1
|
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.
Collapse
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
| |
Collapse
|
2
|
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 DOI: 10.1016/j.virol.2024.110198] [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: 06/06/2024] [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.
Collapse
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.
| |
Collapse
|
3
|
Guenthoer J, Garrett ME, Lilly M, Depierreux DM, Ruiz F, Chi M, Stoddard CI, Chohan V, Yaffe ZA, Sung K, Ralph D, Chu HY, Matsen FA, Overbaugh J. The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2. PLoS Pathog 2024; 20:e1012383. [PMID: 39093891 DOI: 10.1371/journal.ppat.1012383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/14/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
The SARS-CoV-2 virus responsible for the COVID-19 global pandemic has exhibited a striking capacity for viral evolution that drives continued evasion from vaccine and infection-induced immune responses. Mutations in the receptor binding domain of the S1 subunit of the spike glycoprotein have led to considerable escape from antibody responses, reducing the efficacy of vaccines and monoclonal antibody (mAb) therapies. Therefore, there is a need to interrogate more constrained regions of spike, such as the S2 subdomain. Here, we present a collection of S2 mAbs from two SARS-CoV-2 convalescent individuals that target multiple regions in S2, including regions outside of those commonly reported. One of the S2 mAbs, C20.119, which bound to a highly conserved epitope in the fusion peptide, was able to broadly neutralize across SARS-CoV-2 variants, SARS-CoV-1, and closely related zoonotic sarbecoviruses. The majority of the mAbs were non-neutralizing; however, many of them could mediate antibody-dependent cellular cytotoxicity (ADCC) at levels similar to the S1-targeting mAb S309 that was previously authorized for treatment of SARS-CoV-2 infections. Several of the mAbs with ADCC function also bound to spike trimers from other human coronaviruses (HCoVs), such as MERS-CoV and HCoV-HKU1. Our findings suggest S2 mAbs can target diverse epitopes in S2, including functional mAbs with HCoV and sarbecovirus breadth that likely target functionally constrained regions of spike. These mAbs could be developed for potential future pandemics, while also providing insight into ideal epitopes for eliciting a broad HCoV response.
Collapse
Affiliation(s)
- Jamie Guenthoer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Meghan E Garrett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Michelle Lilly
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Delphine M Depierreux
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Felicitas Ruiz
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Margaret Chi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Caitlin I Stoddard
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Zak A Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Duncan Ralph
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Frederick A Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| |
Collapse
|
4
|
Daniels A, Padariya M, Fletcher S, Ball K, Singh A, Carragher N, Hupp T, Tait-Burkard C, Kalathiya U. Molecules targeting a novel homotrimer cavity of Spike protein attenuate replication of SARS-CoV-2. Antiviral Res 2024; 228:105949. [PMID: 38942150 DOI: 10.1016/j.antiviral.2024.105949] [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: 02/20/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
The SARS-CoV-2 Spike glycoprotein (S) utilizes a unique trimeric conformation to interact with the ACE2 receptor on host cells, making it a prime target for inhibitors that block viral entry. We have previously identified a novel proteinaceous cavity within the Spike protein homotrimer that could serve as a binding site for small molecules. However, it is not known whether these molecules would inhibit, stimulate, or have no effect on viral replication. To address this, we employed structural-based screening to identify small molecules that dock into the trimer cavity and assessed their impact on viral replication. Our findings show that a cohort of identified small molecules binding to the Spike trimer cavity effectively reduces the replication of various SARS-CoV-2 variants. These molecules exhibited inhibitory effects on B.1 (European original, D614G, EDB2) and B.1.617.2 (δ) variants, while showing moderate activity against the B.1.1.7 (α) variant. We further categorized these molecules into distinct groups based on their structural similarities. Our experiments demonstrated a dose-dependent viral replication inhibitory activity of these compounds, with some, like BCC0040453 exhibiting no adverse effects on cell viability even at high concentrations. Further investigation revealed that pre-incubating virions with compounds like BCC0031216 at different temperatures significantly inhibited viral replication, suggesting their specificity towards the S protein. Overall, our study highlights the inhibitory impact of a diverse set of chemical molecules on the biological activity of the Spike protein. These findings provide valuable insights into the role of the trimer cavity in the viral replication cycle and aid drug discovery programs aimed at targeting the coronavirus family.
Collapse
Affiliation(s)
- Alison Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland
| | - Sarah Fletcher
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Kathryn Ball
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ashita Singh
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Neil Carragher
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Christine Tait-Burkard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom.
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, ul. Kładki 24, 80-822 Gdańsk, Poland.
| |
Collapse
|
5
|
Datta G, Rezagholizadeh N, Hasler WA, Khan N, Chen X. SLC38A9 regulates SARS-CoV-2 viral entry. iScience 2024; 27:110387. [PMID: 39071889 PMCID: PMC11277692 DOI: 10.1016/j.isci.2024.110387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/13/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
SARS-CoV-2 viral entry into host cells depends on the cleavage of spike (S) protein into S1 and S2 proteins. Such proteolytic cleavage by furin results in the exposure of a multibasic motif on S1, which is critical for SARS-CoV-2 viral infection and transmission; however, how such a multibasic motif contributes to the infection of SARS-CoV-2 remains elusive. Here, we demonstrate that the multibasic motif on S1 is critical for its interaction with SLC38A9, an endolysosome-resident arginine sensor. SLC38A9 knockdown prevents S1-induced endolysosome de-acidification and blocks the S protein-mediated entry of pseudo-SARS-CoV-2 in Calu-3, U87MG, Caco-2, and A549 cells. Our findings provide a novel mechanism in regulating SARS-CoV-2 viral entry; S1 present in endolysosome lumen could interact with SLC38A9, which mediates S1-induced endolysosome de-acidification and dysfunction, facilitating the escape of SARS-CoV-2 from endolysosomes and enhancing viral entry.
Collapse
Affiliation(s)
- Gaurav Datta
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Neda Rezagholizadeh
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Wendie A. Hasler
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Nabab Khan
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Xuesong Chen
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| |
Collapse
|
6
|
Birtles D, Guiyab L, Abbas W, Lee J. Positive residues of the SARS-CoV-2 fusion domain are key contributors to the initiation of membrane fusion. J Biol Chem 2024; 300:107564. [PMID: 39002677 DOI: 10.1016/j.jbc.2024.107564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024] Open
Abstract
SARS-CoV-2 is one of the most infectious viruses ever recorded. Despite a plethora of research over the last several years, the viral life cycle is still not well understood, particularly membrane fusion. This process is initiated by the fusion domain (FD), a highly conserved stretch of amino acids consisting of a fusion peptide (FP) and fusion loop (FL), which in synergy perturbs the target cells' lipid membrane to lower the energetic cost necessary for fusion. In this study, through a mutagenesis-based approach, we have investigated the basic residues within the FD (K825, K835, R847, K854) utilizing an in vitro fusion assay and 19F NMR, validated by traditional 13C 15N techniques. Alanine and charge-conserving mutants revealed every basic residue plays a highly specific role within the mechanism of initiating fusion. Intriguingly, K825A led to increased fusogenecity which was found to be correlated to the number of amino acids within helix one, further implicating the role of this specific helix within the FD's fusion mechanism. This work has found basic residues to be important within the FDs fusion mechanism and highlights K825A, a specific mutation made within the FD of the SARS-CoV-2 spike protein, as requiring further investigation due to its potential to contribute to a more virulent strain of SARS-CoV-2.
Collapse
Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Lijon Guiyab
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Wafa Abbas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA.
| |
Collapse
|
7
|
Quinteros JA, Browning GF, Mardani K, Noormohammadi AH, Stevenson MA, Coppo MJC, Loncoman CA, Ficorilli N, Diaz-Méndez A. Adding yeast extract to culture medium enhances replication of the avian coronavirus infectious bronchitis virus in chicken embryo kidney cells. J Virol Methods 2024; 329:114989. [PMID: 38917942 DOI: 10.1016/j.jviromet.2024.114989] [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: 02/15/2024] [Revised: 06/04/2024] [Accepted: 06/16/2024] [Indexed: 06/27/2024]
Abstract
Infectious bronchitis virus (IBV), an avian coronavirus, can be isolated and cultured in tracheal organ cultures (TOCs), embryonated eggs and cell cultures, the first two of which are commonly used for viral isolation. Previous studies have suggested that foetal bovine serum (FBS) can inhibit coronavirus replication in cell cultures. In this study, the replication of IBV in chicken embryo kidney (CEK) cell cultures and the Leghorn hepatocellular carcinoma (LMH) cell line was assessed using two different cell culture media containing FBS or yeast extract (YE) and two different IBV strains. The highest concentrations of viral genomes were observed when the cell culture medium (CEK) contained YE. Similar results were observed in LMH cells. Examination of the infectivity by titration demonstrated that the cell lysate from CEK cell cultures in a medium including YE contained a higher median embryo infectious dose than that from CEK cell cultures in a medium containing FBS. These results indicate that improved replication of IBV in cell cultures can be achieved by replacing FBS with YE in the cell culture medium.
Collapse
Affiliation(s)
- José A Quinteros
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia.
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Karim Mardani
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC 3030, Australia
| | - Mark A Stevenson
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mauricio J C Coppo
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Carlos A Loncoman
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nino Ficorilli
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrés Diaz-Méndez
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
8
|
Lubinski B, Whittaker GR. Host Cell Proteases Involved in Human Respiratory Viral Infections and Their Inhibitors: A Review. Viruses 2024; 16:984. [PMID: 38932275 PMCID: PMC11209347 DOI: 10.3390/v16060984] [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: 05/13/2024] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Viral tropism is most commonly linked to receptor use, but host cell protease use can be a notable factor in susceptibility to infection. Here we review the use of host cell proteases by human viruses, focusing on those with primarily respiratory tropism, particularly SARS-CoV-2. We first describe the various classes of proteases present in the respiratory tract, as well as elsewhere in the body, and incorporate the targeting of these proteases as therapeutic drugs for use in humans. Host cell proteases are also linked to the systemic spread of viruses and play important roles outside of the respiratory tract; therefore, we address how proteases affect viruses across the spectrum of infections that can occur in humans, intending to understand the extrapulmonary spread of SARS-CoV-2.
Collapse
Affiliation(s)
- Bailey Lubinski
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA;
| | - Gary R. Whittaker
- Department of Microbiology & Immunology and Public & Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| |
Collapse
|
9
|
Aktaş E, Özdemir Özgentürk N. A comprehensive examination of ACE2 receptor and prediction of spike glycoprotein and ACE2 interaction based on in silico analysis of ACE2 receptor. J Biomol Struct Dyn 2024; 42:4412-4428. [PMID: 37349943 DOI: 10.1080/07391102.2023.2220814] [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: 02/12/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
The ACE2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in various other diseases, including cardiovascular diseases and ARDS. While studies have explored the interactions between ACE2 and SARS-CoV proteins, comprehensive research utilizing bioinformatic tools on the ACE2 protein has been lacking. The one aim of present study was to extensively analyze the regions of the ACE2 protein. After utilizing all bioinformatics tools especially G104 and L108 regions on ACE2 were come forward. The results of our analysis revealed that possible mutations or deletions in the G104 and L108 regions play a critical role in both the biological functioning and the determination of the chemical-physical properties of ACE2. Additionally, these regions were found to be more susceptible to mutations or deletions compared to other regions of the ACE2 protein. Notably, the randomly selected peptide, LQQNGSSVLS (100-109), which includes G104 and L108, exhibited a crucial role in binding the RBD of the spike protein, as supported by docking scores. Furthermore, both MDs and iMODs results provided evidence that G104 and L108 influence the dynamics of ACE2-spike complexes. This study is expected to offer a new perspective on the ACE2-SARS-CoV interaction and other research areas where ACE2 plays a significant role, such as biotechnology (protein engineering, enzyme optimization), medicine (RAS, pulmonary and cardiac diseases), and basic research (structural motifs, stabilizing protein folds, or facilitating important inter molecular contacts, protein's proper structure and function).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Emre Aktaş
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Nehir Özdemir Özgentürk
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| |
Collapse
|
10
|
Wang S, Ran W, Sun L, Fan Q, Zhao Y, Wang B, Yang J, He Y, Wu Y, Wang Y, Chen L, Chuchuay A, You Y, Zhu X, Wang X, Chen Y, Wang Y, Chen YQ, Yuan Y, Zhao J, Mao Y. Sequential glycosylations at the multibasic cleavage site of SARS-CoV-2 spike protein regulate viral activity. Nat Commun 2024; 15:4162. [PMID: 38755139 PMCID: PMC11099032 DOI: 10.1038/s41467-024-48503-x] [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: 05/18/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
The multibasic furin cleavage site at the S1/S2 boundary of the spike protein is a hallmark of SARS-CoV-2 and plays a crucial role in viral infection. However, the mechanism underlying furin activation and its regulation remain poorly understood. Here, we show that GalNAc-T3 and T7 jointly initiate clustered O-glycosylations in the furin cleavage site of the SARS-CoV-2 spike protein, which inhibit furin processing, suppress the incorporation of the spike protein into virus-like-particles and affect viral infection. Mechanistic analysis reveals that the assembly of the spike protein into virus-like particles relies on interactions between the furin-cleaved spike protein and the membrane protein of SARS-CoV-2, suggesting a possible mechanism for furin activation. Interestingly, mutations in the spike protein of the alpha and delta variants of the virus confer resistance against glycosylation by GalNAc-T3 and T7. In the omicron variant, additional mutations reverse this resistance, making the spike protein susceptible to glycosylation in vitro and sensitive to GalNAc-T3 and T7 expression in human lung cells. Our findings highlight the role of glycosylation as a defense mechanism employed by host cells against SARS-CoV-2 and shed light on the evolutionary interplay between the host and the virus.
Collapse
Affiliation(s)
- Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lingyu Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingchi Fan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanqi Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Foshan Institute for Food and Drug Control, Foshan, China
| | - Bowen Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Jinghong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqi He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Luoyi Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Arpaporn Chuchuay
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuyu You
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinhai Zhu
- Instrumental Analysis & Research Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ye Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanqiu Yuan
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Bio-island, Guangzhou, China.
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
| | - Yang Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, China.
| |
Collapse
|
11
|
Lei R, Qing E, Odle A, Yuan M, Gunawardene CD, Tan TJC, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. Nat Commun 2024; 15:4056. [PMID: 38744813 PMCID: PMC11094058 DOI: 10.1038/s41467-024-48104-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we perform a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identify mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we show that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
Collapse
Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chaminda D Gunawardene
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wenhao O Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA.
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA.
- Center for Virus-Host Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
| |
Collapse
|
12
|
Xiang Q, Wu J, Zhou Y, Li L, Tian M, Li G, Zhang Z, Fu Y. SARS-CoV-2 Membrane protein regulates the function of Spike by inhibiting its plasma membrane localization and enzymatic activity of Furin. Microbiol Res 2024; 282:127659. [PMID: 38430890 DOI: 10.1016/j.micres.2024.127659] [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: 01/08/2024] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024]
Abstract
The presence of a multibasic cleavage site in the Spike protein of SARS-CoV-2 makes it prone to be cleaved by Furin at the S1/S2 junction (aa. 685-686), which enhances the usage of TMPRSS2 to promote cell-cell fusion to form syncytia. Syncytia may contribute to pathology by facilitating viral dissemination, cytopathicity, immune evasion, and inflammation. However, the role of other SARS-CoV-2 encoding viral proteins in syncytia formation remains largely unknown. Here, we report that SARS-CoV-2 M protein effectively inhibits syncytia formation triggered by Spike or its variants (Alpha, Delta, Omicron, etc.) and prevents Spike cleavage into S1 and S2 based on a screen assay of 20 viral proteins. Mechanistically, M protein interacts with Furin and inhibits its enzymatic activity, preventing the cleavage of Spike. In addition, M interacts with Spike independent of its cytoplasmic tail, retaining it within the cytoplasm and reducing cell membrane localization. Our findings offer new insights into M protein's role in regulating Spike's function and underscore the importance of functional interplay among viral proteins, highlighting potential avenues for SARS-CoV-2 therapy development.
Collapse
Affiliation(s)
- Qi Xiang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Jie Wu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Yuzheng Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518112, China
| | - Linhao Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Miao Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Guobao Li
- Department of Tuberculosis, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen 518112, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518112, China.
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China.
| |
Collapse
|
13
|
Kılıç G, Demirkan E, Yücel F. Development of Anti-idiotypic Monoclonal Antibody Mimicking SARS-CoV-2 Receptor Binding Domain. Mol Biotechnol 2024:10.1007/s12033-024-01138-1. [PMID: 38662257 DOI: 10.1007/s12033-024-01138-1] [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: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 04/26/2024]
Abstract
Using the hybridoma technique, we developed a panel of anti-idiotypic monoclonal antibodies (aId-mAb) that mimic The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Receptor-Binding Domain (RBD) molecule against Fragment antigen-binding (Fab) of anti-SARS-CoV-2 (S1, RBD) antibodies. Investigated the in vivo and in vitro effects of these aId-mAbs we developed and examined their antigenic mimicry abilities. Among these 12 antibodies, 6 aId-mAbs (designated FY1B4, FY2A6, H9F3, E6G7, FY7E11, and FY8H3) were selected for further characterization in a series of experiments. First, competitive receptor binding assay results confirmed that six aId-mAbs could specifically bind to the ACE2 receptor in target cells and block the interaction between the RBD molecule and the ACE receptor. Moreover, we examined the immunological activities of these aId-mAbs in female BALB/c and showed that E6G7, H7E11, and H8H3 aId-mAbs induce an antibody response by mimicking RBD and stimulating the immune system. It is considered that these three aId-mAbs will be evaluated as SARS-CoV-2 vaccine candidate molecules in future studies.
Collapse
Affiliation(s)
- Gamze Kılıç
- Bursa Uludag University, Faculty of Arts and Sciences, Biology Department, Görükle Campus, Bursa, Turkey
- TUBITAK, Marmara Research Center, Life Sciences, Genetic Engineering and Biotechnology, Kocaeli, Turkey
| | - Elif Demirkan
- Bursa Uludag University, Faculty of Arts and Sciences, Biology Department, Görükle Campus, Bursa, Turkey
| | - Fatıma Yücel
- TUBITAK, Marmara Research Center, Life Sciences, Genetic Engineering and Biotechnology, Kocaeli, Turkey.
| |
Collapse
|
14
|
Kakavandi E, Sadeghi K, Shayestehpour M, Mirhendi H, Rahimi Foroushani A, Mokhtari-Azad T, Shafiei Jandaghi NZ, Yavarian J. Evaluation of angiotensin converting enzyme 2 (ACE2), angiotensin II (Ang II), miR-141-3p, and miR-421 levels in SARS-CoV-2 patients: a case-control study. BMC Infect Dis 2024; 24:429. [PMID: 38649818 PMCID: PMC11036566 DOI: 10.1186/s12879-024-09310-3] [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: 07/23/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious virus that uses angiotensin converting enzyme 2 (ACE2), a pivotal member of the renin-angiotensin system (RAS), as its cell-entry receptor. Another member of the RAS, angiotensin II (Ang II), is the major biologically active component in this system. There is growing evidence suggesting that serum miRNAs could serve as prognostic biomarkers for SARS-CoV-2 infection and regulate ACE2 expression. Therefore, the aim of this study is to evaluate the changes in the serum levels of sACE2 and Ang II, as well as the expression level of miR-141-3p and miR-421 in SARS-CoV-2 positive and negative subjects. METHODS In the present study, the serum levels of sACE2 and Ang II were measured in 94 SARS-CoV-2 positive patients and 94 SARS-CoV-2 negative subjects with some symptoms similar to those of SARS-CoV-2 positive patients using the ELISA method. In addition, the expression level of miR-141-3p and miR-421 as ACE2 regulators and biomarkers was evaluated using quantitative real-time PCR (qRT-PCR) method. RESULTS The mean serum sACE2 concentration in the SARS-CoV-2-positive group was 3.268 ± 0.410 ng/ml, whereas in the SARS-CoV-2 negative group, it was 3.564 ± 0.437 ng/ml. Additionally, the mean serum Ang II level in the SARS-CoV-2 positive and negative groups were 60.67 ± 6.192 ng/L and 67.97 ± 6.837 ng/L, respectively. However, there was no significant difference in the serum levels of sACE2 (P value: 0.516) and Ang II (P value: 0.134) between the SARS-CoV-2 positive and negative groups. Meanwhile, our findings indicated that the expression levels of miR-141-3p and miR-421 in SARS-CoV-2 positive group were significantly lower and higher than SARS-CoV-2 negative group, respectively (P value < 0.001). CONCLUSIONS Taken together, the results of this study showed that the serum levels of sACE2 and Ang II in SARS-CoV-2 positive and negative subjects were not significantly different, but the expression levels of miR-141-3p and miR-421 were altered in SARS-CoV-2 positive patients which need more investigation to be used as biomarkers for COVID-19 diagnosis.
Collapse
Affiliation(s)
- Ehsan Kakavandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kaveh Sadeghi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Shayestehpour
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Jila Yavarian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Research Center for Antibiotic Stewardship and Antimicrobial Resistance, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
15
|
Vajdi M, Karimi A, Hassanizadeh S, Farhangi MA, Bagherniya M, Askari G, Roufogalis BD, Davies NM, Sahebkar A. Effect of polyphenols against complications of COVID-19: current evidence and potential efficacy. Pharmacol Rep 2024; 76:307-327. [PMID: 38498260 DOI: 10.1007/s43440-024-00585-6] [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: 09/23/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The COVID-19 pandemic that started in 2019 and resulted in significant morbidity and mortality continues to be a significant global health challenge, characterized by inflammation, oxidative stress, and immune system dysfunction.. Developing therapies for preventing or treating COVID-19 remains an important goal for pharmacology and drug development research. Polyphenols are effective against various viral infections and can be extracted and isolated from plants without losing their therapeutic potential. Researchers have developed methods for separating and isolating polyphenols from complex matrices. Polyphenols are effective in treating common viral infections, including COVID-19, and can also boost immunity. Polyphenolic-based antiviral medications can mitigate SARS-CoV-2 enzymes vital to virus replication and infection. Individual polyphenolic triterpenoids, flavonoids, anthraquinonoids, and tannins may also inhibit the SARS-CoV-2 protease. Polyphenol pharmacophore structures identified to date can explain their action and lead to the design of novel anti-COVID-19 compounds. Polyphenol-containing mixtures offer the advantages of a well-recognized safety profile with few known severe side effects. However, studies to date are limited, and further animal studies and randomized controlled trials are needed in future studies. The purpose of this study was to review and present the latest findings on the therapeutic impact of plant-derived polyphenols on COVID-19 infection and its complications. Exploring alternative approaches to traditional therapies could aid in developing novel drugs and remedies against coronavirus infection.
Collapse
Affiliation(s)
- Mahdi Vajdi
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Arash Karimi
- Traditional Medicine and Hydrotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Shirin Hassanizadeh
- Department of Community Nutrition, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahdieh Abbasalizad Farhangi
- Department of Community Nutrition, Faculty of Nutrition and Food Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Bagherniya
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Gholamreza Askari
- Department of Community Nutrition, Food Security Research Center, School of Nutrition and Food Science, Isfahan University of Medical Sciences, Isfahan, Iran
- Anesthesia and Critical Care Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Basil D Roufogalis
- Discipline of Pharmacology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
- NICM Health Research Institute, Western Sydney University, Penrith, NSW, Australia
| | - Neal M Davies
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
16
|
Bridge HN, Leiter W, Frazier CL, Weeks AM. An N terminomics toolbox combining 2-pyridinecarboxaldehyde probes and click chemistry for profiling protease specificity. Cell Chem Biol 2024; 31:534-549.e8. [PMID: 37816350 PMCID: PMC10960722 DOI: 10.1016/j.chembiol.2023.09.009] [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: 02/22/2023] [Revised: 07/10/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
Proteomic profiling of protease-generated N termini provides key insights into protease function and specificity. However, current technologies have sequence limitations or require specialized synthetic reagents for N-terminal peptide isolation. Here, we introduce an N terminomics toolbox that combines selective N-terminal biotinylation using 2-pyridinecarboxaldehyde (2PCA) reagents with chemically cleavable linkers to enable efficient enrichment of protein N termini. By incorporating a commercially available alkyne-modified 2PCA in combination with Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), our strategy eliminates the need for chemical synthesis of N-terminal probes. Using these reagents, we developed PICS2 (Proteomic Identification of Cleavage Sites with 2PCA) to profile the specificity of subtilisin/kexin-type proprotein convertases (PCSKs). We also implemented CHOPPER (chemical enrichment of protease substrates with purchasable, elutable reagents) for global sequencing of apoptotic proteolytic cleavage sites. Based on their broad applicability and ease of implementation, PICS2 and CHOPPER are useful tools that will advance our understanding of protease biology.
Collapse
Affiliation(s)
- Haley N Bridge
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - William Leiter
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Clara L Frazier
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Amy M Weeks
- Department of Biochemistry, University of Wisconsin - Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA.
| |
Collapse
|
17
|
Birtles D, Abbas W, Lee J. Bis(Monoacylglycero)Phosphate Promotes Membrane Fusion Facilitated by the SARS-CoV-2 Fusion Domain. J Phys Chem B 2024; 128:2675-2683. [PMID: 38466655 DOI: 10.1021/acs.jpcb.3c07863] [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: 03/13/2024]
Abstract
Membrane fusion is a critical component of the viral lifecycle. For SARS-CoV-2, fusion is facilitated by the spike glycoprotein and can take place via either the plasma membrane or the endocytic pathway. The fusion domain (FD), which is found within the spike glycoprotein, is primarily responsible for the initiation of fusion as it embeds itself within the target cell's membrane. A preference for SARS-CoV-2 to fuse at low pH akin to the environment of the endocytic pathway has already been established; however, the impact of the target cell's lipid composition on the FD has yet to be explored. Here, we have shown that the SARS-CoV-2 FD preferentially initiates fusion at the late endosomal membrane over the plasma membrane, on the basis of lipid composition alone. A positive, fusogenic relationship with anionic lipids from the plasma membrane (POPS: 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine) and endosomal membrane (BMP: bis(monoacylglycero)phosphate) was established, with a large preference demonstrated for the latter. When comparing the binding affinity and secondary structure of the FD in the presence of different anionic lipids, little deviation was evident while the charge was maintained. However, it was discovered that BMP had a subtle, negative impact on lipid packing in comparison to that of POPS. Furthermore, an inverse relationship between lipid packing and the fusogenecity of the SARS-CoV-2 FD was witnessed. In conclusion, the SARS-CoV-2 FD preferentially initiates fusion at a membrane resembling that of the late endosomal compartment, predominately due to the presence of BMP and its impact on lipid packing.
Collapse
Affiliation(s)
- Daniel Birtles
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
| | - Wafa Abbas
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
| | - Jinwoo Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, Maryland, United States
| |
Collapse
|
18
|
Su S, Hu W, Chen X, Ren Y, Lu Y, Shi J, Zhang T, Zhang H, Wang M, Wang Y, Zhao F, Jin R, Liu Y, Zhang H, Liu G. Cardiac injury progression in children with multisystem inflammatory syndrome associated with SARS-CoV-2 infection: a review. Front Pediatr 2024; 12:1348016. [PMID: 38510081 PMCID: PMC10950994 DOI: 10.3389/fped.2024.1348016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
The symptoms and signs of infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are milder in children than in adults. However, in April 2020, British pediatricians first reported that coronavirus disease 2019 (COVID-19) may present as multisystem inflammatory syndrome in children and adolescents (MIS-C), similar to that observed in Kawasaki disease. MIS-C can be associated with multiple systemic injuries and even death in children. In addition to digestive system involvement, cardiac injury is prominent. This article reviews the pathogenesis, clinical manifestations, and treatment of cardiac injury caused by MIS-C, which may help clinicians in early diagnosis and timely commencement of treatment.
Collapse
Affiliation(s)
- Song Su
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Wandong Hu
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Xiao Chen
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Ying Ren
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Yi Lu
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Jianguo Shi
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Tong Zhang
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Huan Zhang
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Meng Wang
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Yaping Wang
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Fen Zhao
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Ruifeng Jin
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Yong Liu
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Hongwei Zhang
- Epilepsy Center, Children’s Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Epilepsy Center, Jinan Children's Hospital, Jinan, Shandong, China
| | - Guohua Liu
- Department of Ophthalmology, Children's Hospital Affiliated to Shandong University, Jinan, Shandong, China
- Department of Ophthalmology, Jinan Children's Hospital, Jinan, Shandong, China
| |
Collapse
|
19
|
Yang X, Zheng X, Zhu Y, Zhao X, Liu J, Xun J, Yuan S, Chen J, Pan H, Yang J, Wang J, Liang Z, Shen X, Liang Y, Lin Q, Liang H, Li M, Peng F, Lu D, Xu J, Lu H, Jiang S, Zhao P, Zhu H. Asialoglycoprotein receptor 1 promotes SARS-CoV-2 infection of human normal hepatocytes. Signal Transduct Target Ther 2024; 9:42. [PMID: 38355848 PMCID: PMC10866945 DOI: 10.1038/s41392-024-01754-y] [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: 08/29/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes multi-organ damage, which includes hepatic dysfunction, as observed in over 50% of COVID-19 patients. Angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 (ACE2) is the primary receptor for SARS-CoV-2 entry into host cells, and studies have shown the presence of intracellular virus particles in human hepatocytes that express ACE2, but at extremely low levels. Consequently, we asked if hepatocytes might express receptors other than ACE2 capable of promoting the entry of SARS-CoV-2 into cells. To address this question, we performed a genome-wide CRISPR-Cas9 activation library screening and found that Asialoglycoprotein receptor 1 (ASGR1) promoted SARS-CoV-2 pseudovirus infection of HeLa cells. In Huh-7 cells, simultaneous knockout of ACE2 and ASGR1 prevented SARS-CoV-2 pseudovirus infection. In the immortalized THLE-2 hepatocyte cell line and primary hepatic parenchymal cells, both of which barely expressed ACE2, SARS-CoV-2 pseudovirus could successfully establish an infection. However, after treatment with ASGR1 antibody or siRNA targeting ASGR1, the infection rate significantly dropped, suggesting that SARS-CoV-2 pseudovirus infects hepatic parenchymal cells mainly through an ASGR1-dependent mechanism. We confirmed that ASGR1 could interact with Spike protein, which depends on receptor binding domain (RBD) and N-terminal domain (NTD). Finally, we also used Immunohistochemistry and electron microscopy to verify that SARS-CoV-2 could infect primary hepatic parenchymal cells. After inhibiting ASGR1 in primary hepatic parenchymal cells by siRNA, the infection efficiency of the live virus decreased significantly. Collectively, these findings indicate that ASGR1 is a candidate receptor for SARS-CoV-2 that promotes infection of hepatic parenchymal cells.
Collapse
Affiliation(s)
- Xinyi Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Xu Zheng
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Xiaying Zhao
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jun Liu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jiangna Xun
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Songhua Yuan
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Chen
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hanyu Pan
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jinlong Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jing Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Zhimin Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Xiaoting Shen
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Yue Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Qinru Lin
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Huitong Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Min Li
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Fei Peng
- Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China
| | - Jianqing Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Nursing Research Institution, National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Shenzhen, Guangdong, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping Zhao
- Department of Microbiology, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, China.
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Yiwu Research Institute, Fudan University, Shanghai, China.
| |
Collapse
|
20
|
Carten JD, Khelashvili G, Bidon MK, Straus MR, Tang T, Jaimes JA, Whittaker GR, Weinstein H, Daniel S. A Mechanistic Understanding of the Modes of Ca 2+ Ion Binding to the SARS-CoV-1 Fusion Peptide and Their Role in the Dynamics of Host Membrane Penetration. ACS Infect Dis 2024; 10:398-411. [PMID: 38270149 DOI: 10.1021/acsinfecdis.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The SARS-CoV-1 spike glycoprotein contains a fusion peptide (FP) segment that mediates the fusion of the viral and host cell membranes. Calcium ions are thought to position the FP optimally for membrane insertion by interacting with negatively charged residues in this segment (E801, D802, D812, E821, D825, and D830); however, which residues bind to calcium and in what combinations supportive of membrane insertion are unknown. Using biological assays and molecular dynamics studies, we have determined the functional configurations of FP-Ca2+ binding that likely promote membrane insertion. We first individually mutated the negatively charged residues in the SARS CoV-1 FP to assay their roles in cell entry and syncytia formation, finding that charge loss in the D802A or D830A mutants greatly reduced syncytia formation and pseudoparticle transduction of VeroE6 cells. Interestingly, one mutation (D812A) led to a modest increase in cell transduction, further indicating that FP function likely depends on calcium binding at specific residues and in specific combinations. To interpret these results mechanistically and identify specific modes of FP-Ca2+ binding that modulate membrane insertion, we performed molecular dynamics simulations of the SARS-CoV-1 FP and Ca2+ions. The preferred residue pairs for Ca2+ binding we identified (E801/D802, E801/D830, and D812/E821) include the two residues found to be essential for S function in our biological studies (D802 and D830). The three preferred Ca2+ binding pairs were also predicted to promote FP membrane insertion. We also identified a Ca2+ binding pair (E821/D825) predicted to inhibit FP membrane insertion. We then carried out simulations in the presence of membranes and found that binding of Ca2+ to SARS-CoV-1 FP residue pairs E801/D802 and D812/E821 facilitates membrane insertion by enabling the peptide to adopt conformations that shield the negative charges of the FP to reduce repulsion by the membrane phospholipid headgroups. This calcium binding mode also optimally positions the hydrophobic LLF region of the FP for membrane penetration. Conversely, Ca2+ binding to the FP E801/D802 and D821/D825 pairs eliminates the negative charge screening and instead creates a repulsive negative charge that hinders membrane penetration of the LLF motif. These computational results, taken together with our biological studies, provide an improved and nuanced mechanistic understanding of the dymanics of SARS-CoV-1 calcium binding and their potential effects on host cell entry.
Collapse
Affiliation(s)
- Juliana Debrito Carten
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - George Khelashvili
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Miya K Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Marco R Straus
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Javier A Jaimes
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
| | - Gary R Whittaker
- Departments of Microbiology & Immunology, Cornell University, Ithaca, New York 14853, United States
- Public & Ecosystem Health, Cornell University, Ithaca, New York 14853, United States
| | - Harel Weinstein
- Department of Physiology & Biophysics, Weill Cornell Medicine, New York, New York 10065, United States
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
21
|
Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
Collapse
Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| |
Collapse
|
22
|
Dong M, Galvan Achi JM, Du R, Rong L, Cui Q. Development of SARS-CoV-2 entry antivirals. CELL INSIGHT 2024; 3:100144. [PMID: 38323318 PMCID: PMC10844678 DOI: 10.1016/j.cellin.2023.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 02/08/2024]
Abstract
The global outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatened human health and public safety. The development of anti-SARS-CoV-2 therapies have been essential to curb the spread of SARS-CoV-2. Particularly, antivirals targeting viral entry have become an attractive target for the development of anti-SARS-CoV-2 therapies. In this review, we elucidate the mechanism of SARS-CoV-2 viral entry and summarize the development of antiviral inhibitors targeting viral entry. Moreover, we speculate upon future directions toward more potent inhibitors of SARS-CoV-2 entry. This study is expected to provide novel insights for the efficient discovery of promising candidate drugs against the entry of SARS-CoV-2, and contribute to the development of broad-spectrum anti-coronavirus drugs.
Collapse
Affiliation(s)
- Meiyue Dong
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Jazmin M. Galvan Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL60612, USA
| | - Ruikun Du
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, Shandong, 266122, China
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL60612, USA
| | - Qinghua Cui
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
- Qingdao Academy of Chinese Medical Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, Shandong, 266122, China
| |
Collapse
|
23
|
Noh HE, Rha MS. Mucosal Immunity against SARS-CoV-2 in the Respiratory Tract. Pathogens 2024; 13:113. [PMID: 38392851 PMCID: PMC10892713 DOI: 10.3390/pathogens13020113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The respiratory tract, the first-line defense, is constantly exposed to inhaled allergens, pollutants, and pathogens such as respiratory viruses. Emerging evidence has demonstrated that the coordination of innate and adaptive immune responses in the respiratory tract plays a crucial role in the protection against invading respiratory pathogens. Therefore, a better understanding of mucosal immunity in the airways is critical for the development of novel therapeutics and next-generation vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses. Since the coronavirus disease 2019 pandemic, our knowledge of mucosal immune responses in the airways has expanded. In this review, we describe the latest knowledge regarding the key components of the mucosal immune system in the respiratory tract. In addition, we summarize the host immune responses in the upper and lower airways following SARS-CoV-2 infection and vaccination, and discuss the impact of allergic airway inflammation on mucosal immune responses against SARS-CoV-2.
Collapse
Affiliation(s)
- Hae-Eun Noh
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea;
| | - Min-Seok Rha
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea;
- Department of Biomedical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| |
Collapse
|
24
|
Majeed M, Nagabhushanam K, Lawrence L, Prakasan P, Mundkur L. The Mechanism of Anti-Viral Activity of a Novel, Hydroponically Selenium-Enriched Garlic Powder (SelenoForce ®) Against SARS-CoV-2 Virus. GLOBAL ADVANCES IN INTEGRATIVE MEDICINE AND HEALTH 2024; 13:27536130241268100. [PMID: 39130207 PMCID: PMC11311149 DOI: 10.1177/27536130241268100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 08/13/2024]
Abstract
Abstract The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is far from over as new strains are emerging all over the world. Selenium as a micronutrient is important for immunity and also has anti-viral activity. Objective The study evaluated the activity of a Selenium enriched garlic powder (SeGP or SelenoForce®) against SARS-CoV-2 viral replication in vitro and explored its possible mechanism of action. Methods The anti-SARS-CoV-2 activity assay was carried out in Vero E6 cells in vitro. Human lung carcinoma A549 cells were used to study the antioxidant activity, expression of angiotensin converting enzyme (ACE), transmembrane protease, serine 2 (TMPRSS2) and the activity of proprotein convertase, and furin. Anti-inflammatory activity was evaluated in lipopolysaccharide-activated RAW 264.7 cells. Results SeGP inhibited the replication of SARS-CoV-2 in Vero E6 cells with an IC50 of 19.59 μg/ml. It exhibited significant antioxidant activity in vitro with IC50 value determined as 43.45 μg/ml. The Selenium enriched product inhibited the expression of ACE and TMPRSS2 and also showed inhibition of furin protease activity. In the presence of SeGP, the secretion of nitric oxide, interleukin -6 and TNF-α were reduced in activated RAW 264.7 macrophages. Conclusion The results of the study suggest that Selenium enriched garlic powder could inhibit SARS-CoV-2 multiplication in vitro, reduce oxidative stress and inflammatory mediators suggesting that it could be developed as an effective supplement or adjunct therapy to combat viral infections.
Collapse
Affiliation(s)
- Muhammed Majeed
- Sami-Sabinsa Group Limited, Bangalore, India
- Sabinsa Corporation, East Windsor, NJ, USA
| | | | | | | | | |
Collapse
|
25
|
Chaudhury S, Kaur P, Gupta D, Anand P, Chaudhary M, Tiwari S, Mittal A, Gupta J, Kaur S, Singh VD, Dhawan D, Singh P, Sahu SK. Therapeutic Management with Repurposing Approaches: A Mystery During COVID-19 Outbreak. Curr Mol Med 2024; 24:712-733. [PMID: 37312440 DOI: 10.2174/1566524023666230613141746] [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: 08/31/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/15/2023]
Abstract
The ubiquitous pandemic that emerged due to COVID-19 affected the whole planet. People all over the globe became vulnerable to the unpredictable emergence of coronavirus. The sudden emergence of respiratory disease in coronavirus infected several patients. This affected human life drastically, from mild symptoms to severe illness, leading to mortality. COVID-19 is an exceptionally communicable disease caused by SARS-CoV-2. According to a genomic study, the viral spike RBD interactions with the host ACE2 protein from several coronavirus strains and the interaction between RBD and ACE2 highlighted the potential change in affinity from the virus causing the COVID-19 outbreak to a progenitor type of SARS-CoV-2. SARS-CoV-2, which could be the principal reservoir, is phylogenetically related to the SARS-like bat virus. Other research works reported that intermediary hosts for the transmission of viruses to humans could include cats, bats, snakes, pigs, ferrets, orangutans, and monkeys. Even with the arrival of vaccines and individuals getting vaccinated and treated with FDAapproved repurposed drugs like Remdesivir, the first and foremost steps aimed towards the possible control and minimization of community transmission of the virus include social distancing, self-realization, and self-health care. In this review paper, we discussed and summarized various approaches and methodologies adopted and proposed by researchers all over the globe to help with the management of this zoonotic outbreak by following repurposed approaches.
Collapse
Affiliation(s)
- Soumik Chaudhury
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Paranjeet Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Deepali Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Palak Anand
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Manish Chaudhary
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Siddhita Tiwari
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Amit Mittal
- Faculty of Pharmaceutical Sciences, Desh Bhagat University, Amloh Road, Mandi Gobindgarh, 147301, Punjab, India
| | - Jeena Gupta
- School of Bioscience, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sukhmeen Kaur
- Department of Opthalmology, Punjab Institute of Medical Sciences, Jalandhar, 144001, Punjab, India
| | - Varsh Deep Singh
- American University of Barbados, Wildey, St. Michael, BB11100, Barbados
| | - Dakshita Dhawan
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Princejyot Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sanjeev Kumar Sahu
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| |
Collapse
|
26
|
Logue J, Melville VM, Ardanuy J, Frieman MB. CNP blocks mitochondrial depolarization and inhibits SARS-CoV-2 replication in vitro and in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544327. [PMID: 37333151 PMCID: PMC10274905 DOI: 10.1101/2023.06.09.544327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The COVID-19 pandemic has claimed over 6.5 million lives worldwide and continues to have lasting impacts on the world's healthcare and economic systems. Several approved and emergency authorized therapeutics that inhibit early stages of the virus replication cycle have been developed however, effective late-stage therapeutical targets have yet to be identified. To that end, our lab identified that 2',3' cyclic-nucleotide 3'-phosphodiesterase (CNP) inhibits SARS-CoV-2 virion assembly. We show that CNP inhibits the generation of new SARS-CoV-2 virions, reducing intracellular titers without inhibiting viral structural protein translation. Additionally, we show that targeting of CNP to mitochondria is necessary for inhibition, blocking mitochondrial depolarization and implicating CNP's proposed role as an inhibitor of the mitochondrial permeabilization transition pore (mPTP) as the mechanism of virion assembly inhibition. We also demonstrate that an adenovirus expressing virus expressing both human ACE2 and CNP inhibits SARS-CoV-2 titers to undetectable levels in lungs of mice. Collectively, this work shows the potential of CNP to be a new SARS-CoV-2 antiviral target.
Collapse
Affiliation(s)
- James Logue
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Victoria M. Melville
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Jeremy Ardanuy
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| | - Matthew B. Frieman
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore,Maryland, USA
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore,Maryland, USA
| |
Collapse
|
27
|
Islam MA. A review of SARS-CoV-2 variants and vaccines: Viral properties, mutations, vaccine efficacy, and safety. INFECTIOUS MEDICINE 2023; 2:247-261. [PMID: 38205179 PMCID: PMC10774670 DOI: 10.1016/j.imj.2023.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 01/12/2024]
Abstract
The severe acute respiratory syndrome coronavirus disease 2 instigated by coronavirus disease of 2019 (COVID-19) has delivered an unfathomable obstruction that has touched all sectors worldwide. Despite new vaccine technologies and mass administration of booster doses, the virus persists, and unknown the ending of the pandemic for new variants and sub-variants. Moreover, whether leaning on home medications or using plant extracts is sufficient often to combat the virus has generated tremendous interest in the scientific fraternity. Different databases including PubMed, Scopus, Web of Science, and Google Scholar used to find published articles linked with related topics. Currently, COVID-19 third and fourth shots of vaccines are progressively administered worldwide, where some countries trail others by a significant margin. Many proteins related to viral activity have changed, possibly boosting the virus infectivity and making antibodies ineffective. This study will reminisce the viral genome, associated pathways for viral protein functions, variants, and their mutations. The current, comprehensive review will also provide information on vaccine technologies developed by several biotech companies and the efficacy of their doses, costs including boosters on a mass level. As no vaccine is working to protect fully against all the variants, the new proactive vaccine research needs to be conducted based on all variants, their sub-lineage, and mutations.
Collapse
Affiliation(s)
- Md. Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj 2310, Bangladesh
- COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| |
Collapse
|
28
|
Logue J, Melville VM, Ardanuy J, Frieman MB. CNP blocks mitochondrial depolarization and inhibits SARS-CoV-2 replication in vitro and in vivo. PLoS Pathog 2023; 19:e1011870. [PMID: 38117830 PMCID: PMC10766180 DOI: 10.1371/journal.ppat.1011870] [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: 06/16/2023] [Revised: 01/04/2024] [Accepted: 11/28/2023] [Indexed: 12/22/2023] Open
Abstract
The COVID-19 pandemic has claimed over 6.5 million lives worldwide and continues to have lasting impacts on the world's healthcare and economic systems. Several approved and emergency authorized therapeutics that inhibit early stages of the virus replication cycle have been developed however, effective late-stage therapeutical targets have yet to be identified. To that end, our lab identified that 2',3' cyclic-nucleotide 3'-phosphodiesterase (CNP) inhibits SARS-CoV-2 virion assembly. We show that CNP inhibits the generation of new SARS-CoV-2 virions, reducing intracellular titers without inhibiting viral structural protein translation. Additionally, we show that targeting of CNP to mitochondria is necessary for inhibition, blocking mitochondrial depolarization and implicating CNP's proposed role as an inhibitor of the mitochondrial permeabilization transition pore (mPTP) as the mechanism of virion assembly inhibition. We also demonstrate that an adenovirus expressing virus expressing both human ACE2 and CNP inhibits SARS-CoV-2 titers to undetectable levels in lungs of mice. Collectively, this work shows the potential of CNP to be a new SARS-CoV-2 antiviral target.
Collapse
Affiliation(s)
- James Logue
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Victoria M. Melville
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeremy Ardanuy
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew B. Frieman
- The Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Pathogen Research, The University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| |
Collapse
|
29
|
Guo N, Li X, Han Z, Yu Q, Zhang Y, Liu S, Xu H, Han G, Li Q. Expression of angiotensin converting enzyme 2 mRNA in different SARS-CoV-2 infection states and times. J Biomol Struct Dyn 2023; 41:11255-11261. [PMID: 36625725 DOI: 10.1080/07391102.2022.2160821] [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: 08/26/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
To measure the expression of angiotensin converting enzyme 2 (ACE2) mRNA in SARS-CoV-2 infection with different infection status and at different stages during infection, we used RT-qP CR to measure the expression of ACE2 mRNA. Measurements were analyzed by two-way repeated measures analysis of variance (RMANOVA). Expression of ACE2 mRNA was downregulated in initial stages of SARS-CoV-2 infection both in the asymptomatic infection (ASY) group and the confirmed cases (CON) group (t=-8.0845, P < 0.0001; t=-8.1904, P < 0.0001, respectively). The expression of ACE2 mRNA in the incubation period of CON group was lower compared with the intinal period of ASY group (F = 6.084, p = 0.016, partialη2 = 0.070). Relative expression of ACE2 mRNA was upregulated at the late stage of SARS-CoV-2 infection in the ASY and CON groups (F = 23.489, p = 0.000, partialη2 = 0.225; F = 46.555, p = 0.000, partialη2 = 0.365, respectively). The relative expression of ACE2 mRNA was down-regulated (mean ± SEM:0.69 ± 0.03) after inoculation with SARSCoV- 2 Spike pseudovirus, and there was a statistical difference (one-way t test, mean diffience =-0.31, 95%CI: -0.37˜-0.24, t=-8.1904, P < 0.0001). The expression of ACE2 mRNA is downregulated in the initial stage of SARS-CoV-2 infection, and then upregulated in the late stage of SARS-CoV-2 infection. The lower expression of ACE2 mRNA during the incubation period can lead to clinical symptoms. Downregulation of ACE2 mRNA was related to the interaction between SARS-CoV-2 S protein and ACE2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nana Guo
- Hebei Medical University, Shijiazhang, People's Republic of China
- bHandan Center for Disease Control and Prevention, Handan, People's Republic of China
| | - Xue Li
- Hebei Medical University, Shijiazhang, People's Republic of China
| | - Zhanying Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhang, People's Republic of China
| | - Qiuli Yu
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhang, People's Republic of China
| | - Yanbo Zhang
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhang, People's Republic of China
| | - Shiyou Liu
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhang, People's Republic of China
| | - Han Xu
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhang, People's Republic of China
| | - Guangyue Han
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhang, People's Republic of China
| | - Qi Li
- Hebei Medical University, Shijiazhang, People's Republic of China
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhang, People's Republic of China
| |
Collapse
|
30
|
Olarte-Castillo XA, Plimpton L, McQueary H, Sun Y, Yu YT, Cover S, Richardson AN, Jin Y, Grenier JK, Cummings KJ, Bunting E, Diuk-Wasser M, Needle D, Schuler K, Stanhope MJ, Whittaker G, Goodman LB. Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, in saliva and feces of meso-carnivores in the northeastern United States. J Virol 2023; 97:e0082923. [PMID: 37882520 PMCID: PMC10688340 DOI: 10.1128/jvi.00829-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Several coronaviruses (CoVs) have been detected in domesticated, farmed, and wild meso-carnivores, causing a wide range of diseases and infecting diverse species, highlighting their important but understudied role in the epidemiology of these viruses. Assessing the viral diversity hosted in wildlife species is essential to understand their significance in the cross-species transmission of CoVs. Our focus here was on CoV discovery in meso-carnivores in the Northeast United States as a potential "hotspot" area with high density of humans and urban wildlife. This study identifies novel alphacoronaviruses circulating in multiple free-ranging wild and domestic species in this area and explores their potential epidemiological importance based on regions of the Spike gene, which are relevant for virus-host interactions.
Collapse
Affiliation(s)
- Ximena A. Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Laura Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yining Sun
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Y. Tina Yu
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Sarah Cover
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Amy N. Richardson
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Yuhan Jin
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Elizabeth Bunting
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire, Durham, USA
| | - Krysten Schuler
- Cornell Wildlife Health Lab, Animal Health Diagnostic Center, Cornell College of Veterinary Medicine, Ithaca, New York, USA
| | - Michael J. Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| |
Collapse
|
31
|
Lei R, Qing E, Odle A, Yuan M, Tan TJ, So N, Ouyang WO, Wilson IA, Gallagher T, Perlman S, Wu NC, Wong LYR. Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569051. [PMID: 38076875 PMCID: PMC10705381 DOI: 10.1101/2023.11.28.569051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we performed a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identified mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we showed that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.
Collapse
Affiliation(s)
- Ruipeng Lei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Natalie So
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wenhao O. Ouyang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
- Center for Virus-Host-Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| |
Collapse
|
32
|
Desai PJ. Expression and fusogenic activity of SARS CoV-2 Spike protein displayed in the HSV-1 Virion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.568860. [PMID: 38076893 PMCID: PMC10705244 DOI: 10.1101/2023.11.28.568860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is a zoonotic pathogen that can cause severe respiratory disease in humans. The new SARS-CoV-2 is the cause of the current global pandemic termed coronavirus disease 2019 (COVID-19) that has resulted in many millions of deaths world-wide. The virus is a member of the Betacoronavirus family, its genome is a positive strand RNA molecule that encodes for many genes which are required for virus genome replication as well as for structural proteins that are required for virion assembly and maturation. A key determinant of this virus is the Spike (S) protein embedded in the virion membrane and mediates attachment of the virus to the receptor (ACE2). This protein also is required for cell-cell fusion (syncytia) that is an important pathogenic determinant. We have developed a pseudotyped herpes simplex virus type 1 (HSV-1) recombinant virus expressing S protein in the virion envelop. This virus has also been modified to express a Venus fluorescent protein fusion to VP16, a virion protein of HSV-1. The virus expressing Spike can enter cells and generates large multi-nucleated syncytia which are evident by the Venus fluorescence. The HSV-1 recombinant virus is genetically stable and virus amplification can be easily done by infecting cells. This recombinant virus provides a reproducible platform for Spike function analysis and thus adds to the repertoire of pseudotyped viruses expressing Spike.
Collapse
Affiliation(s)
- Prashant J. Desai
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
33
|
Yu S, Zheng X, Zhou Y, Gao Y, Zhou B, Zhao Y, Li T, Li Y, Mou J, Cui X, Yang Y, Li D, Chen M, Lavillette D, Meng G. Antibody-mediated spike activation promotes cell-cell transmission of SARS-CoV-2. PLoS Pathog 2023; 19:e1011789. [PMID: 37948454 PMCID: PMC10664894 DOI: 10.1371/journal.ppat.1011789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/22/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
The COVID pandemic fueled by emerging SARS-CoV-2 new variants of concern remains a major global health concern, and the constantly emerging mutations present challenges to current therapeutics. The spike glycoprotein is not only essential for the initial viral entry, but is also responsible for the transmission of SARS-CoV-2 components via syncytia formation. Spike-mediated cell-cell transmission is strongly resistant to extracellular therapeutic and convalescent antibodies via an unknown mechanism. Here, we describe the antibody-mediated spike activation and syncytia formation on cells displaying the viral spike. We found that soluble antibodies against receptor binding motif (RBM) are capable of inducing the proteolytic processing of spike at both the S1/S2 and S2' cleavage sites, hence triggering ACE2-independent cell-cell fusion. Mechanistically, antibody-induced cell-cell fusion requires the shedding of S1 and exposure of the fusion peptide at the cell surface. By inhibiting S1/S2 proteolysis, we demonstrated that cell-cell fusion mediated by spike can be re-sensitized towards antibody neutralization in vitro. Lastly, we showed that cytopathic effect mediated by authentic SARS-CoV-2 infection remain unaffected by the addition of extracellular neutralization antibodies. Hence, these results unveil a novel mode of antibody evasion and provide insights for antibody selection and drug design strategies targeting the SARS-CoV-2 infected cells.
Collapse
Affiliation(s)
- Shi Yu
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Xu Zheng
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Yanqiu Zhou
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yuhui Gao
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Bingjie Zhou
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Yapei Zhao
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
| | - Tingting Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yunyi Li
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jiabin Mou
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoxian Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yuying Yang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS), Shanghai, China
| | - Min Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Dimitri Lavillette
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
- Pasteurien College, Soochow University, Suzhou, Jiangsu, China
- Applied Molecular Virology Laboratory, Discovery Biology Department, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Guangxun Meng
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, University of Chinese Academy of Sciences, Shanghai, China
- Pasteurien College, Soochow University, Suzhou, Jiangsu, China
- Nanjing Advanced Academy of Life and Health, Nanjing, Jiangsu, China
| |
Collapse
|
34
|
Chen Y, Liu X, Zheng JN, Yang LJ, Luo Y, Yao YL, Liu MQ, Xie TT, Lin HF, He YT, Zhou P, Hu B, Tian RJ, Shi ZL. N-linked glycoproteins and host proteases are involved in swine acute diarrhea syndrome coronavirus entry. J Virol 2023; 97:e0091623. [PMID: 37772826 PMCID: PMC10617469 DOI: 10.1128/jvi.00916-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
IMPORTANCE Gaining insight into the cell-entry mechanisms of swine acute diarrhea syndrome coronavirus (SADS-CoV) is critical for investigating potential cross-species infections. Here, we demonstrated that pretreatment of host cells with tunicamycin decreased SADS-CoV attachment efficiency, indicating that N-linked glycosylation of host cells was involved in SADS-CoV entry. Common N-linked sugars Neu5Gc and Neu5Ac did not interact with the SADS-CoV S1 protein, suggesting that these molecules were not involved in SADS-CoV entry. Additionally, various host proteases participated in SADS-CoV entry into diverse cells with different efficiencies. Our findings suggested that SADS-CoV may exploit multiple pathways to enter cells, providing insights into intervention strategies targeting the cell entry of this virus.
Collapse
Affiliation(s)
- Ying Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiang-Nan Zheng
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Li-Jun Yang
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Yun Luo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Lin Yao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Mei-Qin Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ting-ting Xie
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao-Feng Lin
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Tong He
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhou
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Rui-Jun Tian
- Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen, China
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
35
|
Dabrell SN, Li YC, Yamaguchi H, Chen HF, Hung MC. Herbal Compounds Dauricine and Isoliensinine Impede SARS-CoV-2 Viral Entry. Biomedicines 2023; 11:2914. [PMID: 38001915 PMCID: PMC10669532 DOI: 10.3390/biomedicines11112914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Targeting viral entry has been the focal point for the last 3 years due to the continued threat posed by SARS-CoV-2. SARS-CoV-2's entry is highly dependent on the interaction between the virus's Spike protein and host receptors. The virus's Spike protein is a key modulator of viral entry, allowing sequential cleavage of ACE2 at the S1/S2 and S2 sites, resulting in the amalgamation of membranes and subsequent entry of the virus. A Polybasic insertion (PRRAR) conveniently located at the S1/S2 site can also be cleaved by furin or by serine protease, TMPRSS2, at the cell surface. Since ACE2 and TMPRSS2 are conveniently located on the surface of host cells, targeting one or both receptors may inhibit receptor-ligand interaction. Here, we show that Dauricine and Isoliensinine, two commonly used herbal compounds, were capable of inhibiting SARS-CoV-2 viral entry by reducing Spike-ACE2 interaction but not suppressing TMPRSS2 protease activity. Further, our biological assays using pseudoviruses engineered to express Spike proteins of different variants revealed a reduction in infection rates following treatment with these compounds. The molecular modeling revealed an interconnection between R403 of Spike protein and both two compounds. Spike mutations at residue R403 are critical, and often utilized by ACE2 to gain cell access. Overall, our findings strongly suggest that Dauricine and Isoliensinine are effective in blocking Spike-ACE2 interaction and may serve as effective therapeutic agents for targeting SARS-CoV-2's viral entry.
Collapse
Affiliation(s)
- Shaneek Natoya Dabrell
- International Master's Program of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
| | - Yi-Chuan Li
- Department of Biological Science and Technology, China Medical University, Taichung 406040, Taiwan
| | - Hirohito Yamaguchi
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Center for Molecular Medicine, China Medical University Hospital, China Medical University, Taichung 406040, Taiwan
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 406040, Taiwan
- Institute of Biochemistry and Molecular Biology, China Medical University, Taichung 406040, Taiwan
- Department of Biotechnology, Asia University, Taichung 413305, Taiwan
| |
Collapse
|
36
|
Khatri R, Lohiya B, Kaur G, Maithil V, Goswami A, Sarmadhikari D, Asthana S, Samal S. Understanding the role of conserved proline and serine residues in the SARS-CoV-2 spike cleavage sites in the virus entry, fusion, and infectivity. 3 Biotech 2023; 13:323. [PMID: 37663753 PMCID: PMC10469153 DOI: 10.1007/s13205-023-03749-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
The spike (S) glycoprotein of the SARS-CoV-2 virus binds to the host cell receptor and promotes the virus's entry into the target host cell. This interaction is primed by host cell proteases like furin and TMPRSS2, which act at the S1/S2 and S2´ cleavage sites, respectively. Both cleavage sites have serine or proline residues flanking either the single or polybasic region and were found to be conserved in coronaviruses. Unravelling the effects of these conserved residues on the virus entry and infectivity might facilitate the development of novel therapeutics. Here, we have investigated the role of the conserved serine and proline residues in the SARS-CoV-2 spike mediated entry, fusogenicity, and viral infectivity by using the HIV-1/spike-based pseudovirus system. A conserved serine residue mutation to alanine (S2´S-A) at the S2´ cleavage site resulted in the complete loss of spike cleavage. Exogenous treatment with trypsin or overexpression of TMPRSS2 protease could not rescue the loss of spike cleavage and biological activity. The S2´S-A mutant showed no significant responses against E-64d, TMPRSS2 or other relevant inhibitors. Taken together, serine at the S2´ site in the spike protein was indispensable for spike protein cleavage and virus infectivity. Thus, novel interventions targeting the conserved serine at the S2´ cleavage site should be explored to reduce severe disease caused by SARS-CoV-2-and novel emerging variants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03749-y.
Collapse
Affiliation(s)
- Ritika Khatri
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Bharat Lohiya
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Gurleen Kaur
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Vikas Maithil
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Abhishek Goswami
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Debapriyo Sarmadhikari
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Shailendra Asthana
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Sweety Samal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| |
Collapse
|
37
|
Odongo L, Habtegebrael BH, Kiessling V, White JM, Tamm LK. A novel in vitro system of supported planar endosomal membranes (SPEMs) reveals an enhancing role for cathepsin B in the final stage of Ebola virus fusion and entry. Microbiol Spectr 2023; 11:e0190823. [PMID: 37728342 PMCID: PMC10581071 DOI: 10.1128/spectrum.01908-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/17/2023] [Indexed: 09/21/2023] Open
Abstract
Ebola virus (EBOV) causes a hemorrhagic fever with fatality rates up to 90%. The EBOV entry process is complex and incompletely understood. Following attachment to host cells, EBOV is trafficked to late endosomes/lysosomes where its glycoprotein (GP) is processed to a 19-kDa form, which binds to the EBOV intracellular receptor Niemann-Pick type C1. We previously showed that the cathepsin protease inhibitor, E-64d, blocks infection by pseudovirus particles bearing 19-kDa GP, suggesting that further cathepsin action is needed to trigger fusion. This, however, has not been demonstrated directly. Since 19-kDa Ebola GP fusion occurs in late endosomes, we devised a system in which enriched late endosomes are used to prepare supported planar endosomal membranes (SPEMs), and fusion of fluorescent (pseudo)virus particles is monitored by total internal reflection fluorescence microscopy. We validated the system by demonstrating the pH dependencies of influenza virus hemagglutinin (HA)-mediated and Lassa virus (LASV) GP-mediated fusion. Using SPEMs, we showed that fusion mediated by 19-kDa Ebola GP is dependent on low pH, enhanced by Ca2+, and augmented by the addition of cathepsins. Subsequently, we found that E-64d inhibits full fusion, but not lipid mixing, mediated by 19-kDa GP, which we corroborated with the reversible cathepsin inhibitor VBY-825. Hence, we provide both gain- and loss-of-function evidence that further cathepsin action enhances the fusion activity of 19-kDa Ebola GP. In addition to providing new insights into how Ebola GP mediates fusion, the approach we developed employing SPEMs can now be broadly used for studies of virus and toxin entry through endosomes. IMPORTANCE Ebola virus is the causative agent of Ebola virus disease, which is severe and frequently lethal. EBOV gains entry into cells via late endosomes/lysosomes. The events immediately preceding fusion of the viral and endosomal membranes are incompletely understood. In this study, we report a novel in vitro system for studying virus fusion with endosomal membranes. We validated the system by demonstrating the low pH dependencies of influenza and Lassa virus fusion. Moreover, we show that further cathepsin B action enhances the fusion activity of the primed Ebola virus glycoprotein. Finally, this model endosomal membrane system should be useful in studying the mechanisms of bilayer breaching by other enveloped viruses, by non-enveloped viruses, and by acid-activated bacterial toxins.
Collapse
Affiliation(s)
- Laura Odongo
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Betelihem H. Habtegebrael
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Volker Kiessling
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Judith M. White
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Lukas K. Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| |
Collapse
|
38
|
Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
Collapse
Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| |
Collapse
|
39
|
Olarte-Castillo XA, Plimpton L, McQueary H, Sun Y, Yu YT, Cover S, Richardson AN, Jin Y, Grenier JK, Cummings KJ, Bunting E, Diuk-Wasser M, Needle D, Schuler K, Stanhope MJ, Whittaker G, Goodman LB. Detection and characterization of novel luchacoviruses, genus Alphacoronavirus, shed in saliva and feces of meso-carnivores in the northeastern United States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.541188. [PMID: 37745528 PMCID: PMC10515766 DOI: 10.1101/2023.05.31.541188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Small to mid-sized carnivores, or meso-carnivores, comprise a group of diverse mammals, many of which can adapt to anthropogenically disturbed environments. Wild meso-carnivores living in urban areas may get exposed to or spread pathogens to other species, including stray/feral domestic animals. Several coronaviruses (CoVs) have been detected in domesticated and farmed meso-carnivores, but knowledge of CoVs circulating in free-ranging wild meso-carnivores remains limited. In this study, we analyzed 321 samples collected between 2016 and 2022 from 9 species of free-ranging wild meso-carnivores and stray/feral domestic cats in the northeastern United States. Using a pan-CoV PCR, we screened tissues, feces, and saliva, nasal, and rectal swabs. We detected CoV RNA in fecal and saliva samples of animals in four species: fisher (Pekania pennanti), bobcat (Lynx rufus), red fox (Vulpes vulpes), and domestic cat (Felis catus). Next-generation sequencing revealed that all these viruses belonged to the Luchacovirus subgenus (Alphacoronavirus genus), previously reported only in rodents and lagomorphs (i.e., rabbits). Genetic comparison of the 3'-end of the genome (~12,000bp) revealed that although the viruses detected group with, and have a genetic organization similar to other luchacoviruses, they are genetically distinct from those from rodents and lagomorphs. Genetic characterization of the spike protein revealed that the meso-carnivore luchacoviruses do not have an S1/S2 cleavage motif but do have highly variable structural loops containing cleavage motifs similar to those identified in certain pathogenic CoVs. This study highlights the importance of characterizing the spike protein of CoVs in wild species for further targeted epidemiologic monitoring.
Collapse
Affiliation(s)
- Ximena A. Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Laura Plimpton
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Holly McQueary
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Yining Sun
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Y. Tina Yu
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Sarah Cover
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Amy N. Richardson
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Yuhan Jin
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Jennifer K. Grenier
- Transcriptional Regulation and Expression Facility, Biotechnology Resource Center, Institute of Biotechnology, Cornell University
| | - Kevin J. Cummings
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Elizabeth Bunting
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Maria Diuk-Wasser
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - David Needle
- New Hampshire Veterinary Diagnostic Laboratory, College of Life Sciences and Agriculture, University of New Hampshire
| | - Krysten Schuler
- Cornell Wildlife Health Lab, Animal Health Diagnostic Center, Cornell College of Veterinary Medicine, 240 Farrier Road, Ithaca, NY 14853
| | - Michael J. Stanhope
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gary Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Laura B. Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| |
Collapse
|
40
|
Niort K, Dancourt J, Boedec E, Al Amir Dache Z, Lavieu G, Tareste D. Cholesterol and Ceramide Facilitate Membrane Fusion Mediated by the Fusion Peptide of the SARS-CoV-2 Spike Protein. ACS OMEGA 2023; 8:32729-32739. [PMID: 37720777 PMCID: PMC10500581 DOI: 10.1021/acsomega.3c03610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 09/19/2023]
Abstract
SARS-CoV-2 entry into host cells is mediated by the Spike (S) protein of the viral envelope. The S protein is composed of two subunits: S1 that induces binding to the host cell via its interaction with the ACE2 receptor of the cell surface and S2 that triggers fusion between viral and cellular membranes. Fusion by S2 depends on its heptad repeat domains that bring membranes close together and its fusion peptide (FP) that interacts with and perturbs the membrane structure to trigger fusion. Recent studies have suggested that cholesterol and ceramide lipids from the cell surface may facilitate SARS-CoV-2 entry into host cells, but their exact mode of action remains unknown. We have used a combination of in vitro liposome-liposome and in situ cell-cell fusion assays to study the lipid determinants of S-mediated membrane fusion. Our findings reveal that both cholesterol and ceramide lipids facilitate fusion, suggesting that targeting these lipids could be effective against SARS-CoV-2. As a proof of concept, we examined the effect of chlorpromazine (CPZ), an antipsychotic drug known to perturb membrane structure. Our results show that CPZ effectively inhibits S-mediated membrane fusion, thereby potentially impeding SARS-CoV-2 entry into the host cell.
Collapse
Affiliation(s)
- Kristina Niort
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Julia Dancourt
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Erwan Boedec
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| | - Zahra Al Amir Dache
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - Grégory Lavieu
- Université
Paris Cité, Inserm U 1316, CNRS UMR 7057, Laboratoire Matières
et Systèmes Complexes (MSC), Paris 75006, France
| | - David Tareste
- Université
Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and
Neuroscience of Paris (IPNP), Paris 75014, France
| |
Collapse
|
41
|
Landry SJ, Mettu RR, Kolls JK, Aberle JH, Norton E, Zwezdaryk K, Robinson J. Structural Framework for Analysis of CD4+ T-Cell Epitope Dominance in Viral Fusion Proteins. Biochemistry 2023; 62:2517-2529. [PMID: 37554055 PMCID: PMC10483696 DOI: 10.1021/acs.biochem.3c00335] [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: 06/28/2023] [Revised: 07/31/2023] [Indexed: 08/10/2023]
Abstract
Antigen conformation shapes CD4+ T-cell specificity through mechanisms of antigen processing, and the consequences for immunity may rival those from conformational effects on antibody specificity. CD4+ T cells initiate and control immunity to pathogens and cancer and are at least partly responsible for immunopathology associated with infection, autoimmunity, and allergy. The primary trigger for CD4+ T-cell maturation is the presentation of an epitope peptide in the MHC class II antigen-presenting protein (MHCII), most commonly on an activated dendritic cell, and then the T-cell responses are recalled by subsequent presentations of the epitope peptide by the same or other antigen-presenting cells. Peptide presentation depends on the proteolytic fragmentation of the antigen in an endosomal/lysosomal compartment and concomitant loading of the fragments into the MHCII, a multistep mechanism called antigen processing and presentation. Although the role of peptide affinity for MHCII has been well studied, the role of proteolytic fragmentation has received less attention. In this Perspective, we will briefly summarize evidence that antigen resistance to unfolding and proteolytic fragmentation shapes the specificity of the CD4+ T-cell response to selected viral envelope proteins, identify several remarkable examples in which the immunodominant CD4+ epitopes most likely depend on the interaction of processing machinery with antigen conformation, and outline how knowledge of antigen conformation can inform future efforts to design vaccines.
Collapse
Affiliation(s)
- Samuel J. Landry
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Ramgopal R. Mettu
- Department
of Computer Science, Tulane University, New Orleans, Louisiana 70118, United States
| | - Jay K. Kolls
- John
W. Deming Department of Internal Medicine, Center for Translational
Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Judith H. Aberle
- Center
for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elizabeth Norton
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Kevin Zwezdaryk
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - James Robinson
- Department
of Pediatrics, Tulane University School
of Medicine, New Orleans, Louisiana 70112, United States
| |
Collapse
|
42
|
Paul DC, Bhattacharjee M, Mahato DR, Sarma MP. Natural furin inhibitor(s) as potent therapeutic molecule to mitigate SARS-CoV-2 infection. J Biomol Struct Dyn 2023; 41:7365-7371. [PMID: 36099195 DOI: 10.1080/07391102.2022.2121760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/29/2022] [Indexed: 10/14/2022]
Abstract
The COVID 2019 has had been going pandemic as per WHO situation reports. The major differentiating point in this virus is the presence of a unique furin cleavage site. Our insilico study points out to the effectiveness of a potent plant origin furin inhibitor. We exploited the aspect of the cleavage machinery of furin subunits which is critical and indispensible to the entry of SARS-CoV-2 in human cells and subsequent massive contagion. In-silico analysis was done to observe the interactions of proposed analogs of protease inhibitor of plant origin against furin protein as well as the furin spike glycoprotein (SGP) binding machinery. This was done by docking protocols using Hex 6.0 software followed by molecular Dynamic simulation (MDS) analysis in 100 ns scale using Amber94. Further, the images were analysed with PyMol software. The analogs I, II and III included in our study showed strong interactivity against furin individually, as well as the furin-Spike Glycoprotein 1 binding machinery. The findings were confirmed using molecular dynamic simulation analysis which indicated good structural stability and ability to neutralise furin and furin-spike glycoprotein 1. Analog II was found to be the best interactive molecule against furin, showing the least deviation (1.484 ± 0.0064). Also, it was the most effective against furin + Spike glycoprotein I machinery [1.575 ± 0.01]. We report the first of its kind of natural furin inhibitor(s) which would disrupt the furin machinery of SARS-CoV-2 and help in controlling the COVID-19 contagion.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Dhiman Chandra Paul
- Department of Biotechnology, Assam Down Town University, Guwahati, Assam, India
| | | | - Dhani Ram Mahato
- Institut de Química Computacional i Catàlisi, Universitat de Girona, Girona, Spain
| | - Manash Pratim Sarma
- Department of Biotechnology, Assam Down Town University, Guwahati, Assam, India
| |
Collapse
|
43
|
Bader SM, Cooney JP, Sheerin D, Taiaroa G, Harty L, Davidson KC, Mackiewicz L, Dayton M, Wilcox S, Whitehead L, Rogers KL, Georgy SR, Coussens AK, Grimley SL, Corbin V, Pitt M, Coin L, Pickering R, Thomas M, Allison CC, McAuley J, Purcell DFJ, Doerflinger M, Pellegrini M. SARS-CoV-2 mouse adaptation selects virulence mutations that cause TNF-driven age-dependent severe disease with human correlates. Proc Natl Acad Sci U S A 2023; 120:e2301689120. [PMID: 37523564 PMCID: PMC10410703 DOI: 10.1073/pnas.2301689120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023] Open
Abstract
The diversity of COVID-19 disease in otherwise healthy people, from seemingly asymptomatic infection to severe life-threatening disease, is not clearly understood. We passaged a naturally occurring near-ancestral SARS-CoV-2 variant, capable of infecting wild-type mice, and identified viral genomic mutations coinciding with the acquisition of severe disease in young adult mice and lethality in aged animals. Transcriptomic analysis of lung tissues from mice with severe disease elucidated a host antiviral response dominated mainly by interferon and IL-6 pathway activation in young mice, while in aged animals, a fatal outcome was dominated by TNF and TGF-β signaling. Congruent with our pathway analysis, we showed that young TNF-deficient mice had mild disease compared to controls and aged TNF-deficient animals were more likely to survive infection. Emerging clinical correlates of disease are consistent with our preclinical studies, and our model may provide value in defining aberrant host responses that are causative of severe COVID-19.
Collapse
Affiliation(s)
- Stefanie M. Bader
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - James P. Cooney
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Dylan Sheerin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - George Taiaroa
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Leigh Harty
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Kathryn C. Davidson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Liana Mackiewicz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
| | - Merle Dayton
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Lachlan Whitehead
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Kelly L. Rogers
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Smitha Rose Georgy
- Anatomic Pathology, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Melbourne, VIC3030, Australia
| | - Anna K. Coussens
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Samantha L. Grimley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Vincent Corbin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Miranda Pitt
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Lachlan Coin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Raelene Pickering
- Department of Diabetes, Monash University, Central Clinical School, Level 5, Alfred Centre, Melbourne, VIC3004, Australia
| | - Merlin Thomas
- Department of Diabetes, Monash University, Central Clinical School, Level 5, Alfred Centre, Melbourne, VIC3004, Australia
| | - Cody C. Allison
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Damian F. J. Purcell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC3000, Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC3052, Australia
| |
Collapse
|
44
|
Ou X, Xu G, Li P, Liu Y, Zan F, Liu P, Hu J, Lu X, Dong S, Zhou Y, Mu Z, Wu Z, Wang J, Jin Q, Liu P, Lu J, Wang X, Qian Z. Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses. Cell Discov 2023; 9:78. [PMID: 37507385 PMCID: PMC10382498 DOI: 10.1038/s41421-023-00581-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
The bat coronaviruses (CoV) BANAL-20-52 and BANAL-20-236 are two newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) closely related coronaviruses (SC2r-CoV) and the genome of BANAL-20-52 shares the highest homology with SARS-CoV-2. However, the risk of their potential zoonotic transmission has not been fully evaluated. Here, we determined their potential host susceptibility among 13 different bat species and 26 different animal species, and found that both might have extensive host ranges, indicating high zoonotic transmission potential. We also determined the cryo-EM structures of BANAL-20-52 and BANAL-20-236 S proteins at pH 5.5 and the complex of BANAL-20-236 S1 and Rhinolophus affinis ACE2, and found that both trimeric S proteins adopt all three receptor binding domains (RBDs) in "closed" conformation and are more compact than SARS-CoV-2. Strikingly, the unique sugar moiety at N370 of bat SC2r-CoVs acts like a "bolt" and crosses over two neighboring subunits, facilitating the S proteins in the locked conformation and underpinning the architecture stability. Removal of the glycosylation at N370 by a T372A substitution substantially enhances virus infectivity but becomes highly sensitive to trypsin digestion at pH 5.5, a condition roughly mimicking the insectivorous bat's stomach digestion. In contrast, WT S proteins of SC2r-CoVs showed considerable resistance to trypsin digestion at pH 5.5, indicating that the highly conserved T372 in bat CoVs might result from the selective advantages in stability during the fecal-oral transmission over A372. Moreover, the results of cross-immunogenicity among S proteins of SARS-CoV-2, BANAL-20-52, and BANAL-20-236 showed that A372 pseudoviruses are more sensitive to anti-S sera than T372, indicating that immune evasion might also play a role in the natural selection of T372 over A372 during evolution. Finally, residues 493 and 498 of the S protein affect host susceptibility, and residue 498 also influences the immunogenicity of the S protein. Together, our findings aid a better understanding of the molecular basis of CoV entry, selective evolution, and immunogenicity and highlight the importance of surveillance of susceptible hosts of these viruses to prevent potential outbreaks.
Collapse
Affiliation(s)
- Xiuyuan Ou
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ge Xu
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Pei Li
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yan Liu
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fuwen Zan
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Pan Liu
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiaxin Hu
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xing Lu
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Siwen Dong
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yao Zhou
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhixia Mu
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhiqiang Wu
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi Jin
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Pinghuang Liu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jian Lu
- College of Life Sciences, Peking University, Beijing, China
| | - Xiangxi Wang
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Zhaohui Qian
- Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| |
Collapse
|
45
|
Xia X. Identification of host receptors for viral entry and beyond: a perspective from the spike of SARS-CoV-2. Front Microbiol 2023; 14:1188249. [PMID: 37560522 PMCID: PMC10407229 DOI: 10.3389/fmicb.2023.1188249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
Identification of the interaction between the host membrane receptor and viral receptor-binding domain (RBD) represents a crucial step for understanding viral pathophysiology and for developing drugs against pathogenic viruses. While all membrane receptors and carbohydrate chains could potentially be used as receptors for viruses, prioritized searches focus typically on membrane receptors that are known to have been used by the relatives of the pathogenic virus, e.g., ACE2 used as a receptor for SARS-CoV is a prioritized candidate receptor for SARS-CoV-2. An ideal receptor protein from a viral perspective is one that is highly expressed in epithelial cell surface of mammalian respiratory or digestive tracts, strongly conserved in evolution so many mammalian species can serve as potential hosts, and functionally important so that its expression cannot be readily downregulated by the host in response to the infection. Experimental confirmation of host receptors includes (1) infection studies with cell cultures/tissues/organs with or without candidate receptor expression, (2) experimental determination of protein structure of the complex between the putative viral RDB and the candidate host receptor, and (3) experiments with mutant candidate receptor or homologues of the candidate receptor in other species. Successful identification of the host receptor opens the door for mechanism-based development of candidate drugs and vaccines and facilitates the inference of what other animal species are vulnerable to the viral pathogen. I illustrate these approaches with research on identification of the receptor and co-factors for SARS-CoV-2.
Collapse
Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
46
|
Xie E, Ahmad S, Smyth RP, Sieben C. Advanced fluorescence microscopy in respiratory virus cell biology. Adv Virus Res 2023; 116:123-172. [PMID: 37524480 DOI: 10.1016/bs.aivir.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Respiratory viruses are a major public health burden across all age groups around the globe, and are associated with high morbidity and mortality rates. They can be transmitted by multiple routes, including physical contact or droplets and aerosols, resulting in efficient spreading within the human population. Investigations of the cell biology of virus replication are thus of utmost importance to gain a better understanding of virus-induced pathogenicity and the development of antiviral countermeasures. Light and fluorescence microscopy techniques have revolutionized investigations of the cell biology of virus infection by allowing the study of the localization and dynamics of viral or cellular components directly in infected cells. Advanced microscopy including high- and super-resolution microscopy techniques available today can visualize biological processes at the single-virus and even single-molecule level, thus opening a unique view on virus infection. We will highlight how fluorescence microscopy has supported investigations on virus cell biology by focusing on three major respiratory viruses: respiratory syncytial virus (RSV), Influenza A virus (IAV) and SARS-CoV-2. We will review our current knowledge of virus replication and highlight how fluorescence microscopy has helped to improve our state of understanding. We will start by introducing major imaging and labeling modalities and conclude the chapter with a perspective discussion on remaining challenges and potential opportunities.
Collapse
Affiliation(s)
- Enyu Xie
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Shazeb Ahmad
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany; Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Christian Sieben
- Nanoscale Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany; Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany.
| |
Collapse
|
47
|
Li Y, Shen Y, Zhang Y, Yan R. Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants. Viruses 2023; 15:1398. [PMID: 37376697 PMCID: PMC10304477 DOI: 10.3390/v15061398] [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: 05/13/2023] [Revised: 06/08/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S protein) compared to the original wild-type (WT) strain. Here we report the cryo-EM structures of the trimeric S proteins from the BA.1, BA.2, BA.3, and BA.4/BA.5 subvariants, with BA.4 and BA.5 sharing the same S protein mutations, each in complex with the surface receptor ACE2. All three receptor-binding domains of the S protein from BA.2 and BA.4/BA.5 are "up", while the BA.1 S protein has two "up" and one "down". The BA.3 S protein displays increased heterogeneity, with the majority in the all "up" RBD state. The different conformations preferences of the S protein are consistent with their varied transmissibility. By analyzing the position of the glycan modification on Asn343, which is located at the S309 epitopes, we have uncovered the underlying immune evasion mechanism of the Omicron subvariants. Our findings provide a molecular basis of high infectivity and immune evasion of Omicron subvariants, thereby offering insights into potential therapeutic interventions against SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Yaning Li
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yaping Shen
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yuanyuan Zhang
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Renhong Yan
- Key University Laboratory of Metabolism and Health of Guangdong, Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
48
|
Mubashshir M, Ahmad N, Negi T, Rawal R, Singhvi N, Khatoon H, Laxmi V, Dubey O, Sharma RB, Negi G, Ovais M. Therapeutic Benefits of Melatonin against COVID-19. Neuroimmunomodulation 2023; 30:196-205. [PMID: 37336193 PMCID: PMC10614475 DOI: 10.1159/000531550] [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: 03/23/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
The assumption of the pineal hormone melatonin as a therapeutic use for COVID-19-affected people seems promising. Its intake has shown significant improvement in the patients' conditions. Higher melatonin titers in children may provide a protective shield against this disease. The hormone melatonin works as an anti-inflammatory, antioxidant, immunomodulator, and strategically slows down the cytokine release which is observed in the COVID-19 disease, thereby improving the overall health of afflicted patients. The medical community is expected shortly to use remedial attributes like anti-inflammatory, antioxidant, antivirals, etc., of melatonin in the successful prevention and cure of COVID-19 morbidity. Thus, the administration of melatonin seems auspicious in the cure and prevention of this COVID-19 fatality. Moreover, melatonin does not seem to reduce the efficiency of approved vaccines against the SARS-CoV-2 virus. Melatonin increases the production of inflammatory cytokines and Th1 and enhances both humoral and cell-mediated responses. Through the enhanced humoral immunity, melatonin exhibits antiviral activities by suppressing multiple inflammatory products such as IL-6, IL1β, and tumor necrosis factor α, which are immediately released during lung injury of severe COVID-19. Hence, the novel use of melatonin along with other antivirals as an early treatment option against COVID-19 infection is suggested. Here, we have chalked out the invasion mechanisms and appropriate implications of the latest findings concerned with melatonin against the virus SARS-CoV-2. Nevertheless, within the setting of a clinical intervention, the promising compounds must go through a series of studies before their recommendation. In the clinical field, this is done in a time-ordered sequence, in line with the phase label affixed to proper protocol of trials: phase I-phase II and the final phase III. Nevertheless, while medical recommendations can only be made on the basis of reassuring evidence, there are still three issues worth considering before implementation: representativeness, validity, and lastly generalizability.
Collapse
Affiliation(s)
- Muhammad Mubashshir
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Nabeel Ahmad
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Tripti Negi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Renu Rawal
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Hina Khatoon
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Vijya Laxmi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Om Dubey
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Renu Bala Sharma
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Ganga Negi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, India
| | - Mohd Ovais
- Department of Bio-Science, Barkatullah University, Bhopal, India
| |
Collapse
|
49
|
Qiu R, Chen F, Álvarez Z, Clemons TD, Biswas S, Karver MR, Takata N, Sai H, Peng H, Weigand S, Palmer LC, Stupp SI. Supramolecular Nanofibers Block SARS-CoV-2 Entry into Human Host Cells. ACS APPLIED MATERIALS & INTERFACES 2023; 15:26340-26348. [PMID: 37235485 DOI: 10.1021/acsami.3c02447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection relies on its spike protein binding to angiotensin-converting enzyme 2 (ACE2) on host cells to initiate cellular entry. Blocking the interactions between the spike protein and ACE2 offers promising therapeutic opportunities to prevent infection. We report here on peptide amphiphile supramolecular nanofibers that display a sequence from ACE2 in order to promote interactions with the SARS-CoV-2 spike receptor binding domain. We demonstrate that displaying this sequence on the surface of supramolecular assemblies preserves its α-helical conformation and blocks the entry of a pseudovirus and its two variants into human host cells. We also found that the chemical stability of the bioactive structures was enhanced in the supramolecular environment relative to the unassembled peptide molecules. These findings reveal unique advantages of supramolecular peptide therapies to prevent viral infections and more broadly for other targets as well.
Collapse
Affiliation(s)
- Ruomeng Qiu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Feng Chen
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Zaida Álvarez
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Medicine, Northwestern University, 676 N. St. Clair Street, Chicago, Illinois 60611, United States
| | - Tristan D Clemons
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Suvendu Biswas
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Mark R Karver
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Nozomu Takata
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Hiroaki Sai
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Han Peng
- Department of Dermatology, Northwestern University, 303 E. Superior Street, Chicago, Illinois 60611, United States
| | - Steven Weigand
- DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) Synchrotron Research Center, Advanced Photon Source (APS)/Argonne National Laboratory 432-A004, Northwestern University, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Liam C Palmer
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Samuel I Stupp
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Medicine, Northwestern University, 676 N. St. Clair Street, Chicago, Illinois 60611, United States
| |
Collapse
|
50
|
Guenthoer J, Lilly M, Starr TN, Dadonaite B, Lovendahl KN, Croft JT, Stoddard CI, Chohan V, Ding S, Ruiz F, Kopp MS, Finzi A, Bloom JD, Chu HY, Lee KK, Overbaugh J. Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection. Proc Natl Acad Sci U S A 2023; 120:e2220948120. [PMID: 37253011 PMCID: PMC10265947 DOI: 10.1073/pnas.2220948120] [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: 01/27/2023] [Accepted: 04/28/2023] [Indexed: 06/01/2023] Open
Abstract
The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor-binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are unique in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
Collapse
Affiliation(s)
- Jamie Guenthoer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Michelle Lilly
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Tyler N. Starr
- Department of Biochemistry, University of Utah, Salt Lake City, UT84112
| | | | - Klaus N. Lovendahl
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Jacob T. Croft
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | | | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
| | - Felicitas Ruiz
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Mackenzie S. Kopp
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QCH2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QCH2X 0A9, Canada
| | - Jesse D. Bloom
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- HHMI, Seattle, WA98195
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA98195
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA98195
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| |
Collapse
|