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 COVID-19 vaccines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.11.628030. [PMID: 39713412 PMCID: PMC11661243 DOI: 10.1101/2024.12.11.628030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Current COVID-19 vaccines are largely limited in their ability to induce broad, durable immunity against emerging viral variants. Design and development of improved vaccines utilizing existing platforms requires an in-depth understanding of the antigenic and immunogenic properties of available vaccines. Here we examined the antigenicity of two of the original COVID-19 vaccines, mRNA-1273 and NVX-CoV2373, by electron microscopy-based polyclonal epitope mapping (EMPEM) of serum from immunized non-human primates (NHPs) and clinical trial donors. Both vaccines induce diverse polyclonal antibody (pAb) responses to the N-terminal domain (NTD) in addition to the receptor-binding domain (RBD) of the Spike protein, with the NTD supersite being an immunodominant epitope. High-resolution cryo-EMPEM studies revealed extensive pAb responses to and around the supersite with unique angles of approach and engagement. NTD supersite pAbs were also the most susceptible to variant mutations compared to other specificities, indicating that ongoing Spike ectodomain-based vaccine design strategies should consider immuno-masking this site to prevent induction of these strain-specific responses.
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Affiliation(s)
- Sandhya Bangaru
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Abigail M. Jackson
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Monica L. Fernández-Quintero
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Jonathan L. Torres
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Sara T. Richey
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Bartek Nogal
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Leigh M. Sewall
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Alba Torrents de la Peña
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
| | - Asma Rehman
- Novavax, Inc; 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | | | | | | | - Kizzmekia S. Corbett-Helaire
- Vaccine Research Center; National Institutes of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892, USA
- Current affiliation: Department of Immunology and Infectious Diseases; Harvard T.H. Chan School of Public Health; Boston, Massachusetts, 02115, USA
- Current affiliation: Howard Hughes Medical Institute; Chevy Chase, Maryland, 20815, USA
| | - Robert A. Seder
- Vaccine Research Center; National Institutes of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892, USA
| | - Barney S. Graham
- Vaccine Research Center; National Institutes of Allergy and Infectious Diseases; National Institutes of Health; Bethesda, Maryland, 20892, USA
- Current affiliation: Department of Microbiology, Biochemistry & Immunology; Morehouse School of Medicine; Atlanta, Georgia, 30310, USA
| | | | - Nita Patel
- Novavax, Inc; 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Gale Smith
- Novavax, Inc; 21 Firstfield Road, Gaithersburg, MD, 20878, USA
| | - Andrew B. Ward
- Dept. of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA, 92037, USA
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52
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Minigulov N, Boranbayev K, Bekbossynova A, Gadilgereyeva B, Filchakova O. Structural proteins of human coronaviruses: what makes them different? Front Cell Infect Microbiol 2024; 14:1458383. [PMID: 39711780 PMCID: PMC11659265 DOI: 10.3389/fcimb.2024.1458383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 10/17/2024] [Indexed: 12/24/2024] Open
Abstract
Following COVID-19 outbreak with its unprecedented effect on the entire world, the interest to the coronaviruses increased. The causative agent of the COVID-19, severe acute respiratory syndrome coronavirus - 2 (SARS-CoV-2) is one of seven coronaviruses that is pathogenic to humans. Others include SARS-CoV, MERS-CoV, HCoV-HKU1, HCoV-OC43, HCoV-NL63 and HCoV-229E. The viruses differ in their pathogenicity. SARS-CoV, MERS-CoV, and SARS-CoV-2 are capable to spread rapidly and cause epidemic, while HCoV-HKU1, HCoV-OC43, HCoV-NL63 and HCoV-229E cause mild respiratory disease. The difference in the viral behavior is due to structural and functional differences. All seven human coronaviruses possess four structural proteins: spike, envelope, membrane, and nucleocapsid. Spike protein with its receptor binding domain is crucial for the entry to the host cell, where different receptors on the host cell are recruited by different viruses. Envelope protein plays important role in viral assembly, and following cellular entry, contributes to immune response. Membrane protein is an abundant viral protein, contributing to the assembly and pathogenicity of the virus. Nucleocapsid protein encompasses the viral RNA into ribonucleocapsid, playing important role in viral replication. The present review provides detailed summary of structural and functional characteristics of structural proteins from seven human coronaviruses, and could serve as a practical reference when pathogenic human coronaviruses are compared, and novel treatments are proposed.
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Affiliation(s)
| | | | | | | | - Olena Filchakova
- Biology Department, School of Sciences and Humanities, Nazarbayev
University, Astana, Kazakhstan
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53
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Xiang Q, Wouters C, Chang P, Lu YN, Liu M, Wang H, Yang J, Pekosz A, Zhang Y, Wang J. Ubiquitin Ligase ITCH Regulates Life Cycle of SARS-CoV-2 Virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.04.624804. [PMID: 39677672 PMCID: PMC11642887 DOI: 10.1101/2024.12.04.624804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
SARS-CoV-2 infection poses a major threat to public health, and understanding the mechanism of viral replication and virion release would help identify therapeutic targets and effective drugs for combating the virus. Herein, we identified E3 ubiquitin-protein ligase Itchy homolog (ITCH) as a central regulator of SARS-CoV-2 at multiple steps and processes. ITCH enhances the ubiquitination of viral envelope and membrane proteins and mutual interactions of structural proteins, thereby aiding in virion assembly. ITCH-mediated ubiquitination also enhances the interaction of viral proteins to the autophagosome receptor p62, promoting their autophagosome-dependent secretion. Additionally, ITCH disrupts the trafficking of the protease furin and the maturation of cathepsin L, thereby suppressing their activities in cleaving and destabilizing the viral spike protein. Furthermore, ITCH exhibits robust activation during the SARS-CoV-2 replication stage, and SARS-CoV-2 replication is significantly decreased by genetic or pharmacological inhibition of ITCH. These findings provide new insights into the mechanisms of the SARS-CoV-2 life cycle and identify a potential target for developing treatments for the virus-related diseases.
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Affiliation(s)
- Qiwang Xiang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Camille Wouters
- Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Peixi Chang
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Yu-Ning Lu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Mingming Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Haocheng Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Junqin Yang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Yanjin Zhang
- Department of Veterinary Medicine, University of Maryland, College Park, MD, 20742, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
- Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
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54
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Pandey RP, Kumar S, Rao DN, Gupta DL. Emerging severe acute respiratory syndrome coronavirus 2 variants and their impact on immune evasion and vaccine-induced immunity. Trans R Soc Trop Med Hyg 2024; 118:761-772. [PMID: 39297227 DOI: 10.1093/trstmh/trae060] [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: 04/25/2024] [Revised: 07/24/2024] [Accepted: 08/30/2024] [Indexed: 12/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants harboring mutations in the structural protein, especially in the receptor binding domain (RBD) of spike protein, have raised concern about potential immune escape. The spike protein of SARS-CoV-2 plays a vital role in infection and is an important target for neutralizing antibodies. The mutations that occur in the structural proteins, especially in the spike protein, lead to changes in the virus attributes of transmissibility, an increase in disease severity, a notable reduction in neutralizing antibodies generated and thus a decreased response to vaccines and therapy. The observed multiple mutations in the RBD of the spike protein showed immune escape because it increases the affinity of spike protein binding with the ACE-2 receptor of host cells and increases resistance to neutralizing antibodies. Cytotoxic T-cell responses are crucial in controlling SARS-CoV-2 infections from the infected tissues and clearing them from circulation. Cytotoxic T cells efficiently recognized the infected cells and killed them by releasing soluble mediator's perforin and granzymes. However, the overwhelming response of T cells and, subsequently, the overproduction of inflammatory mediators during severe infections with SARS-CoV-2 may lead to poor outcomes. This review article summarizes the impact of mutations in the spike protein of SARS-CoV-2, especially mutations of RBD, on immunogenicity, immune escape and vaccine-induced immunity, which could contribute to future studies focusing on vaccine design and immunotherapy.
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Affiliation(s)
- Ramendra Pati Pandey
- School of Health Sciences and Technology (SOHST), UPES, Dehradun, Uttarakhand, India-248007
| | - Sachin Kumar
- School of Allied Health Sciences and Management, Delhi Pharmaceutical Sciences and Research University, New Delhi, India-110017
| | - D N Rao
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India-110029
| | - Dablu Lal Gupta
- Department of Biochemistry, All India Institute of Medical Sciences, Raipur, Chhattisgarh, India-492099
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55
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Escalera A, Laporte M, Turner S, Karakus U, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khalil Z, van Bakel H, Smith D, García-Sastre A, Aydillo T. The impact of S2 mutations on Omicron SARS-CoV-2 cell surface expression and fusogenicity. Emerg Microbes Infect 2024; 13:2297553. [PMID: 38112266 PMCID: PMC10866063 DOI: 10.1080/22221751.2023.2297553] [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: 07/06/2023] [Accepted: 12/17/2023] [Indexed: 12/21/2023]
Abstract
SARS-CoV-2 Omicron subvariants are still emerging and spreading worldwide. These variants contain a high number of polymorphisms in the spike (S) glycoprotein that could potentially impact their pathogenicity and transmission. We have previously shown that the S:655Y and P681H mutations enhance S protein cleavage and syncytia formation. Interestingly, these polymorphisms are present in Omicron S protein. Here, we characterized the cleavage efficiency and fusogenicity of the S protein of different Omicron sublineages. Our results showed that Omicron BA.1 subvariant is efficiently cleaved but it is poorly fusogenic compared to previous SARS-CoV-2 strains. To understand the basis of this phenotype, we generated chimeric S protein using combinations of the S1 and S2 domains from WA1, Delta and Omicron BA.1 variants. We found that the S2 domain of Omicron BA.1 hindered efficient cell-cell fusion. Interestingly, this domain only contains six unique polymorphisms never detected before in ancestral SARS-CoV-2 variants. WA1614G S proteins containing the six individuals S2 Omicron mutations were assessed for their fusogenicity and S surface expression after transfection in cells. Results showed that the S:N856K and N969K substitutions decreased syncytia formation and impacted S protein cell surface levels. However, we observed that "first-generation" Omicron sublineages that emerged subsequently, had convergently evolved to an enhanced fusogenic activity and S expression on the surface of infected cells while "second-generation" Omicron variants have highly diverged and showed lineage-specific fusogenic properties. Importantly, our findings could have potential implications in the improvement and redesign of COVID-19 vaccines.
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Affiliation(s)
- Alba Escalera
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manon Laporte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sam Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Umut Karakus
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Derek Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Teresa Aydillo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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56
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Ke Z, Peacock TP, Brown JC, Sheppard CM, Croll TI, Kotecha A, Goldhill DH, Barclay WS, Briggs JAG. Virion morphology and on-virus spike protein structures of diverse SARS-CoV-2 variants. EMBO J 2024; 43:6469-6495. [PMID: 39543395 PMCID: PMC11649927 DOI: 10.1038/s44318-024-00303-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 10/23/2024] [Accepted: 10/25/2024] [Indexed: 11/17/2024] Open
Abstract
The evolution of SARS-CoV-2 variants with increased fitness has been accompanied by structural changes in the spike (S) proteins, which are the major target for the adaptive immune response. Single-particle cryo-EM analysis of soluble S protein from SARS-CoV-2 variants has revealed this structural adaptation at high resolution. The analysis of S trimers in situ on intact virions has the potential to provide more functionally relevant insights into S structure and virion morphology. Here, we characterized B.1, Alpha, Beta, Gamma, Delta, Kappa, and Mu variants by cryo-electron microscopy and tomography, assessing S cleavage, virion morphology, S incorporation, "in-situ" high-resolution S structures, and the range of S conformational states. We found no evidence for adaptive changes in virion morphology, but describe multiple different positions in the S protein where amino acid changes alter local protein structure. Taken together, our data are consistent with a model where amino acid changes at multiple positions from the top to the base of the spike cause structural changes that can modulate the conformational dynamics of the S protein.
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Affiliation(s)
- Zunlong Ke
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
- The Pirbright Institute, Woking, UK
| | - Jonathan C Brown
- Department of Infectious Disease, Imperial College London, London, UK
| | - Carol M Sheppard
- Department of Infectious Disease, Imperial College London, London, UK
| | - Tristan I Croll
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Altos Labs, Cambridge, UK
| | - Abhay Kotecha
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Daniel H Goldhill
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - John A G Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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57
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Siwak KC, LeBlanc EV, Scott HM, Kim Y, Pellizzari-Delano I, Ball AM, Temperton NJ, Capicciotti CJ, Colpitts CC. Cellular sialoglycans are differentially required for endosomal and cell-surface entry of SARS-CoV-2 in lung cell lines. PLoS Pathog 2024; 20:e1012365. [PMID: 39625989 PMCID: PMC11642992 DOI: 10.1371/journal.ppat.1012365] [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: 06/22/2024] [Revised: 12/13/2024] [Accepted: 11/17/2024] [Indexed: 12/14/2024] Open
Abstract
Cell entry of severe acute respiratory coronavirus-2 (SARS-CoV-2) and other CoVs can occur via two distinct routes. Following receptor binding by the spike glycoprotein, membrane fusion can be triggered by spike cleavage either at the cell surface in a transmembrane serine protease 2 (TMPRSS2)-dependent manner or within endosomes in a cathepsin-dependent manner. Cellular sialoglycans have been proposed to aid in CoV attachment and entry, although their functional contributions to each entry pathway are unknown. In this study, we used genetic and enzymatic approaches to deplete sialic acid from cell surfaces and compared the requirement for sialoglycans during endosomal and cell-surface CoV entry using lentiviral particles pseudotyped with the spike proteins of different sarbecoviruses. We show that entry of SARS-CoV-1, WIV1-CoV and WIV16-CoV, like the SARS-CoV-2 omicron variant, depends on endosomal cathepsins and requires cellular sialoglycans for entry. Ancestral SARS-CoV-2 and the delta variant can use either pathway for entry, but only require sialic acid for endosomal entry in cells lacking TMPRSS2. Binding of SARS-CoV-2 spike protein to cells did not require sialic acid, nor was sialic acid required for SARS-CoV-2 entry in TMRPSS2-expressing cells. These findings suggest that cellular sialoglycans are not strictly required for SARS-CoV-2 attachment, receptor binding or fusion, but rather promote endocytic entry of SARS-CoV-2 and related sarbecoviruses. In contrast, the requirement for sialic acid during entry of MERS-CoV pseudoparticles and authentic HCoV-OC43 was not affected by TMPRSS2 expression, consistent with a described role for sialic acid in merbecovirus and embecovirus cell attachment. Overall, these findings clarify the role of sialoglycans in SARS-CoV-2 entry and suggest that cellular sialoglycans mediate endosomal, but not cell-surface, SARS-CoV-2 entry.
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Affiliation(s)
- Kimberley C. Siwak
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada
| | - Emmanuelle V. LeBlanc
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada
| | - Heidi M. Scott
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada
| | - Youjin Kim
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada
| | | | - Alice M. Ball
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada
| | - Nigel J. Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich at Medway, Chatham, United Kingdom
| | - Chantelle J. Capicciotti
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada
- Department of Chemistry, Queen’s University, Kingston, Canada
- Department of Surgery, Queen’s University, Kingston, Canada
| | - Che C. Colpitts
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Canada
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58
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Indra S, Chalak K, Das P, Mukhopadhyay A. Placenta a potential gateway of prenatal SARS-CoV-2 infection: A review. Eur J Obstet Gynecol Reprod Biol 2024; 303:123-131. [PMID: 39461078 DOI: 10.1016/j.ejogrb.2024.10.027] [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: 08/13/2024] [Revised: 10/15/2024] [Accepted: 10/17/2024] [Indexed: 10/29/2024]
Abstract
SARS-CoV-2, the causative agent of COVID-19, can infect various tissues in the body apart from the lungs. Although placental infection remains controversial, COVID-19-associated placental abnormalities have been reported worldwide. Therefore, COVID-19 poses a significant risk for fetal distress as well. Scientists are currently debating whether such distress results from direct viral induced assault or placental damage caused by the mother's immune response. The placenta develops different histopathological lesions in response to maternal SARS-CoV-2 infection. While some studies support both theories, the transmission rate through the placenta remains low. Therefore, a more in-depth study is necessary to determine the primary cause of maternal SARS-CoV-2-induced fetal distress. This comprehensive review is aimed to shed light on the possible reasons towards fetal distress among mothers with COVID-19. This review describes the various mechanisms of viral entry along with the mechanisms by which the virus could affect the placenta. Reported cases of placental abnormalities and fetal distress symptoms have been collated to provide an overview of the current state of knowledge on vertical transmission of COVID-19.
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Affiliation(s)
- Subhashis Indra
- Department of Life Sciences, Presidency University, Kolkata 700073, India
| | - Kuheli Chalak
- Department of Life Sciences, Presidency University, Kolkata 700073, India
| | - Purbasha Das
- Department of Life Sciences, Presidency University, Kolkata 700073, India
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59
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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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60
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Cao X, Huang L, Tang M, Liang Y, Liu X, Hou H, Liang S. Antibiotics daptomycin interacts with S protein of SARS-CoV-2 to promote cell invasion of Omicron (B1.1.529) pseudovirus. Virulence 2024; 15:2339703. [PMID: 38576396 PMCID: PMC11057663 DOI: 10.1080/21505594.2024.2339703] [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: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has posed enormous challenges to global public health. The use of antibiotics has greatly increased during the SARS-CoV-2 epidemic owing to the presence of bacterial co-infection and secondary bacterial infections. The antibiotics daptomycin (DAP) is widely used in the treatment of infectious diseases caused by gram-positive bacteria owing to its highly efficient antibacterial activity. It is pivotal to study the antibiotics usage options for patients of coronavirus infectious disease (COVID-19) with pneumonia those need admission to receive antibiotics treatment for bacterial co-infection in managing COVID-19 disease. Herein, we have revealed the interactions of DAP with the S protein of SARS-CoV-2 and the variant Omicron (B1.1.529) using the molecular docking approach and Omicron (B1.1.529) pseudovirus (PsV) mimic invasion. Molecular docking analysis shows that DAP has a certain degree of binding ability to the S protein of SARS-CoV-2 and several derived virus variants, and co-incubation of 1-100 μM DAP with cells promotes the entry of the PsV into human angiotensin-converting enzyme 2 (hACE2)-expressing HEK-293T cells (HEK-293T-hACE2), and this effect is related to the concentration of extracellular calcium ions (Ca2+). The PsV invasion rate in the HEK-293T-hACE2 cells concurrently with DAP incubation was 1.7 times of PsV infection alone. In general, our findings demonstrate that DAP promotes the infection of PsV into cells, which provides certain reference of antibiotics selection and usage optimization for clinicians to treat bacterial coinfection or secondary infection during SARS-CoV-2 infection.
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Affiliation(s)
- Xu Cao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lan Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Min Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xinpeng Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Huijin Hou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shufang Liang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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61
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Mao B, Le-Trilling VTK, Tang H, Hu J, Schmitz MS, Barbet K, Xu D, Wei Z, Guo B, Mennerich D, Yao C, Liu J, Li Z, Wan Y, Zhang X, Wang K, Tang N, Yu Z, Trilling M, Lin Y. Diphyllin elicits a doubled-pronged attack on the entry of SARS-CoV-2 by inhibiting cathepsin L and furin. Virus Res 2024; 350:199485. [PMID: 39424146 PMCID: PMC11532987 DOI: 10.1016/j.virusres.2024.199485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 10/09/2024] [Accepted: 10/15/2024] [Indexed: 10/21/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic, posing serious threats to global health. Effective broad-spectrum antiviral drugs for the treatment of COVID-19 are not sufficiently available. In the present study, we investigated the antiviral activity of the natural lignan diphyllin (PubChem CID 100492) against different SARS-CoV-2 variants and explored the underlying molecular mechanisms. We found that diphyllin dose-dependently inhibits the SARS-CoV-2 spike (S)-mediated entry into different types of cells. The potent inhibition was evident against spike proteins derived from the original SARS-CoV-2 and from variants of concern such as Alpha, Beta, Delta or Omicron. Accordingly, diphyllin also significantly inhibited the in vitro infection of a clinical SARS-CoV-2 virus isolate. Mechanistically, diphyllin simultaneously inhibited the endosomal entry of SARS-CoV-2 by neutralizing the endosomal acidification and reducing the activity of the cysteine protease cathepsin L (CTSL) as well as S-meditated cell surface entry by impairing furin activity. Collectively, our findings establish diphyllin as novel inhibitor of CTSL and furin proteases, resulting in a double-pronged attack on SARS-CoV-2 entry along endosomal as well as cell surface routes. Therefore, diphyllin has the potential to be advanced as an inhibitor of SARS-CoV-2 entry.
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Affiliation(s)
- Binli Mao
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China; Department of Blood Transfusion, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Vu Thuy Khanh Le-Trilling
- Institute for the Research on HIV and AIDS-associated Diseases, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany; Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Haihuan Tang
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Jie Hu
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China; Department of Laboratory Medicine, Bishan Hospital of Chongqing Medical University, Chongqing 402760, China
| | - Mona S Schmitz
- Department of Pulmonary Medicine, University Medical Center Essen, Ruhrlandklinik, Essen 45239, Germany
| | - Kimberly Barbet
- Department of Pulmonary Medicine, University Medical Center Essen, Ruhrlandklinik, Essen 45239, Germany
| | - Dan Xu
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Zhen Wei
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Beinu Guo
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Denise Mennerich
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany
| | - Chun Yao
- Chongqing Yucai Secondary School, Chongqing 400050, China
| | - Jinxin Liu
- Chongqing Yucai Secondary School, Chongqing 400050, China
| | - Zhenghan Li
- Chongqing Yucai Secondary School, Chongqing 400050, China
| | - Yushun Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoyong Zhang
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Kai Wang
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Ni Tang
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China
| | - Zebo Yu
- Department of Blood Transfusion, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Mirko Trilling
- Institute for the Research on HIV and AIDS-associated Diseases, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany; Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen 45147, Germany.
| | - Yong Lin
- Key Laboratory of Molecular Biology of Infectious Diseases (Chinese Ministry of Education), Chongqing Medical University, Chongqing 400016, China.
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62
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Evers P, Uguccioni SM, Ahmed N, Francis ME, Kelvin AA, Pezacki JP. miR-24-3p Is Antiviral Against SARS-CoV-2 by Downregulating Critical Host Entry Factors. Viruses 2024; 16:1844. [PMID: 39772154 PMCID: PMC11680362 DOI: 10.3390/v16121844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 11/20/2024] [Accepted: 11/26/2024] [Indexed: 01/11/2025] Open
Abstract
Despite all the progress in treating SARS-CoV-2, escape mutants to current therapies remain a constant concern. Promising alternative treatments for current and future coronaviruses are those that limit escape mutants by inhibiting multiple pathogenic targets, analogous to the current strategies for treating HCV and HIV. With increasing popularity and ease of manufacturing of RNA technologies for vaccines and drugs, therapeutic microRNAs represent a promising option. In the present work, miR-24-3p was identified to inhibit SARS-CoV-2 entry, replication, and production; furthermore, this inhibition was retained against common mutations improving SARS-CoV-2 fitness. To determine the mechanism of action, bioinformatic tools were employed, identifying numerous potential effectors promoting infection targeted by miR-24-3p. Of these targets, several key host proteins for priming and facilitating SARS-CoV-2 entry were identified: furin, NRP1, NRP2, and SREBP2. With further experimental analysis, we show that miR-24-3p directly downregulates these viral entry factors to impede infection when producing virions and when infecting the target cell. Furthermore, we compare the findings with coronavirus, HCoV-229E, which relies on different factors strengthening the miR-24-3p mechanism. Taken together, the following work suggests that miR-24-3p could be an avenue to treat current coronaviruses and those likely to emerge.
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Affiliation(s)
- Parrish Evers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N6, Canada; (P.E.); (S.M.U.)
| | - Spencer M. Uguccioni
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N6, Canada; (P.E.); (S.M.U.)
| | - Nadine Ahmed
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N6, Canada; (P.E.); (S.M.U.)
| | - Magen E. Francis
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (M.E.F.); (A.A.K.)
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Alyson A. Kelvin
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (M.E.F.); (A.A.K.)
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - John P. Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N6, Canada; (P.E.); (S.M.U.)
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63
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Norton TD, Thakur M, Ganguly S, Ali S, Chao J, Waldron A, Xiao J, Turner KC, Davis JD, Irvin SC, Pan C, Atmodjo D, Hooper AT, Hamilton JD, Hussein M, Subramaniam D, Roque-Guerrero L, Kohli A, Mylonakis E, Geba GP, Cox E, Braunstein N, Dakin P, Kowal B, Bhore R, DiCioccio AT, Hughes D, Herman GA, for the Trial Investigators. Safety and Pharmacokinetics of Casirivimab and Imdevimab (CAS + IMD) in Pediatric Outpatients With COVID-19. J Pediatric Infect Dis Soc 2024; 13:589-593. [PMID: 39351798 PMCID: PMC11599144 DOI: 10.1093/jpids/piae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/30/2024] [Indexed: 11/28/2024]
Abstract
The safety of casirivimab + imdevimab (CAS + IMD) (anti-severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] monoclonal antibodies [mAbs]) in pediatric outpatients with coronavirus disease 2019 (COVID-19) was evaluated in a randomized phase 1/2/3 trial. Consistent with adults, CAS + IMD was generally well tolerated with low drug-induced immunogenicity rates. The findings support the development of next-generation anti-SARS-CoV-2 mAbs for at-risk pediatric patients.
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MESH Headings
- Humans
- Child
- Antibodies, Monoclonal, Humanized/pharmacokinetics
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibodies, Monoclonal, Humanized/adverse effects
- COVID-19 Drug Treatment
- Male
- Adolescent
- Female
- SARS-CoV-2/immunology
- Child, Preschool
- Antiviral Agents/pharmacokinetics
- Antiviral Agents/therapeutic use
- Antiviral Agents/adverse effects
- COVID-19/immunology
- Drug Combinations
- Outpatients
- Antibodies, Monoclonal/pharmacokinetics
- Antibodies, Monoclonal/adverse effects
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing
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Affiliation(s)
| | - Mazhar Thakur
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Samit Ganguly
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Shazia Ali
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Jesse Chao
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Alpana Waldron
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Jing Xiao
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | | | - John D Davis
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Susan C Irvin
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Cynthia Pan
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | | | | | | | | | | | | | | | - Eleftherios Mylonakis
- Infectious Diseases Division, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Gregory P Geba
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Edward Cox
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Ned Braunstein
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Paula Dakin
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Bari Kowal
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Rafia Bhore
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | | | - Diana Hughes
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
| | - Gary A Herman
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, USA
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64
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Hu J, Huynh DT, Boyce M. Sugar Highs: Recent Notable Breakthroughs in Glycobiology. Biochemistry 2024; 63:2937-2947. [PMID: 39475524 DOI: 10.1021/acs.biochem.4c00418] [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: 11/20/2024]
Abstract
Glycosylation is biochemically complex and functionally critical to a wide range of processes and disease states, making it a vibrant area of contemporary research. Here, we highlight a selection of notable recent advances in the glycobiology of SARS-CoV-2 infection and immunity, cancer biology and immunotherapy, and newly discovered glycosylated RNAs. Together, these studies illustrate the significance of glycosylation in normal biology and the great promise of manipulating glycosylation for therapeutic benefit in disease.
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Affiliation(s)
- Jimin Hu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Duc T Huynh
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
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65
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Hoffmann M, Kleine-Weber H, Graichen L, Nehlmeier I, Kempf A, Moldenhauer AS, Braun E, Assiri AM, Kirchhoff F, Sauter D, Alkharsah KR, Pöhlmann S. Acquisition of a multibasic cleavage site does not increase MERS-CoV entry into Calu-3 human lung cells. J Virol 2024; 98:e0130524. [PMID: 39470207 PMCID: PMC11575293 DOI: 10.1128/jvi.01305-24] [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: 07/26/2024] [Accepted: 09/18/2024] [Indexed: 10/30/2024] Open
Abstract
Human-to-human transmission of the highly pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV) is currently inefficient. However, there is concern that the virus might mutate and thereby increase its transmissibility and thus pandemic potential. The pandemic SARS-CoV-2 depends on a highly cleavable furin motif at the S1/S2 site of the viral spike (S) protein for efficient lung cell entry, transmission, and pathogenicity. Here, by employing pseudotyped particles, we investigated whether augmented cleavage at the S1/S2 site also increases MERS-CoV entry into Calu-3 human lung cells. We report that polymorphism T746K at the S1/S2 cleavage site or optimization of the furin motif increases S protein cleavage but not lung cell entry. These findings suggest that, unlike what has been reported for SARS-CoV-2, a highly cleavable S1/S2 site might not augment MERS-CoV infectivity for human lung cells.IMPORTANCEThe highly cleavable furin motif in the spike protein is required for robust lung cell entry, transmission, and pathogenicity of SARS-CoV-2. In contrast, it is unknown whether optimization of the furin motif in the spike protein of the pre-pandemic MERS-CoV increases lung cell entry and allows for robust human-human transmission. The present study indicates that this might not be the case. Thus, neither a naturally occurring polymorphism that increased MERS-CoV spike protein cleavage nor artificial optimization of the cleavage site allowed for increased spike-protein-driven entry into Calu-3 human lung cells.
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Affiliation(s)
- Markus Hoffmann
- Infection Biology Unit, German Primate Center- Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
| | - Hannah Kleine-Weber
- Infection Biology Unit, German Primate Center- Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center- Leibniz Institute for Primate Research, Göttingen, Germany
| | - Inga Nehlmeier
- Infection Biology Unit, German Primate Center- Leibniz Institute for Primate Research, Göttingen, Germany
| | - Amy Kempf
- Infection Biology Unit, German Primate Center- Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
| | - Anna-Sophie Moldenhauer
- Infection Biology Unit, German Primate Center- Leibniz Institute for Primate Research, Göttingen, Germany
| | - Elisabeth Braun
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Khaled R. Alkharsah
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University (IAU), Dammam, Saudi Arabia
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center- Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, Göttingen, Germany
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66
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Stearns K, Lampe G, Hanan R, Marcink T, Niewiesk S, Sternberg SH, Greninger AL, Porotto M, Moscona A. Human parainfluenza virus 3 field strains undergo extracellular fusion protein cleavage to activate entry. mBio 2024; 15:e0232724. [PMID: 39382296 PMCID: PMC11559058 DOI: 10.1128/mbio.02327-24] [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: 08/02/2024] [Accepted: 08/23/2024] [Indexed: 10/10/2024] Open
Abstract
Human parainfluenza virus 3 (HPIV3) infection is driven by the coordinated action of viral surface glycoproteins hemagglutinin-neuraminidase (HN) and fusion protein (F). Receptor-engaged HN activates F to insert into the target cell membrane and drive virion-cell membrane fusion. For F to mediate entry, its precursor (F0) must first be cleaved by host proteases. F0 cleavage has been thought to be executed during viral glycoprotein transit through the trans-Golgi network by the ubiquitously expressed furin because F0 proteins of laboratory-adapted viruses contain a furin recognition dibasic cleavage motif RXKR around residue 108. Here, we show that the F proteins of field strains have a different cleavage motif from laboratory-adapted strains and are cleaved by unidentified proteases expressed in only a narrow subset of cell types. We demonstrate that extracellular serine protease inhibitors block HPIV3 F0 cleavage for field strains, suggesting F0 cleavage occurs at the cell surface facilitated by transmembrane proteases. Candidate proteases that may process HPIV3 F in vivo were identified by a genome-wide CRISPRa screen in HEK293/dCas9-VP64 + MPH cells. The lung-expressed extracellular serine proteases TMPRSS2 and TMPRSS13 are both sufficient to cleave HPIV3 F and enable infectious virus release by otherwise non-permissive cells. Our findings support an alternative mechanism of F activation in vivo, reliant on extracellular membrane-bound serine proteases expressed in a narrow subset of cells. The proportion of HPIV3 F proteins cleaved and infectious virus release is determined by host cell expression of requisite proteases, allowing just-in-time activation of F and positioning F cleavage as another key regulator of HPIV3 spread. IMPORTANCE Enveloped viruses cause a wide range of diseases in humans. At the first step of infection, these viruses must fuse their envelope with a cell membrane to initiate infection. This fusion is mediated by viral proteins that require a critical activating cleavage event. It was previously thought that for parainfluenza virus 3, an important cause of respiratory disease and a representative of a group of important pathogens, this cleavage event was mediated by furin in the cell secretory pathways prior to formation of the virions. We show that this is only true for laboratory strain viruses, and that clinical viruses that infect humans utilize extracellular proteases that are only made by a small subset of cells. These results highlight the importance of studying authentic clinical viruses that infect human tissues for understanding natural infection.
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Affiliation(s)
- Kyle Stearns
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Center for Host–Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Physiology & Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - George Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Rachel Hanan
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Center for Host–Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Tara Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Center for Host–Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Samuel H. Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Center for Host–Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Center for Host–Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Physiology & Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Microbiology & Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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67
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Dey S, Pahari P, Mukherjee S, Munro JB, Das DK. Conformational dynamics of SARS-CoV-2 Omicron spike trimers during fusion activation at single molecule resolution. Structure 2024; 32:1910-1925.e6. [PMID: 39366371 PMCID: PMC11560620 DOI: 10.1016/j.str.2024.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/26/2024] [Accepted: 09/09/2024] [Indexed: 10/06/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron entry involves spike (S) glycoprotein-mediated fusion of viral and late endosomal membranes. Here, using single-molecule Förster resonance energy transfer (sm-FRET) imaging and biochemical measurements, we directly visualized conformational changes of individual spike trimers on the surface of SARS-CoV-2 Omicron pseudovirions during fusion activation. We observed that the S2 domain of the Omicron spike is a dynamic fusion machine. S2 reversibly interchanges between the pre-fusion conformation and two previously undescribed intermediate conformations. Acidic pH shifts the conformational equilibrium of S2 toward an intermediate conformation and promotes the membrane hemi-fusion reaction. Moreover, we captured conformational reversibility in the S2 domain, which suggests that spike can protect itself from pre-triggering. Furthermore, we determined that Ca2+ directly promotes the S2 conformational change from an intermediate conformation to post-fusion conformation. In the presence of a target membrane, low pH and Ca2+ stimulate the irreversible transition to S2 post-fusion state and promote membrane fusion.
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Affiliation(s)
- Shuvankar Dey
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Purba Pahari
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Srija Mukherjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - James B Munro
- Department of Microbiology, University of Massachusetts Chan Medical School, Worcester, MA, USA; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dibyendu Kumar Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India; Center for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India.
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68
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Zhang H, Wang Z, Nguyen HTT, Cornejo Pontelli M, Qi W, Rao L, Liu Z, Whelan SPJ, Zhu J. Facilitating and restraining virus infection using cell-attachable soluble viral receptors. Proc Natl Acad Sci U S A 2024; 121:e2414583121. [PMID: 39480852 PMCID: PMC11551432 DOI: 10.1073/pnas.2414583121] [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: 07/19/2024] [Accepted: 10/02/2024] [Indexed: 11/02/2024] Open
Abstract
SARS-CoV-2 uses the receptor binding domain (RBD) of its spike protein to recognize and infect host cells by binding to the cell surface receptor angiotensin converting enzyme 2 (ACE2). The ACE2 receptor is composed of peptidase domain (PD), collectrin-like domain, transmembrane domain, and short cytoplasmic domain, and may exist as a dimer on cell surface. The RBD binding site is located atop of the ACE2 PD, but the involvement of other domains in virus infection is uncertain. We found that the ACE2 PD alone, whether anchored to cell membrane via a glycosylphosphatidylinositol anchor or attached to another surface protein, is fully functional as a receptor for spike-mediated cell fusion and virus infection. However, for ACE2 to function as the viral receptor, the RBD binding site must be positioned in close proximity to the cell membrane. Elevating the surface height of ACE2 using long and rigid protein spacers reduces or eliminates cell fusion and virus infection. Moreover, we found that the RBD-targeting neutralizing antibodies, nanobodies, and de novo designed miniprotein binders, when present on cell surface, also act as viral receptors, facilitating cell fusion and virus infection. Our data demonstrate that RBD binding and close membrane proximity are essential properties for a receptor to effectively mediate SARS-CoV-2 infection. Importantly, we show that soluble RBD-binders can be engineered to make cells either susceptible or resistant to virus infection, which has significant implications for antiviral therapy and various virus-mediated applications.
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Affiliation(s)
- Heng Zhang
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Zhengli Wang
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Huong T. T. Nguyen
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | | | - Wanrong Qi
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Liem Rao
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO63110
| | - Sean P. J. Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO63110
| | - Jieqing Zhu
- Thrombosis and Hemostasis Program, Versiti Blood Research Institute, Milwaukee, WI53226
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
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69
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Ngo VN, Winski DP, Aho B, Kamath PL, King BL, Waters H, Zimmerberg J, Sodt A, Hess ST. Conserved sequence features in intracellular domains of viral spike proteins. Virology 2024; 599:110198. [PMID: 39116647 PMCID: PMC11383743 DOI: 10.1016/j.virol.2024.110198] [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: 06/06/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
Viral spike proteins mutate frequently, but conserved features within these proteins often have functional importance and can inform development of anti-viral therapies which circumvent the effects of viral sequence mutations. Through analysis of large numbers of viral spike protein sequences from several viral families, we found highly (>99%) conserved patterns within their intracellular domains. The patterns generally consist of one or more basic amino acids (arginine or lysine) adjacent to a cysteine, many of which are known to undergo acylation. These patterns were not enriched in cellular proteins in general. Molecular dynamics simulations show direct electrostatic and hydrophobic interactions between these conserved residues in hemagglutinin (HA) from influenza A and B and the phosphoinositide PIP2. Super-resolution microscopy shows nanoscale colocalization of PIP2 and several of the same viral proteins. We propose the hypothesis that these conserved viral spike protein features can interact with phosphoinositides such as PIP2.
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Affiliation(s)
- Vinh-Nhan Ngo
- Department of Physics and Astronomy, 120 Bennett Hall, University of Maine, Orono, ME, 04469-5709, USA
| | - David P Winski
- Department of Physics and Astronomy, 120 Bennett Hall, University of Maine, Orono, ME, 04469-5709, USA
| | - Brandon Aho
- Department of Physics and Astronomy, 120 Bennett Hall, University of Maine, Orono, ME, 04469-5709, USA
| | - Pauline L Kamath
- School of Food and Agriculture, 342 Hitchner Hall, University of Maine, And Maine Center for Genetics in the Environment, Orono, ME, USA.
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, 5735 Hitchner Hall, University of Maine, Orono, ME, USA.
| | - Hang Waters
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alexander Sodt
- Unit on Membrane Chemical Physics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Samuel T Hess
- Department of Physics and Astronomy, 120 Bennett Hall, University of Maine, Orono, ME, 04469-5709, USA.
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70
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Zhang L, Cheng HH, Krüger N, Hörnich B, Graichen L, Hahn AS, Schulz SR, Jäck HM, Stankov MV, Behrens GMN, Müller MA, Drosten C, Mörer O, Winkler MS, Qian Z, Pöhlmann S, Hoffmann M. ACE2-independent sarbecovirus cell entry can be supported by TMPRSS2-related enzymes and can reduce sensitivity to antibody-mediated neutralization. PLoS Pathog 2024; 20:e1012653. [PMID: 39536058 PMCID: PMC11559990 DOI: 10.1371/journal.ppat.1012653] [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: 09/26/2024] [Accepted: 10/10/2024] [Indexed: 11/16/2024] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, demonstrated that zoonotic transmission of animal sarbecoviruses threatens human health but the determinants of transmission are incompletely understood. Here, we show that most spike (S) proteins of horseshoe bat and Malayan pangolin sarbecoviruses employ ACE2 for entry, with human and raccoon dog ACE2 exhibiting broad receptor activity. The insertion of a multibasic cleavage site into the S proteins increased entry into human lung cells driven by most S proteins tested, suggesting that acquisition of a multibasic cleavage site might increase infectivity of diverse animal sarbecoviruses for the human respiratory tract. In contrast, two bat sarbecovirus S proteins drove cell entry in an ACE2-independent, trypsin-dependent fashion and several ACE2-dependent S proteins could switch to the ACE2-independent entry pathway when exposed to trypsin. Several TMPRSS2-related cellular proteases but not the insertion of a multibasic cleavage site into the S protein allowed for ACE2-independent entry in the absence of trypsin and may support viral spread in the respiratory tract. Finally, the pan-sarbecovirus antibody S2H97 enhanced cell entry driven by two S proteins and this effect was reversed by trypsin while trypsin protected entry driven by a third S protein from neutralization by S2H97. Similarly, plasma from quadruple vaccinated individuals neutralized entry driven by all S proteins studied, and availability of the ACE2-independent, trypsin-dependent pathway reduced neutralization sensitivity. In sum, our study reports a pathway for entry into human cells that is ACE2-independent, can be supported by TMPRSS2-related proteases and may be associated with antibody evasion.
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Affiliation(s)
- Lu Zhang
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Hsiu-Hsin Cheng
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Nadine Krüger
- Platform Infection Models, German Primate Center, Göttingen, Germany
| | - Bojan Hörnich
- Junior Research Group Herpesviruses, German Primate Center, Göttingen, Germany
| | - Luise Graichen
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Alexander S. Hahn
- Junior Research Group Herpesviruses, German Primate Center, Göttingen, Germany
| | - Sebastian R. Schulz
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Department of Internal Medicine 3, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Metodi V. Stankov
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Georg M. N. Behrens
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Marcel A. Müller
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), partner site Berlin, Berlin, Germany
| | - Onnen Mörer
- Department of Anesthesiology, University of Göttingen Medical Center, Göttingen, Georg-August University of Göttingen, Göttingen, Germany
| | - Martin Sebastian Winkler
- Department of Anesthesiology, University of Göttingen Medical Center, Göttingen, Georg-August University of Göttingen, Göttingen, Germany
| | - ZhaoHui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center–Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
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71
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Oliveira BR, Nehlmeier I, Kempf AM, Venugopalan V, Rehders M, Ceniza MEP, Cavalcanti PADTPV, Hoffmann M, Pöhlmann S, Brix K. Cytoskeletal β-tubulin and cysteine cathepsin L deregulation by SARS-CoV-2 spike protein interaction with the neuronal model cell line SH-SY5Y. Biochimie 2024; 226:49-61. [PMID: 38432290 DOI: 10.1016/j.biochi.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
SARS-CoV-2 mainly infects the respiratory tract but can also target other organs, including the central nervous system. While it was recently shown that cells of the blood-brain-barrier are permissive to SARS-CoV-2 infection in vitro, it remains debated whether neurons can be infected. In this study, we demonstrate that vesicular stomatitis virus particles pseudotyped with the spike protein of SARS-CoV-2 variants WT, Alpha, Delta and Omicron enter the neuronal model cell line SH-SY5Y. Cell biological analyses of the pseudo-virus treated cultures showed marked alterations in microtubules of SH-SY5Y cells. Because the changes in β-tubulin occurred in most cells, but only few were infected, we further asked whether interaction of the cells with spike protein might be sufficient to cause molecular and structural changes. For this, SH-SY5Y cells were incubated with trimeric spike proteins for time intervals of up to 24 h. CellProfiler™-based image analyses revealed changes in the intensities of microtubule staining in spike protein-incubated cells. Furthermore, expression of the spike protein-processing protease cathepsin L was found to be up-regulated by wild type, Alpha and Delta spike protein pseudotypes and cathepsin L was found to be secreted from spike protein-treated cells. We conclude that the mere interaction of the SARS-CoV-2 with neuronal cells can affect cellular architecture and proteolytic capacities. The molecular mechanisms underlying SARS-CoV-2 spike protein induced cytoskeletal changes in neuronal cells remain elusive and require future studies.
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Affiliation(s)
- Bernardo R Oliveira
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany
| | - Inga Nehlmeier
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany.
| | - Amy Madeleine Kempf
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August University Göttingen, Wilhelmsplatz 1, D-37073, Göttingen, Germany.
| | | | - Maren Rehders
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany.
| | - Marianne E P Ceniza
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany.
| | | | - Markus Hoffmann
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August University Göttingen, Wilhelmsplatz 1, D-37073, Göttingen, Germany.
| | - Stefan Pöhlmann
- Deutsches Primatenzentrum - Leibniz-Institut für Primatenforschung, Abteilung Infektionsbiologie, Kellnerweg 4, D-37077, Göttingen, Germany; Faculty of Biology and Psychology, Georg-August University Göttingen, Wilhelmsplatz 1, D-37073, Göttingen, Germany.
| | - Klaudia Brix
- Constructor University, School of Science, Campus Ring 1, D-28759, Bremen, Germany.
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72
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Kumar P, Zhang X, Shaha R, Kschischo M, Dobbelstein M. Identification of antibody-resistant SARS-CoV-2 mutants via N4-Hydroxycytidine mutagenesis. Antiviral Res 2024; 231:106006. [PMID: 39293594 DOI: 10.1016/j.antiviral.2024.106006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 08/31/2024] [Accepted: 09/12/2024] [Indexed: 09/20/2024]
Abstract
Monoclonal antibodies targeting the Spike protein of SARS-CoV-2 are effective against COVID-19 and might mitigate future pandemics. However, their efficacy is challenged by the emergence of antibody-resistant virus variants. We developed a method to efficiently identify such resistant mutants based on selection from mutagenized virus pools. By inducing mutations with the active compound of Molnupiravir, N4-hydroxycytidine (NHC), and subsequently passaging the virus in the presence of antibodies, we identified specific Spike mutations linked to resistance. Validation of these mutations was conducted using pseudotypes and immunofluorescence analysis. From a Wuhan-like strain of SARS-CoV-2, we identified the following mutations conferring strong resistance towards the corresponding antibodies: Bamlanivimab - E484K, F490S and S494P; Sotrovimab - E340K; Cilgavimab - K444R/E and N450D. From the Omicron B.1.1.529 variant, the strongly selected mutations were: Bebtelovimab - V445A; Sotrovimab - E340K and K356M; Cilgavimab - K444R, V445A and N450D. We also identified escape mutations in the Wuhan-like Spike for the broadly neutralizing antibodies S2K146 - combined G485S and Q493R - and S2H97 - D428G, K462E and S514F. Structural analysis revealed that the selected mutations occurred at antibody-binding residues within the receptor-binding domains of the Spike protein. Most of the selected mutants largely maintained ACE2 binding and infectivity. Notably, many of the identified resistance-conferring mutations are prevalent in real-world SARS-CoV-2 variants, but some of them (G485S, D428G, and K462E) have not yet been observed in circulating strains. Our approach offers a strategy for predicting the therapeutic efficacy of antibodies against emerging virus variants.
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MESH Headings
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/drug effects
- Cytidine/analogs & derivatives
- Cytidine/pharmacology
- Cytidine/genetics
- Humans
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Drug Resistance, Viral/genetics
- Mutation
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Mutagenesis
- COVID-19/virology
- COVID-19/immunology
- Antiviral Agents/pharmacology
- COVID-19 Drug Treatment
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/pharmacology
- Hydroxylamines
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Affiliation(s)
- Priya Kumar
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, 37077, Göttingen, Germany
| | - Xiaoxiao Zhang
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, 53424, Remagen, Germany; Department of Informatics, Technical University of Munich, 81675, Munich, Germany
| | - Rahul Shaha
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences (GZMB), University of Göttingen, 37077, Göttingen, Germany
| | - Maik Kschischo
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, 53424, Remagen, Germany
| | - Matthias Dobbelstein
- Department of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, 37077, Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
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73
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Lee YJ, Easwaran M, Jung YS, Qian Y, Shin HJ. Enhanced Humoral and Cellular Immune Responses Elicited by Adenoviral Delivery of SARS-CoV-2 Receptor-Binding Motif Fused to Human Fc. Vaccines (Basel) 2024; 12:1247. [PMID: 39591150 PMCID: PMC11598816 DOI: 10.3390/vaccines12111247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 10/28/2024] [Accepted: 10/29/2024] [Indexed: 11/28/2024] Open
Abstract
Background/Objectives: The receptor binding motif (RBM) of the SARS-CoV-2 spike protein is critical for viral entry into host cells. Development of a vaccine targeting this region is a promising strategy for COVID-19 prevention. To enhance the immunogenicity of SARS-CoV-2 vaccines, we developed an adenoviral vector expressing the RBM from the SARS-CoV-2 spike protein that fused to the human Fc (hFc) domain. Methods: The recombinant RBM_hFc fusion protein was successfully cloned into the pacAd5CMV-N-pA (pAd5) vector and expressed in HEK293 cells as a ~40 kDa protein. A recombinant adenovirus encoding RBM_hFc was subsequently generated and confirmed by cytopathic effect assay. Results: Western blot analysis verified the expression of RBM_hFc in the adenovirus (AdV). ELISA assays, validated for IgG detection, demonstrated a twofold increase in IgG antibody levels (M-1.090 at 450 nm; SD-±0.326; and 95% CI-0.250 [0.839 to 1.340]) in sera from BALB/c mice immunized with Ad/RBM_hFc, compared to the negative control group. Result suggests a robust humoral immune response induced by the Ad/RBM_hFc vaccine. Moreover, ELISpot assays demonstrated a tenfold increase in IFN-γ -producing cells (M-440 spot-forming cells; SD-±124.976; and 95% CI-75.522 [364.478 to 515.522]) in mice immunized with AdV/RBM_hFc compared to the negative control group. Result proved that AdV/RBM_hFc-stimulated a robust cellular immune response in animal model. Conclusions: Our findings indicate that the RBM_hFc fusion protein enhances both humoral and cellular immune responses. These results suggest the potential of adenoviral vectors carrying RBM_hFc as vaccine candidates. However, comprehensive evaluation of the protective efficacy of these adenoviral vectors will necessitate rigorous experimental studies.
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Affiliation(s)
- Yea-Jin Lee
- Laboratory of Infectious Disease, College of Veterinary Medicine, Research Institute of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon 34134, Republic of Korea;
| | - Maheswaran Easwaran
- Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India;
| | - Yong-Sam Jung
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Foreign Expert Workshop, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (Y.-S.J.); (Y.Q.)
| | - Yingjuan Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Foreign Expert Workshop, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (Y.-S.J.); (Y.Q.)
| | - Hyun-Jin Shin
- Laboratory of Infectious Disease, College of Veterinary Medicine, Research Institute of Veterinary Medicine, Chungnam National University, Yuseong-gu, Daejeon 34134, Republic of Korea;
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74
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Tse AL, Acreman CM, Ricardo-Lax I, Berrigan J, Lasso G, Balogun T, Kearns FL, Casalino L, McClain GL, Chandran AM, Lemeunier C, Amaro RE, Rice CM, Jangra RK, McLellan JS, Chandran K, Miller EH. Distinct pathways for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses. PLoS Pathog 2024; 20:e1012704. [PMID: 39546542 PMCID: PMC11602109 DOI: 10.1371/journal.ppat.1012704] [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: 07/05/2024] [Revised: 11/27/2024] [Accepted: 10/29/2024] [Indexed: 11/17/2024] Open
Abstract
Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014-CoV, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the S1 N-terminal domain, uncovered through the rescue and serial passage of a virus bearing the FPPR substitution, further enhanced spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles' heels that could be targeted with countermeasures.
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Affiliation(s)
- Alexandra L. Tse
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Cory M. Acreman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Inna Ricardo-Lax
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Jacob Berrigan
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Gorka Lasso
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Toheeb Balogun
- Department of Molecular Biology, University of California San Diego, La Jolla, California, United States of America
| | - Fiona L. Kearns
- Department of Molecular Biology, University of California San Diego, La Jolla, California, United States of America
| | - Lorenzo Casalino
- Department of Molecular Biology, University of California San Diego, La Jolla, California, United States of America
| | - Georgia L. McClain
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Amartya Mudry Chandran
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Charlotte Lemeunier
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Rommie E. Amaro
- Department of Molecular Biology, University of California San Diego, La Jolla, California, United States of America
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, United States of America
| | - Rohit K. Jangra
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Present address: Department of Microbiology and Immunology, Louisiana State University Health Sciences Center-Shreveport, Shreveport, Louisiana, United States of America
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Kartik Chandran
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Emily Happy Miller
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
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75
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Lin CH, Yang XR, Lin MW, Chang HJ, Lee CH, Lin CS. Engineering a NanoBiT biosensor for detecting angiotensin-converting enzyme-2 (hACE2) interaction with SARS-CoV-2 spike protein and screening the inhibitors to block hACE2 and spike interaction. Biosens Bioelectron 2024; 263:116630. [PMID: 39102773 DOI: 10.1016/j.bios.2024.116630] [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: 05/21/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is facilitated by its trimeric surface spike protein, which binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. This critical interaction facilitates viral entry and is a primary target for therapeutic intervention against COVID-19. However, it is difficult to fully optimize viral infection using existing protein-protein interaction methods. Herein, we introduce a nano-luciferase binary technology (NanoBiT)-based pseudoviral sensor designed to stimulate the dynamics of viral infection in both living cells and animals. Infection progression can be dynamically visualized via a rapid increase in luminescence within 3 h using an in vivo imaging system (IVIS). Inhibition of viral infection by baicalein and baicalin was evaluated using a NanoBiT-based pseudoviral sensor. These results indicate that the inhibitory efficacy of baicalein was strengthened by targeting the spike protein, whereas baicalin targeted the hACE2 protein. Additionally, under optimized conditions, baicalein and baicalin provided a synergistic combination to inhibit pseudoviral infection. Live bioluminescence imaging was used to evaluate the in vivo effects of baicalein and baicalin treatment on LgBiT-hACE2 mice infected with the BA.2-SmBiT spike pseudovirus. This innovative bioluminescent system functions as a sensitive and early-stage quantitative viral transduction in vitro and in vivo. This platform provides novel opportunities for studying the molecular biology of animal models.
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Affiliation(s)
- Cheng-Han Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Xin-Rui Yang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Meng-Wei Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ho-Ju Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Che-Hsiung Lee
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan; Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan, 333, Taiwan
| | - Chih-Sheng Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan; Center for Intelligent Drug Systems and Smart Bio-devices (IDS(2)B), National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan.
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Pellman J, Goldstein A, Słabicki M. Human E3 ubiquitin ligases: accelerators and brakes for SARS-CoV-2 infection. Biochem Soc Trans 2024; 52:2009-2021. [PMID: 39222407 PMCID: PMC11555711 DOI: 10.1042/bst20230324] [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: 06/06/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
E3 ubiquitin ligases regulate the composition of the proteome. These enzymes mono- or poly-ubiquitinate their substrates, directly altering protein function or targeting proteins for degradation by the proteasome. In this review, we discuss the opposing roles of human E3 ligases as effectors and targets in the evolutionary battle between host and pathogen, specifically in the context of SARS-CoV-2 infection. Through complex effects on transcription, translation, and protein trafficking, human E3 ligases can either attenuate SARS-CoV-2 infection or become vulnerabilities that are exploited by the virus to suppress the host's antiviral defenses. For example, the human E3 ligase RNF185 regulates the stability of SARS-CoV-2 envelope protein through the ubiquitin-proteasome pathway, and depletion of RNF185 significantly increases SARS-CoV-2 viral titer (iScience (2023) 26, 106601). We highlight recent advances that identify functions for numerous human E3 ligases in the SARS-CoV-2 life cycle and we assess their potential as novel antiviral agents.
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Affiliation(s)
- Jesse Pellman
- Broad Institute of MIT and Harvard, Cambridge, MA, U.S.A
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, U.S.A
| | - Anna Goldstein
- Broad Institute of MIT and Harvard, Cambridge, MA, U.S.A
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, U.S.A
| | - Mikołaj Słabicki
- Broad Institute of MIT and Harvard, Cambridge, MA, U.S.A
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, U.S.A
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Boston, MA, U.S.A
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Eldin P, David A, Hirtz C, Battini JL, Briant L. SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome. Int J Mol Sci 2024; 25:11614. [PMID: 39519170 PMCID: PMC11546939 DOI: 10.3390/ijms252111614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 10/25/2024] [Accepted: 10/26/2024] [Indexed: 11/16/2024] Open
Abstract
Codon bias analysis of SARS-CoV-2 reveals suboptimal adaptation for translation in human cells it infects. The detailed examination of the codons preferentially used by SARS-CoV-2 shows a strong preference for LysAAA, GlnCAA, GluGAA, and ArgAGA, which are infrequently used in human genes. In the absence of an adapted tRNA pool, efficient decoding of these codons requires a 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2) modification at the U34 wobble position of the corresponding tRNAs (tLysUUU; tGlnUUG; tGluUUC; tArgUCU). The optimal translation of SARS-CoV-2 open reading frames (ORFs) may therefore require several adjustments to the host's translation machinery, enabling the highly biased viral genome to achieve a more favorable "Ready-to-Translate" state in human cells. Experimental approaches based on LC-MS/MS quantification of tRNA modifications and on alteration of enzymatic tRNA modification pathways provide strong evidence to support the hypothesis that SARS-CoV-2 induces U34 tRNA modifications and relies on these modifications for its lifecycle. The conclusions emphasize the need for future studies on the evolution of SARS-CoV-2 codon bias and its ability to alter the host tRNA pool through the manipulation of RNA modifications.
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Affiliation(s)
- Patrick Eldin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), University of Montpellier, CNRS UMR 9004, 1919 route de Mende, 34293 Montpellier, France
| | - Alexandre David
- Institut de Génomique Fonctionnelle (IGF), INSERM U1191, 141 Rue de la Cardonille, 34000 Montpellier, France
- Institute for Regenerative Medicine and Biotherapy (IRMB)-Plateforme de Protéomique Clinique (PPC), Institut des Neurosciences de Montpellier (INM), University of Montpellier, CHU Montpellier, INSERM CNRS, 298 Rue du Truel, 34090 Montpellier, France
| | - Christophe Hirtz
- Institute for Regenerative Medicine and Biotherapy (IRMB)-Plateforme de Protéomique Clinique (PPC), Institut des Neurosciences de Montpellier (INM), University of Montpellier, CHU Montpellier, INSERM CNRS, 298 Rue du Truel, 34090 Montpellier, France
| | - Jean-Luc Battini
- Institut de Recherche en Infectiologie de Montpellier (IRIM), University of Montpellier, CNRS UMR 9004, 1919 route de Mende, 34293 Montpellier, France
| | - Laurence Briant
- Institut de Recherche en Infectiologie de Montpellier (IRIM), University of Montpellier, CNRS UMR 9004, 1919 route de Mende, 34293 Montpellier, France
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Liu Y, Zhao X, Shi J, Wang Y, Liu H, Hu YF, Hu B, Shuai H, Yuen TTT, Chai Y, Liu F, Gong HR, Li J, Wang X, Jiang S, Zhang X, Zhang Y, Li X, Wang L, Hartnoll M, Zhu T, Hou Y, Huang X, Yoon C, Wang Y, He Y, Zhou M, Du L, Zhang X, Chan WM, Chen LL, Cai JP, Yuan S, Zhou J, Huang JD, Yuen KY, To KKW, Chan JFW, Zhang BZ, Sun L, Wang P, Chu H. Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3. Nat Commun 2024; 15:8728. [PMID: 39379369 PMCID: PMC11461813 DOI: 10.1038/s41467-024-53033-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024] Open
Abstract
SARS-CoV-2 JN.1 with an additional L455S mutation on spike when compared with its parental variant BA.2.86 has outcompeted all earlier variants to become the dominant circulating variant. Recent studies investigated the immune resistance of SARS-CoV-2 JN.1 but additional factors are speculated to contribute to its global dominance, which remain elusive until today. Here, we find that SARS-CoV-2 JN.1 has a higher infectivity than BA.2.86 in differentiated primary human nasal epithelial cells (hNECs). Mechanistically, we demonstrate that the gained infectivity of SARS-CoV-2 JN.1 over BA.2.86 associates with increased entry efficiency conferred by L455S and better spike cleavage in hNECs. Structurally, S455 altered the mode of binding of JN.1 spike protein to ACE2 when compared to BA.2.86 spike at ACE2H34, and modified the internal structure of JN.1 spike protein by increasing the number of hydrogen bonds with neighboring residues. These findings indicate that a single mutation (L455S) enhances virus entry in hNECs and increases immune evasiveness, which contribute to the robust transmissibility of SARS-CoV-2 JN.1. We further evaluate the in vitro and in vivo virological characteristics between SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3, and identify key lineage-specific features of the two Omicron sublineages that contribute to our understanding on Omicron antigenicity, transmissibility, and pathogenicity.
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Affiliation(s)
- Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiaoyu Zhao
- Shanghai Sci-Tech Inno Center for Infection & Immunity, National Medical Center for Infectious Diseases, Huashan Hospital, Institute of Infection and Health, Fudan University, Shanghai, China
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yajie Wang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ye-Fan Hu
- BayVax Biotech Limited, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong, China
| | - Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Feifei Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Hua-Rui Gong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiayan Li
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Xun Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Shujun Jiang
- Department of Infectious Diseases, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiang Zhang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yanliang Zhang
- Department of Infectious Diseases, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiangnan Li
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Lei Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Madeline Hartnoll
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yang Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yixin He
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Minmin Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lianzhao Du
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiaojuan Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lin-Lei Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Materials Innovation Institute for Life Sciences and Energy (MILES), HKU-SIRI, Shenzhen, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou, Hainan Province, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou, Hainan Province, China.
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China.
| | - Bao-Zhong Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Lei Sun
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Pengfei Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
- Materials Innovation Institute for Life Sciences and Energy (MILES), HKU-SIRI, Shenzhen, China.
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Norton TD, Thakur M, Ganguly S, Ali S, Chao J, Waldron A, Xiao J, Patel Y, Turner KC, Davis JD, Irvin SC, Pan C, Atmodjo-Watkins D, Hooper AT, Hamilton JD, Subramaniam D, Bocchini JA, Kowal B, DiCioccio AT, Bhore R, Geba GP, Cox E, Braunstein N, Dakin P, Herman GA. Assessing the safety and pharmacokinetics of casirivimab and imdevimab (CAS+IMD) in a cohort of pregnant outpatients with COVID-19: results from an adaptive, multicentre, randomised, double-blind, phase 1/2/3 study. BMJ Open 2024; 14:e087431. [PMID: 39384241 PMCID: PMC11474922 DOI: 10.1136/bmjopen-2024-087431] [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] [Received: 04/17/2024] [Accepted: 08/19/2024] [Indexed: 10/11/2024] Open
Abstract
OBJECTIVE Pregnant women with COVID-19 are at elevated risk for severe outcomes, but clinical data on management of these patients are limited. Monoclonal antibodies, such as casirivimab plus imdevimab (CAS+IMD), have proven effective in treating non-pregnant adults with COVID-19, prompting further evaluation in pregnant women. METHODS A phase 3 portion of an adaptive, multicentre, randomised, double-blind, placebo-controlled trial evaluated the safety, clinical outcomes, pharmacokinetics and immunogenicity of CAS+IMD (1200 mg or 2400 mg) in the treatment of pregnant outpatients with COVID-19 (NCT04425629). Participants were enrolled between December 2020 and November 2021, prior to the emergence of Omicron-lineage variants against which CAS+IMD is not active. Safety was evaluated in randomised participants who received study drug (n=80); clinical outcomes were evaluated in all randomised participants (n=82). Only two pregnant participants received placebo, limiting conclusions regarding treatment effect. Infants born to pregnant participants were followed for developmental outcomes ≤1 year of age. RESULTS In pregnant participants, CAS+IMD was well tolerated, with no grade ≥2 hypersensitivity or infusion-related reactions reported. There were no participant deaths, and only one COVID-19-related medically attended visit. Although two pregnancies (3%) reported issues in the fetus/neonate, they were confounded by maternal history or considered to be due to an alternate aetiology. No adverse developmental outcomes in infants ≤1 year of age were considered related to in utero exposure to the study drug. CAS+IMD 1200 mg and 2400 mg rapidly and similarly reduced viral loads, with a dose-proportional increase in concentrations of CAS+IMD in serum. Pharmacokinetics were consistent with that reported in the general population. Immunogenicity incidence was low. CONCLUSION CAS+IMD treatment of pregnant outpatients with COVID-19 showed similar safety, clinical outcomes and pharmacokinetic profiles to that observed in non-pregnant adults. There was no evidence of an impact on developmental outcomes in infants ≤1 year of age. TRIAL REGISTRATION NUMBER NCT04425629.
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Affiliation(s)
| | - Mazhar Thakur
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Samit Ganguly
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Shazia Ali
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Jesse Chao
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | | | - Jing Xiao
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Yogesh Patel
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | | | - John D Davis
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Susan C Irvin
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Cynthia Pan
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | | | | | | | | | | | - Bari Kowal
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | | | - Rafia Bhore
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | | | - Edward Cox
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | | | - Paula Dakin
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
| | - Gary A Herman
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
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Oduro-Kwateng E, Soliman ME. DON/DRP-104 as potent serine protease inhibitors implicated in SARS-CoV-2 infection: Comparative binding modes with human TMPRSS2 and novel therapeutic approach. J Cell Biochem 2024; 125:e30528. [PMID: 38284235 DOI: 10.1002/jcb.30528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/31/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Human transmembrane serine protease 2 (TMPRSS2) is an important member of the type 2 transmembrane serine protease (TTSP) family with significant therapeutic markings. The search for potent TMPRSS2 inhibitors against severe acute respiratory syndrome coronavirus 2 infection with favorable tissue specificity and off-site toxicity profiles remains limited. Therefore, probing the anti-TMPRSS2 potential of enhanced drug delivery systems, such as nanotechnology and prodrug systems, has become compelling. We report the first in silico study of TMPRSS2 against a prodrug, [isopropyl(S)-2-((S)-2-acetamido-3-(1H-indol-3-yl)-propanamido)-6-diazo-5-oxo-hexanoate] also known as DRP-104 synthesized from 6-Diazo-5-oxo-l-norleucine (DON). We performed comparative studies on DON and DRP-104 against a clinically potent TMPRSS2 inhibitor, nafamostat, and a standard serine protease inhibitor, 4-(2-Aminoethyl) benzenesulfonyl fluoride (AEBSF) against TMPRSS2 and found improved TMPRSS2 inhibition through synergistic binding of the S1/S1' subdomains. Both DON and DRP-104 had better thermodynamic profiles than AEBSF and nafamostat. DON was found to confer structural stability with strong positive correlated inter-residue motions, whereas DRP-104 was found to confer kinetic stability with restricted residue displacements and reduced loop flexibility. Interestingly, the Scavenger Receptor Cysteine-Rich (SRCR) domain of TMPRSS2 may be involved in its inhibition mechanics. Two previously unidentified loops, designated X (270-275) and Y (293-296) underwent minimal and major structural transitions, respectively. In addition, residues 273-277 consistently transitioned to a turn conformation in all ligated systems, whereas unique transitions were identified for other transitioning residue groups in each TMPRSS2-inhibitor complex. Intriguingly, while both DON and DRP-104 showed similar loop transition patterns, DRP-104 preserved loop structural integrity. As evident from our systematic comparative study using experimentally/clinically validated inhibitors, DRP-104 may serve as a potent and novel TMPRSS2 inhibitor and warrants further clinical investigation.
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Affiliation(s)
- Ernest Oduro-Kwateng
- School of Health Sciences, Molecular Bio-Computation and Drug Design Research Group, Westville Campus, University of KwaZulu Natal, Durban, South Africa
| | - Mahmoud E Soliman
- School of Health Sciences, Molecular Bio-Computation and Drug Design Research Group, Westville Campus, University of KwaZulu Natal, Durban, South Africa
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Peña-Bates C, Lascurain R, Ortiz-Navarrete V, Chavez-Galan L. The BCG vaccine and SARS-CoV-2: Could there be a beneficial relationship? Heliyon 2024; 10:e38085. [PMID: 39347386 PMCID: PMC11437859 DOI: 10.1016/j.heliyon.2024.e38085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 09/17/2024] [Accepted: 09/17/2024] [Indexed: 10/01/2024] Open
Abstract
The COVID-19 disease continues to cause complications and deaths worldwide. Identifying effective immune protection strategies remains crucial to address this ongoing challenge. The Bacillus Calmette-Guérin (BCG) vaccine, developed initially to prevent pulmonary tuberculosis, has gained relevance due to its ability to induce cross-protection against other pathogens of the airways. This review summarizes research on the immunological protection provided by BCG, along with its primary clinical and therapeutic uses. It also explores the immunological features of COVID-19, the mechanisms implicated in host cell death, and its association with chronic pulmonary illnesses such as tuberculosis, which has led to complications in diagnosis and management. While vaccines against COVID-19 have been administered globally, uncertainty still exists about its effectiveness. Additionally, it is uncertain whether the utilization of BCG can regulate the immune response to pathogens such as SARS-CoV-2.
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Affiliation(s)
- Carlos Peña-Bates
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
| | - Ricardo Lascurain
- Unidad de Enlace Científico, Faculty of Medicine, Universidad Nacional Autónoma de México en el Instituto Nacional de Medicina Genómica, Mexico City, 14610, Mexico
| | - Vianney Ortiz-Navarrete
- Department of Molecular Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Leslie Chavez-Galan
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico
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Sakurai Y, Okada S, Ozeki T, Yoshikawa R, Kinoshita T, Yasuda J. SARS-CoV-2 Omicron subvariants progressively adapt to human cells with altered host cell entry. mSphere 2024; 9:e0033824. [PMID: 39191389 PMCID: PMC11423564 DOI: 10.1128/msphere.00338-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant exhibits high transmissibility with a strong immune escape ability and causes frequent large-scale global infections by producing predominant subvariants. Here, using human upper/lower airway and intestinal cells, we examined the previously dominant BA.1-BA.5 and BA.2.75 subvariants, together with the recently emerged XBB/BQ lineages, in comparison to the former Delta variant. We observed a tendency for each virus to demonstrate higher growth capability than the previously dominant subvariants. Unlike human bronchial and intestinal cells, nasal epithelial cells accommodated the efficient entry of certain Omicron subvariants, similar to the Delta variant. In contrast to the Delta's reliance on cell-surface transmembrane protease serine 2, all tested Omicron variants depended on endosomal cathepsin L. Moreover, S1/S2 cleavage of early Omicron spikes was less efficient, whereas recent viruses exhibit improved cleavage efficacy. Our results show that the Omicron variant progressively adapts to human cells through continuous endosome-mediated host cell entry.IMPORTANCESARS-CoV-2, the causative agent of coronavirus disease 2019, has evolved into a number of variants/subvariants, which have generated multiple global waves of infection. In order to monitor/predict virological features of emerging variants and determine appropriate strategies for anti-viral development, understanding conserved or altered features of evolving SARS-CoV-2 is important. In this study, we addressed previously or recently predominant Omicron subvariants and demonstrated the gradual adaptation to human cells. The host cell entry route, which was altered from the former Delta variant, was conserved among all tested Omicron subvariants. Collectively, this study revealed both changing and maintained features of SARS-CoV-2 during the Omicron variant evolution.
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Affiliation(s)
- Yasuteru Sakurai
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Sayaka Okada
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Takehiro Ozeki
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Rokusuke Yoshikawa
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Takaaki Kinoshita
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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Hsu JC, Saenkham-Huntsinger P, Huang P, Octaviani CP, Drelich AK, Peng BH, Tseng CTK. Characterizing neuroinvasion and neuropathology of SARS-CoV-2 by using AC70 human ACE2 transgenic mice. Front Microbiol 2024; 15:1455462. [PMID: 39380676 PMCID: PMC11458418 DOI: 10.3389/fmicb.2024.1455462] [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: 06/26/2024] [Accepted: 09/13/2024] [Indexed: 10/10/2024] Open
Abstract
COVID-19 presents with a plethora of neurological signs and symptoms despite being characterized as a respiratory disease, including seizures, anxiety, depression, amnesia, attention deficits, and alterations in consciousness. The olfactory nerve is widely accepted as the neuroinvasive route by which the etiological agent SARS-CoV-2 enters the brain, but the trigeminal nerve is an often-overlooked additional route. Based on this consensus, we initially conducted a pilot experiment investigating the olfactory nerve route of SARS-CoV-2 neuroinvasion via intranasal inoculation in AC70 human ACE2 transgenic mice. Notably, we found that the trigeminal ganglion is an early and highly efficient site of viral replication, which then rapidly spread widely throughout the brain where neurons were primarily targeted. Despite the extensive viral infection across the brain, obvious evidence of tissue pathology including inflammatory infiltration, glial activation, and apoptotic cell deaths were not consistently observed, albeit inflammatory cytokines were significantly induced. However, the expression levels of different genes related to neuronal function, including the neurotransmitter dopamine pathway as well as synaptic function, and markers of neuronal damage were altered as compared to mock-infected mice. Our findings suggest that the trigeminal nerve may serve as a neuroinvasive route complementary to the olfactory nerve and that the ensuing neuroinvasion presented a unique neuropathological profile. This study provides insights into potential neuropathogenic mechanisms utilized by coronaviruses.
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Affiliation(s)
- Jason C. Hsu
- Department of Biochemistry, Cell & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Panatda Saenkham-Huntsinger
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Pinghan Huang
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Cassio Pontes Octaviani
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Aleksandra K. Drelich
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX, United States
| | - Bi-Hung Peng
- Department of Neuroscience, Cell Biology, & Anatomy, The University of Texas Medical Branch, Galveston, TX, United States
| | - Chien-Te K. Tseng
- Department of Biochemistry, Cell & Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX, United States
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, United States
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84
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Domanska-Blicharz K, Lisowska A, Opolska J, Ruszkowski JJ, Gogulski M, Pomorska-Mól M. Whole genome characteristics of hedgehog coronaviruses from Poland and analysis of the evolution of the Spike protein for its interspecies transmission potential. BMC Vet Res 2024; 20:424. [PMID: 39304831 PMCID: PMC11415979 DOI: 10.1186/s12917-024-04277-4] [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: 05/21/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND The hedgehogs have been recently identified as possible reservoir of Middle East respiratory syndrome coronavirus like (MERS-CoV-like). These viruses were classified as a distinct Betacoronavirus erinacei (BCoV-Eri) species within the MerBCoV-Eriirus subgenus. As coronaviruses are known for their ability to jump between different hosts, including humans, this can pose a particular threat to people in direct contact with hedgehogs, such as those working at animal asylums. Our previous studies have shown the presence of BCoV-Eri strains in animals collected in the wildlife rehabilitation centre. This study aimed to investigate the presence of CoV in subsequent hedgehogs collected from the urban area of Poland and their molecular characteristics. RESULTS Monitoring for the presence of coronavirus infection in hedgehogs revealed five positive individuals. The presence of BCoV-Eri was found in a total of 20% of animals tested. Our analyses revealed no correlation between CoVs positivity and animal health conditions but a higher probability of such infection in juveniles and females. The whole genome of two Polish Hedgehog coronavirus 1 strains were sequenced and compared with available counterparts from European and Asian countries. Phylogenetic analysis showed that both CoV strains formed common cluster with other similar MerBCoV-Eriirus, but they were also found to be genetically variable and most changes in the S protein were identified. Our analysis revealed that some S protein sites of the Hedgehog coronavirus 1 strains evolved under positive selection pressure and of five such sites, three are in the S1 region while the other two in the S2 region of the Spike. CONCLUSIONS BCoV-Eri is to some extent prevalent in wildlife asylums in Poland. Given that the S protein of BCoVs-Eri is highly variable and that some sites of this protein evolve under positive selection pressure, these strains could potentially acquire a favourable feature for cross-species transmission. Consequently, the threat to humans working in such asylums is particularly high. Adequate biosecurity safeguards, but also human awareness of such risks, are therefore essential.
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Affiliation(s)
- Katarzyna Domanska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland.
| | - Anna Lisowska
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland
| | - Justyna Opolska
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland
| | - Jakub J Ruszkowski
- Department of Animal Anatomy, University of Life Sciences in Poznań, ul. Wojska Polskiego 71C, Poznań, 60-625, Poland
- University Centre for Veterinary Medicine, University of Life Sciences in Poznań, Szydłowska 43, Poznań, 60-656, Poland
| | - Maciej Gogulski
- Department of Animal Anatomy, University of Life Sciences in Poznań, ul. Wojska Polskiego 71C, Poznań, 60-625, Poland
- University Centre for Veterinary Medicine, University of Life Sciences in Poznań, Szydłowska 43, Poznań, 60-656, Poland
| | - Małgorzata Pomorska-Mól
- Department of Preclinical Sciences and Infectious Diseases, University of Life Sciences in Poznań, ul. Wołyńska 35, Poznań, 60-637, Poland
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Sarkar M, Madabhavi I. COVID-19 mutations: An overview. World J Methodol 2024; 14:89761. [PMID: 39310238 PMCID: PMC11230071 DOI: 10.5662/wjm.v14.i3.89761] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 06/25/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) belongs to the genus Beta coronavirus and the family of Coronaviridae. It is a positive-sense, non-segmented single-strand RNA virus. Four common types of human coronaviruses circulate globally, particularly in the fall and winter seasons. They are responsible for 10%-30% of all mild upper respiratory tract infections in adults. These are 229E, NL63 of the Alfacoronaviridae family, OC43, and HKU1 of the Betacoronaviridae family. However, there are three highly pathogenic human coronaviruses: SARS-CoV-2, Middle East respiratory syndrome coronavirus, and the latest pandemic caused by the SARS-CoV-2 infection. All viruses, including SARS-CoV-2, have the inherent tendency to evolve. SARS-CoV-2 is still evolving in humans. Additionally, due to the development of herd immunity, prior infection, use of medication, vaccination, and antibodies, the viruses are facing immune pressure. During the replication process and due to immune pressure, the virus may undergo mutations. Several SARS-CoV-2 variants, including the variants of concern (VOCs), such as B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617/B.1.617.2 (Delta), P.1 (Gamma), and B.1.1.529 (Omicron) have been reported from various parts of the world. These VOCs contain several important mutations; some of them are on the spike proteins. These mutations may lead to enhanced infectivity, transmissibility, and decreased neutralization efficacy by monoclonal antibodies, convalescent sera, or vaccines. Mutations may also lead to a failure of detection by molecular diagnostic tests, leading to a delayed diagnosis, increased community spread, and delayed treatment. We searched PubMed, EMBASE, Covariant, the Stanford variant Database, and the CINAHL from December 2019 to February 2023 using the following search terms: VOC, SARS-CoV-2, Omicron, mutations in SARS-CoV-2, etc. This review discusses the various mutations and their impact on infectivity, transmissibility, and neutralization efficacy.
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Affiliation(s)
- Malay Sarkar
- Department of Pulmonary Medicine, Indira Gandhi Medical College, Shimla 171001, Himachal Pradesh, India
| | - Irappa Madabhavi
- Department of Medical and Pediatric Oncology and Hematology, J N Medical College, and KAHER, Belagavi, Karnataka 590010, India
- Department of Medical and Pediatric Oncology and Hematology, Kerudi Cancer Hospital, Bagalkot, Karnataka 587103, India
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86
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Assylbekova A, Allayarova M, Konysbekova M, Bekturgan A, Makhanova A, Brown S, Grzegorzek N, Kalbacher H, Kalendar R, Burster T. The Proteolytic Activity of Neutrophil-Derived Serine Proteases Bound to the Cell Surface Arming Lung Epithelial Cells for Viral Defense. Molecules 2024; 29:4449. [PMID: 39339444 PMCID: PMC11434079 DOI: 10.3390/molecules29184449] [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: 07/31/2024] [Revised: 09/12/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
The collaboration between cellular proteases and host cells is pivotal in mounting an effective innate immune defense. Of particular interest is the synergistic interaction between cathepsin G (CatG) and neutrophil elastase (NE), which are proteases secreted by activated neutrophils, and the human alveolar basal epithelial cell line (A549) and the human lung epithelial-like cell line (H1299), because of the potential implications for viral infection. Our study aimed to investigate the binding capacity of CatG and NE on the surface of A549 and H1299 cells through preincubation with purified CatG and NE; thereby, the proteolytic activity could be detected using activity-based probes. Both CatG and NE were capable of binding to the cell surface and exhibited proteolytic activity, leading to increased cell surface levels of MHC I molecules, which is crucial for displaying the endogenous antigenic repertoire. In addition, CatG cleaved the S2' site of the SARS-CoV-2 spike protein at two specific sites (815RS816 and 817FI818) as well as NE (813SK814 and 818IE819), which potentially leads to the destruction of the fusion peptide. Additionally, furin required the presence of Ca2+ ions for the distinct cleavage site necessary to generate the fusion peptide. Overall, the findings suggest that CatG and NE can fortify target cells against viral entry, underscoring the potential significance of cell surface proteases in protecting against viral invasion.
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Affiliation(s)
- Akmaral Assylbekova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Kabanbay Batyr Ave. 53, Astana 010000, Kazakhstan (M.K.); (A.B.); (A.M.)
| | - Maiya Allayarova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Kabanbay Batyr Ave. 53, Astana 010000, Kazakhstan (M.K.); (A.B.); (A.M.)
| | - Moldir Konysbekova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Kabanbay Batyr Ave. 53, Astana 010000, Kazakhstan (M.K.); (A.B.); (A.M.)
| | - Amanbek Bekturgan
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Kabanbay Batyr Ave. 53, Astana 010000, Kazakhstan (M.K.); (A.B.); (A.M.)
| | - Aiya Makhanova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Kabanbay Batyr Ave. 53, Astana 010000, Kazakhstan (M.K.); (A.B.); (A.M.)
| | - Samantha Brown
- Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, 72076 Tübingen, Germany
| | - Norbert Grzegorzek
- Mass Spectrometry Facility, Organic Chemistry, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Hubert Kalbacher
- Institute of Clinical Anatomy and Cell Analysis, University Hospital Tübingen, Eberhard Karls University Tübingen, Österbergstraße 3, 72074 Tübingen, Germany
| | - Ruslan Kalendar
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Kabanbay Batyr Ave. 53, Astana 010000, Kazakhstan;
| | - Timo Burster
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Kabanbay Batyr Ave. 53, Astana 010000, Kazakhstan (M.K.); (A.B.); (A.M.)
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87
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Granatir S, Acosta FM, Pantoja C, Tailor J, Fuori A, Dower B, Marr H, Ramirez PW. Electromagnetic waves destabilize the SARS-CoV-2 Spike protein and reduce SARS-CoV-2 Virus-Like Particle (SC2-VLP) infectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612487. [PMID: 39314332 PMCID: PMC11418983 DOI: 10.1101/2024.09.11.612487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Infection and transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to pose a global public health concern. Using electromagnetic waves represents an alternative strategy to inactivate pathogenic viruses such as SARS-CoV-2 and reduce overall transmission. However, whether electromagnetic waves reduce SARS-CoV-2 infectivity is unclear. Here, we adapted a coplanar waveguide (CPW) to identify electromagnetic waves that could neutralize SARS-CoV-2 virus-like particles (SC2-VLPs). Treatment of SC2-VLPs, particularly at frequencies between 2.5-3.5 GHz at an electric field of 400 V/m for 2 minutes, reduced infectivity. Exposure to a frequency of 3.1 GHz decreased the binding of SC2-VLPs to antibodies directed against the Spike S1 subunit receptor binding domain (RBD). These results suggest that electromagnetic waves alter the conformation of Spike, thereby reducing viral attachment to host cell receptors. Overall, this data provides proof-of-concept in using electromagnetic waves for sanitation and prevention efforts to curb the transmission of SARS-CoV-2 and potentially other pathogenic enveloped viruses.
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Affiliation(s)
| | - Francisco M. Acosta
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA
| | - Christina Pantoja
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA
| | - Johann Tailor
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA
| | - Angus Fuori
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA
| | | | | | - Peter W. Ramirez
- Department of Biological Sciences, California State University Long Beach, Long Beach, CA
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88
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Cone AS, Zhou Y, McNamara RP, Eason AB, Arias GF, Landis JT, Shifflett KW, Chambers MG, Yuan R, Willcox S, Griffith JD, Dittmer DP. CD81 fusion alters SARS-CoV-2 Spike trafficking. mBio 2024; 15:e0192224. [PMID: 39140770 PMCID: PMC11389398 DOI: 10.1128/mbio.01922-24] [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: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic caused the biggest public health crises in recent history. Many expect future coronavirus introductions into the human population. Hence, it is essential to understand the basic biology of these viruses. In natural infection, the SARS-CoV-2 Spike (S) glycoprotein is co-expressed with all other viral proteins, which modify cellular compartments to maximize virion assembly. By comparison, most of S is degraded when the protein is expressed in isolation, as in current molecular vaccines. To probe the maturation pathway of S, we redirected its maturation by fusing S to the tetraspanin protein CD81. CD81 is a defining constituent of extracellular vesicles (EVs) or exosomes. EVs are generated in large numbers by all cells, extruded into blood and lymph, and transfer cargo between cells and systemically (estimated 1012 EVs per mL plasma). EVs, like platelets, can be transfused between unrelated donors. When fusing the proline-stabilized form of strain Delta S into the flexible, large extracellular loop of CD81 rather than being degraded in the lysosome, S was extruded into EVs. CD81-S fusion containing EVs were produced in large numbers and could be isolated to high purity. Purified CD81::S EVs bound ACE2, and S displayed on individual EV was observed by cryogenic electron microscopy (EM). The CD81::S-fusion EVs were non-toxic and elicited an anti-S trimer and anti-RBD antibody response in mice. This report shows a design path to maximize viral glycoprotein assembly and release without relying on the co-expression of potentially pathogenic nonstructural viral proteins. IMPORTANCE The severe acute respiratory syndrome coronavirus 2 pandemic caused the biggest public health crises in recent history. To understand the maturation pathway of S, we fused S to the tetraspanin protein CD81. The resulting molecule is secreted in extracellular vesicles and induces antibodies in mice. This may be a general design path for viral glycoprotein vaccines.
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Affiliation(s)
- Allaura S. Cone
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yijun Zhou
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ryan P. McNamara
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Anthony. B. Eason
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gabriel F. Arias
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin T. Landis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kyle W. Shifflett
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meredith G. Chambers
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Runjie Yuan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P. Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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89
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Singh P, Pahari P, Mukherjee S, Karmakar S, Hoffmann M, Mandal T, Das DK. SARS-CoV-2 spike fusion peptide trans interaction with phosphatidylserine lipid triggers membrane fusion for viral entry. mBio 2024; 15:e0107724. [PMID: 39115315 PMCID: PMC11389415 DOI: 10.1128/mbio.01077-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/30/2024] [Indexed: 09/12/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the fusion machine for host cell entry. Still, the mechanism by which spike protein interacts with the target lipid membrane to facilitate membrane fusion during entry is not fully understood. Here, using steady-state membrane fusion and single-molecule fluorescence resonance energy transfer imaging of spike trimers on the surface of SARS-CoV-2 pseudovirion, we directly show that spike protein interacts with phosphatidylserine (PS) lipid in the target membrane for mediating fusion. We observed that the fusion peptide of the spike S2 domain interacts with the PS lipid of the target membrane. Low pH and Ca2+ trigger the spike conformational change and bring fusion peptide in close proximity to the PS lipid of the membrane. The binding of the spike with PS lipid of its viral membrane (cis interaction) impedes the fusion activation. PS on the target membrane promotes spike binding via trans interaction, prevents the cis interaction, and accelerates fusion. Sequestering or absence of PS lipid abrogates the spike-mediated fusion process and restricts SARS-CoV-2 infectivity. We found that PS-dependent interaction for fusion is conserved across all the SARS-CoV-2 spike variants of concern (D614G, Alpha, Beta, Delta, and Omicron). Our study suggests that PS lipid is indispensable for SARS-CoV-2 spike-mediated virus and target membrane fusion for entry, and restricting PS interaction with spike inhibits the SARS-CoV-2 spike-mediated entry. Therefore, PS is an important cofactor and acts as a molecular beacon in the target membrane for SARS-CoV-2 entry. IMPORTANCE The role of lipids in the host cell target membrane for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is not clear. We do not know whether SARS-CoV-2 spike protein has any specificity in terms of lipid for membrane fusion reaction. Here, using in vitro reconstitution of membrane fusion assay and single-molecule fluorescence resonance energy transfer imaging of SARS-CoV-2 spike trimers on the surface of the virion, we have demonstrated that phosphatidylserine (PS) lipid plays a key role in SARS-CoV-2 spike-mediated membrane fusion reaction for entry. Membrane-externalized PS lipid strongly promotes spike-mediated membrane fusion and COVID-19 infection. Blocking externalized PS lipid with PS-binding protein or in the absence of PS, SARS-CoV-2 spike-mediated fusion is strongly inhibited. Therefore, PS is an important target for restricting viral entry and intervening spike, and PS interaction presents new targets for COVID-19 interventions.
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Affiliation(s)
- Puspangana Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Purba Pahari
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Srija Mukherjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Sharmistha Karmakar
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, USA
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center—Leibniz Institute for Primate Research, Göttingen, Germany
- Faculty of Biology and Psychology, Georg August University, Göttingen, Germany
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Dibyendu Kumar Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
- Center for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
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90
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So-Osman C, Burnouf T, Al-Riyami AZ, Bloch EM, Estcourt L, Goel R, Tiberghien P, Vermeulen M, Wendel S, Wood EM. The role of convalescent plasma and hyperimmune immunoglobulins in the COVID-19 pandemic, including implications for future preparedness. Front Immunol 2024; 15:1448720. [PMID: 39315108 PMCID: PMC11416983 DOI: 10.3389/fimmu.2024.1448720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/21/2024] [Indexed: 09/25/2024] Open
Abstract
Introduction When Coronavirus Disease-19 (COVID-19) struck the world in December 2019, initiatives started to investigate the efficacy of convalescent plasma, a readily available source of passive antibodies, collected from recovered patients as a therapeutic option. This was based on historical observational data from previous virus outbreaks. Methods A scoping review was conducted on the efficacy and safety of convalescent plasma and hyperimmune immunoglobulins for COVID-19 treatment. This review included the latest Cochrane systematic review update on 30-day mortality and safety. We also covered use in pediatric and immunocompromised patients, as well as the logistic challenges faced in donor recruitment and plasma collection in general. Challenges for low resource countries were specifically highlighted. Results A major challenge is the high donation frequency required from first-time donors to ensure a safe product, which minimizes the risk of transfusion-transmitted infectious. This is particularly difficult in low- and middle- income countries due to inadequate infrastructure and insufficient blood product supplies. High-certainty evidence indicates that convalescent plasma does not reduce mortality or significantly improve clinical outcomes in patients with moderate to severe COVID-19 infection. However, CCP may provide a viable treatment for patients unable to mount an endogenous immune response to SARS-CoV-2, based on mostly observational studies and subgroup data of published and ongoing randomized trials. Convalescent plasma has been shown to be safe in adults and children with COVID-19 infection. However, the efficacy in pediatric patients remains unclear. Discussion Data on efficacy and safety of CCP are still underway in ongoing (randomized) studies and by reporting the challenges, limitations and successes encountered to-date, research gaps were identified to be addressed for the future. Conclusion This experience serves as a valuable example for future pandemic preparedness, particularly when therapeutic options are limited, and vaccines are either being developed or ineffective due to underlying immunosuppression.
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Affiliation(s)
- Cynthia So-Osman
- Department Transfusion Medicine, Division Blood Bank, Sanquin Blood Supply Foundation, Amsterdam, Netherlands
- Department Hematology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Thierry Burnouf
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
- International PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan
| | - Arwa Z. Al-Riyami
- Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Evan M. Bloch
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lise Estcourt
- Radcliffe Department of Medicine, University of Oxford and National Health Service (NHS) Blood and Transplant, Oxford, United Kingdom
| | - Ruchika Goel
- Division of Hematology/Oncology, Simmons Cancer Institute at Southern Illinois University (SIU) School of Medicine, Springfield, IL, United States
- Dept Corporate Medical Affairs, Vitalant Corporate Medical Affairs, Scottsdale, AZ, United States
| | - Pierre Tiberghien
- Etablissement Français du Sang, La Plaine-St-Denis and Université de Franche-Comté, Besançon, France
| | - Marion Vermeulen
- Department of Transfusion Medicine and Technical Services, The South African National Blood Service, Roodepoort, South Africa
| | - Silvano Wendel
- Dept Transfusion Medicine, Hospital Sírio-Libanês Blood Bank, São Paulo, Brazil
| | - Erica M. Wood
- Transfusion Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
- Department of Clinical Haematology, Monash Health, Melbourne, VIC, Australia
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91
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DeBarros K, Khan M, Coleman M, Bond VC, Floyd V, Gbodossou E, Diop A, Krumpe LRH, O’Keefe BR, Powell MD. MoMo30 Binds to SARS-CoV-2 Spike Variants and Blocks Infection by SARS-CoV-2 Pseudovirus. Viruses 2024; 16:1433. [PMID: 39339909 PMCID: PMC11437407 DOI: 10.3390/v16091433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
MoMo30 is an antiviral protein isolated from aqueous extracts of Momordica balsamina L. (Senegalese bitter melon). Previously, we demonstrated MoMo30's antiviral activity against HIV-1. Here, we explore whether MoMo30 has antiviral activity against the COVID-19 virus, SARS-CoV-2. MLV particles pseudotyped with the SARS-CoV-2 Spike glycoprotein and a Luciferase reporter gene (SARS2-PsV) were developed from a three-way co-transfection of HEK293-T17 cells. MoMo30's inhibition of SARS2-PsV infection was measured using a luciferase assay and its cytotoxicity using an XTT assay. Additionally, MoMo30's interactions with the variants and domains of Spike were determined by ELISA. We show that MoMo30 inhibits SARS2-PsV infection. We also report evidence of the direct interaction of MoMo30 and SARS-CoV-2 Spike from WH-1, Alpha, Delta, and Omicron variants. Furthermore, MoMo30 interacts with both the S1 and S2 domains of Spike but not the receptor binding domain (RBD), suggesting that MoMo30 inhibits SARS-CoV-2 infection by inhibiting fusion of the virus and the host cell via interactions with Spike.
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Affiliation(s)
- Kenya DeBarros
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA; (K.D.); (M.K.); (M.C.); (V.C.B.)
| | - Mahfuz Khan
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA; (K.D.); (M.K.); (M.C.); (V.C.B.)
| | - Morgan Coleman
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA; (K.D.); (M.K.); (M.C.); (V.C.B.)
| | - Vincent C. Bond
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA; (K.D.); (M.K.); (M.C.); (V.C.B.)
| | - Virginia Floyd
- Department of Community Health and Preventive Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA;
| | | | - Amad Diop
- Malango Traditional Healers Association, Fatick BP 1763, Senegal;
| | - Lauren R. H. Krumpe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA; (L.R.H.K.); (B.R.O.)
| | - Barry R. O’Keefe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA; (L.R.H.K.); (B.R.O.)
- Natural Products Branch, Developmental Therapeutic Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, MD 21702, USA
| | - Michael D. Powell
- Department of Microbiology, Biochemistry and Immunology, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310, USA; (K.D.); (M.K.); (M.C.); (V.C.B.)
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92
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Porebski B, Christ W, Corman A, Haraldsson M, Barz M, Lidemalm L, Häggblad M, Ilmain J, Wright SC, Murga M, Schlegel J, Jarvius M, Lapins M, Sezgin E, Bhabha G, Lauschke VM, Carreras-Puigvert J, Lafarga M, Klingström J, Hühn D, Fernandez-Capetillo O. Discovery of a novel inhibitor of macropinocytosis with antiviral activity. Mol Ther 2024; 32:3012-3024. [PMID: 38956870 PMCID: PMC11403221 DOI: 10.1016/j.ymthe.2024.06.038] [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: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024] Open
Abstract
Several viruses hijack various forms of endocytosis in order to infect host cells. Here, we report the discovery of a molecule with antiviral properties that we named virapinib, which limits viral entry by macropinocytosis. The identification of virapinib derives from a chemical screen using high-throughput microscopy, where we identified chemical entities capable of preventing infection with a pseudotype virus expressing the spike (S) protein from SARS-CoV-2. Subsequent experiments confirmed the capacity of virapinib to inhibit infection by SARS-CoV-2, as well as by additional viruses, such as mpox virus and TBEV. Mechanistic analyses revealed that the compound inhibited macropinocytosis, limiting this entry route for the viruses. Importantly, virapinib has no significant toxicity to host cells. In summary, we present the discovery of a molecule that inhibits macropinocytosis, thereby limiting the infectivity of viruses that use this entry route such as SARS-CoV2.
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Affiliation(s)
- Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Wanda Christ
- Center of Infectious Medicine, Department of Medicine, Karolinska Institutet, 141-86 Huddinge, Sweden
| | - Alba Corman
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Myriam Barz
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Louise Lidemalm
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Maria Häggblad
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Juliana Ilmain
- Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Shane C Wright
- Department of Physiology and Pharmacology, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Matilde Murga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Jan Schlegel
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Malin Jarvius
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Maris Lapins
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Gira Bhabha
- Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, S-171 77 Stockholm, Sweden; Margarete Fischer-Bosch Institute of Clinical Pharmacology, D-70376 Stuttgart, Germany; University of Tuebingen, 72074 Tuebingen, Germany
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden; Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE-751 24 Uppsala, Sweden
| | - Miguel Lafarga
- Departament of Anatomy and Cellular Biology, Neurodegenerative Diseases Network (CIBERNED), University of Cantabria-IDIVAL, 39011 Santander, Spain
| | - Jonas Klingström
- Center of Infectious Medicine, Department of Medicine, Karolinska Institutet, 141-86 Huddinge, Sweden; Department of Biomedical and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden
| | - Daniela Hühn
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden; Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
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93
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Jaganathan R, Kumaradhas P. Structural insights into Furin enzyme inhibition to block SARS-CoV-2 spike protein cleavage: an in-silico approach. 3 Biotech 2024; 14:213. [PMID: 39193012 PMCID: PMC11345345 DOI: 10.1007/s13205-024-04054-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024] Open
Abstract
This study investigates the binding affinity and interactions of the Furin enzyme with two inhibitors, Naphthofluorescein and decanoyl-RVKR-chloromethylketone (CMK), using molecular docking and molecular dynamics (MD) simulations. Molecular docking results showed binding affinities of - 9.18 kcal/mol for CMK and - 5.39 kcal/mol for Naphthofluorescein. To further understand the stability and conformational changes of these complexes, MD simulations were performed. Despite CMK's favorable docking score, MD simulations revealed that its binding interactions at the Furin-active site were unstable, with significant changes observed during the simulation. In contrast, Naphthofluorescein maintained strong and stable interactions throughout the MD simulation, as confirmed by RMSD and RMSF analyses. The binding-free-energy analysis also supported the stability of Naphthofluorescein. These findings indicate that Naphthofluorescein exhibits greater stability and binding affinity as a Furin inhibitor compared to CMK. The results of this in-silico study suggest that Naphthofluorescein, along with CMK, holds the potential for repurposing as a treatment for COVID-19, subject to further validation through clinical studies.
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Affiliation(s)
- Ramakrishnan Jaganathan
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, Tamil Nadu 602 105 India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem, 636 011 India
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94
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Bestle D, Bittel L, Werner AD, Kämper L, Dolnik O, Krähling V, Steinmetzer T, Böttcher-Friebertshäuser E. Novel proteolytic activation of Ebolavirus glycoprotein GP by TMPRSS2 and cathepsin L at an uncharted position can compensate for furin cleavage. Virus Res 2024; 347:199430. [PMID: 38964470 PMCID: PMC11294727 DOI: 10.1016/j.virusres.2024.199430] [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: 03/19/2024] [Revised: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
A multistep priming process involving furin and endosomal cathepsin B and L (CatB/L) has been described for the Orthoebolavirus zairense (EBOV) glycoprotein GP. Inhibition or knockdown of either furin or endosomal cathepsins, however, did not prevent virus multiplication in cell cultures. Moreover, an EBOV mutant lacking the furin cleavage motif (RRTRR→AGTAA) was able to replicate and cause fatal disease in nonhuman primates, indicating that furin cleavage may be dispensable for virus infectivity. Here, by using protease inhibitors and EBOV GP-carrying recombinant vesicular stomatitis virus (VSV) and transcription and replication-competent virus-like particles (trVLPs) we found that processing of EBOV GP is mediated by different proteases in different cell lines depending on the protease repertoire available. Endosomal cathepsins were essential for EBOV GP entry in Huh-7 but not in Vero cells, in which trypsin-like proteases and stably expressed trypsin-like transmembrane serine protease 2 (TMPRSS2) supported wild-type EBOV GP and EBOV GP_AGTAA mutant entry. Furthermore, we show that the EBOV GP_AGTAA mutant is cleaved into fusion-competent GP2 by TMPRSS2 and by CatL at a so far unknown site. Fluorescence microscopy co-localization studies indicate that EBOV GP cleavage by TMPRSS2 may occur in the TGN prior to virus release or in the late endosome at the stage of virus entry into a new cell. Our data show that EBOV GP must be proteolytically activated to support virus entry but has even greater flexibility in terms of proteases and the precise cleavage site than previously assumed.
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Affiliation(s)
- Dorothea Bestle
- Institute of Virology, Philipps-University, Marburg, Germany
| | - Linda Bittel
- Institute of Virology, Philipps-University, Marburg, Germany
| | | | - Lennart Kämper
- Institute of Virology, Philipps-University, Marburg, Germany
| | - Olga Dolnik
- Institute of Virology, Philipps-University, Marburg, Germany
| | - Verena Krähling
- Institute of Virology, Philipps-University, Marburg, Germany; German Center for Infection Research (DZIF), Partner Site Gießen-Marburg-Langen, Marburg, Germany
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95
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Atemin A, Ivanova A, Peppel W, Stamatov R, Gallegos R, Durden H, Uzunova S, Vershinin MD, Saffarian S, Stoynov SS. Kinetic Landscape of Single Virus-like Particles Highlights the Efficacy of SARS-CoV-2 Internalization. Viruses 2024; 16:1341. [PMID: 39205315 PMCID: PMC11359012 DOI: 10.3390/v16081341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/22/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The efficiency of virus internalization into target cells is a major determinant of infectivity. SARS-CoV-2 internalization occurs via S-protein-mediated cell binding followed either by direct fusion with the plasma membrane or endocytosis and subsequent fusion with the endosomal membrane. Despite the crucial role of virus internalization, the precise kinetics of the processes involved remains elusive. We developed a pipeline, which combines live-cell microscopy and advanced image analysis, for measuring the rates of multiple internalization-associated molecular events of single SARS-CoV-2-virus-like particles (VLPs), including endosome ingression and pH change. Our live-cell imaging experiments demonstrate that only a few minutes after binding to the plasma membrane, VLPs ingress into RAP5-negative endosomes via dynamin-dependent scission. Less than two minutes later, VLP speed increases in parallel with a pH drop below 5, yet these two events are not interrelated. By co-imaging fluorescently labeled nucleocapsid proteins, we show that nucleocapsid release occurs with similar kinetics to VLP acidification. Neither Omicron mutations nor abrogation of the S protein polybasic cleavage site affected the rate of VLP internalization, indicating that they do not confer any significant advantages or disadvantages during this process. Finally, we observe that VLP internalization occurs two to three times faster in VeroE6 than in A549 cells, which may contribute to the greater susceptibility of the former cell line to SARS-CoV-2 infection. Taken together, our precise measurements of the kinetics of VLP internalization-associated processes shed light on their contribution to the effectiveness of SARS-CoV-2 propagation in cells.
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Affiliation(s)
- Aleksandar Atemin
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str., 1113 Sofia, Bulgaria; (A.A.); (A.I.); (R.S.); (S.U.)
| | - Aneliya Ivanova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str., 1113 Sofia, Bulgaria; (A.A.); (A.I.); (R.S.); (S.U.)
| | - Wiley Peppel
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA; (W.P.); (R.G.); (H.D.)
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Rumen Stamatov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str., 1113 Sofia, Bulgaria; (A.A.); (A.I.); (R.S.); (S.U.)
| | - Rodrigo Gallegos
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA; (W.P.); (R.G.); (H.D.)
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Haley Durden
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA; (W.P.); (R.G.); (H.D.)
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Sonya Uzunova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str., 1113 Sofia, Bulgaria; (A.A.); (A.I.); (R.S.); (S.U.)
| | - Michael D. Vershinin
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA; (W.P.); (R.G.); (H.D.)
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Saveez Saffarian
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA; (W.P.); (R.G.); (H.D.)
- Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Stoyno S. Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, 21, G. Bontchev Str., 1113 Sofia, Bulgaria; (A.A.); (A.I.); (R.S.); (S.U.)
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96
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Yılmaz Çolak Ç. Bacterial Membrane Vesicles as a Novel Vaccine Platform against SARS-CoV-2. Curr Microbiol 2024; 81:317. [PMID: 39164527 DOI: 10.1007/s00284-024-03846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 08/15/2024] [Indexed: 08/22/2024]
Abstract
Throughout history, infectious diseases have plagued humanity, with outbreaks occurring regularly worldwide. Not every outbreak affects people globally; however, in the case of Coronavirus Disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), it reached a pandemic level within a remarkably short period. Fortunately, advancements in medicine and biotechnology have facilitated swift responses to the disease, resulting in the development of therapeutics and vaccines. Nevertheless, the persistent spread of the virus and the emergence of new variants underscore the necessity for protective interventions, leading researchers to seek more effective vaccines. Despite the presence of various types of vaccines, including mRNA and inactivated vaccines against SARS-CoV-2, new platforms have been investigated since the pandemic, and research on bacterial membrane vesicles (BMVs) has demonstrated their potential as a novel COVID-19 vaccine platform. Researchers have explored different strategies for BMV-based COVID-19 vaccines, such as mixing the vesicles with antigenic components of the virus due to their adjuvant capacity or decorating the vesicles with the viral antigens to create adjuvanted delivery systems. These approaches have presented promising results in inducing robust immune responses, but obstacles such as reproducibility in obtaining and homogeneous characterization of BMVs remain in developing vesicle-based vaccines. Overall, the development of BMV-based vaccines represents a novel and promising strategy in the fight against COVID-19. Additional research and clinical trials are needed to further evaluate the potential of these vaccines to offer long-lasting protection against SARS-CoV-2 and its evolving variants.
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Affiliation(s)
- Çiğdem Yılmaz Çolak
- Life Sciences, Marmara Research Center, TUBITAK, Kocaeli, Türkiye.
- Molecular Biology and Genetics Department, Istanbul Technical University, Istanbul, Türkiye.
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97
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Catanzaro NJ, Wu Z, Fan C, Schäfer A, Yount BL, Bjorkman PJ, Baric R, Letko M. ACE2 from Pipistrellus abramus bats is a receptor for HKU5 coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584892. [PMID: 38559009 PMCID: PMC10980018 DOI: 10.1101/2024.03.13.584892] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The merbecovirus subgenus of coronaviruses includes Middle East Respiratory Syndrome Coronavirus (MERS-CoV), a zoonotic pathogen transmitted from dromedary camels to humans that causes severe respiratory disease. Viral discovery efforts have uncovered hundreds of merbecoviruses in different species across multiple continents, but few have been studied under laboratory conditions, leaving basic questions regarding their human threat potential unresolved. Viral entry into host cells is a critical step for transmission between hosts. Here, a scalable approach that assesses novel merbecovirus cell entry was developed and used to evaluate receptor use across the entire merbecovirus subgenus. Merbecoviruses are sorted into clades based on the receptor-binding domain of the spike glycoprotein. Receptor tropism is clade-specific, with the clade including MERS-CoV using DPP4 and multiple clades using ACE2, including HKU5 bat coronaviruses. Mutational analysis identified possible structural limitations to HKU5 adaptability and a cryo-EM structure of the HKU5-20s spike trimer revealed only 'down' RBDs.
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Affiliation(s)
- Nicholas J. Catanzaro
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Ziyan Wu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Alexandra Schäfer
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Boyd L. Yount
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Ralph Baric
- Department of Epidemiology, Gillings School of Global Public Heath, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99163
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98
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Focosi D, Spezia PG, Maggi F. Subsequent Waves of Convergent Evolution in SARS-CoV-2 Genes and Proteins. Vaccines (Basel) 2024; 12:887. [PMID: 39204013 PMCID: PMC11358953 DOI: 10.3390/vaccines12080887] [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: 07/20/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 09/03/2024] Open
Abstract
Beginning in 2022, following widespread infection and vaccination among the global population, the SARS-CoV-2 virus mainly evolved to evade immunity derived from vaccines and past infections. This review covers the convergent evolution of structural, nonstructural, and accessory proteins in SARS-CoV-2, with a specific look at common mutations found in long-lasting infections that hint at the virus potentially reverting to an enteric sarbecovirus type.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Pietro Giorgio Spezia
- Laboratory of Virology and Laboratory of Biosecurity, National Institute of Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
| | - Fabrizio Maggi
- Laboratory of Virology and Laboratory of Biosecurity, National Institute of Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
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de Souza Goncalves B, Sangani D, Nayyar A, Puri R, Irtiza M, Nayyar A, Khalyfa A, Sodhi K, Pillai SS. COVID-19-Associated Sepsis: Potential Role of Phytochemicals as Functional Foods and Nutraceuticals. Int J Mol Sci 2024; 25:8481. [PMID: 39126050 PMCID: PMC11312872 DOI: 10.3390/ijms25158481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
The acute manifestations of coronavirus disease 2019 (COVID-19) exhibit the hallmarks of sepsis-associated complications that reflect multiple organ failure. The inflammatory cytokine storm accompanied by an imbalance in the pro-inflammatory and anti-inflammatory host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to severe and critical septic shock. The sepsis signature in severely afflicted COVID-19 patients includes cellular reprogramming and organ dysfunction that leads to high mortality rates, emphasizing the importance of improved clinical care and advanced therapeutic interventions for sepsis associated with COVID-19. Phytochemicals of functional foods and nutraceutical importance have an incredible impact on the healthcare system, which includes the prevention and/or treatment of chronic diseases. Hence, in the present review, we aim to explore the pathogenesis of sepsis associated with COVID-19 that disrupts the physiological homeostasis of the body, resulting in severe organ damage. Furthermore, we have summarized the diverse pharmacological properties of some potent phytochemicals, which can be used as functional foods as well as nutraceuticals against sepsis-associated complications of SARS-CoV-2 infection. The phytochemicals explored in this article include quercetin, curcumin, luteolin, apigenin, resveratrol, and naringenin, which are the major phytoconstituents of our daily food intake. We have compiled the findings from various studies, including clinical trials in humans, to explore more into the therapeutic potential of each phytochemical against sepsis and COVID-19, which highlights their possible importance in sepsis-associated COVID-19 pathogenesis. We conclude that our review will open a new research avenue for exploring phytochemical-derived therapeutic agents for preventing or treating the life-threatening complications of sepsis associated with COVID-19.
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Affiliation(s)
- Bruno de Souza Goncalves
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
| | - Darshan Sangani
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
| | - Aleen Nayyar
- Department of Medicine, Sharif Medical and Dental College, Lahore 55150, Pakistan;
| | - Raghav Puri
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
| | - Mahir Irtiza
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
| | - Asma Nayyar
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
| | - Abdelnaby Khalyfa
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
| | - Komal Sodhi
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
| | - Sneha S. Pillai
- Department of Surgery, Internal Medicine and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25701, USA; (B.d.S.G.); (D.S.); (R.P.); (M.I.); (A.N.); (A.K.); (K.S.)
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Michaels TM, Essop MF, Joseph DE. Potential Effects of Hyperglycemia on SARS-CoV-2 Entry Mechanisms in Pancreatic Beta Cells. Viruses 2024; 16:1243. [PMID: 39205219 PMCID: PMC11358987 DOI: 10.3390/v16081243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
The COVID-19 pandemic has revealed a bidirectional relationship between SARS-CoV-2 infection and diabetes mellitus. Existing evidence strongly suggests hyperglycemia as an independent risk factor for severe COVID-19, resulting in increased morbidity and mortality. Conversely, recent studies have reported new-onset diabetes following SARS-CoV-2 infection, hinting at a potential direct viral attack on pancreatic beta cells. In this review, we explore how hyperglycemia, a hallmark of diabetes, might influence SARS-CoV-2 entry and accessory proteins in pancreatic β-cells. We examine how the virus may enter and manipulate such cells, focusing on the role of the spike protein and its interaction with host receptors. Additionally, we analyze potential effects on endosomal processing and accessory proteins involved in viral infection. Our analysis suggests a complex interplay between hyperglycemia and SARS-CoV-2 in pancreatic β-cells. Understanding these mechanisms may help unlock urgent therapeutic strategies to mitigate the detrimental effects of COVID-19 in diabetic patients and unveil if the virus itself can trigger diabetes onset.
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Affiliation(s)
- Tara M. Michaels
- Centre for Cardio-Metabolic Research in Africa, Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa;
| | - M. Faadiel Essop
- Centre for Cardio-Metabolic Research in Africa, Division of Medical Physiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
| | - Danzil E. Joseph
- Centre for Cardio-Metabolic Research in Africa, Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa;
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