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Viruses
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Mechanism of Receptor Recognition in Coronavirus
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Mechanism of Receptor Recognition in Coronavirus

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Coronaviruses".

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 10818

Special Issue Editor

Dr. Qibin Geng

E-Mail Website
Guest Editor
Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
Interests: virus; host; structure; biology; cells; biochemistry; protein; gene; vaccines; immunology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, the scientific community has made remarkable advancements in unraveling the mechanisms of receptor recognition in coronaviruses, a critical facet in the field of virology. Early research delineated the pivotal role of spike (S) proteins in facilitating virus entry into host cells, laying a solid foundation for subsequent, more detailed investigations. A significant breakthrough came in the early 2000s with the identification of the ACE2 receptor as a key entry point for SARS-CoV. This was followed by the discovery of DPP4 as the receptor for MERS-CoV, further underscoring the receptor diversity among different coronaviruses. More recently, during the COVID-19 pandemic, the critical role of the ACE2 receptor in SARS-CoV-2 entry was elucidated, marking a pivotal moment in contemporary research. The rapid response to the COVID-19 outbreak saw an unprecedented focus in this field, with researchers swiftly pinpointing the involvement of proteases like TMPRSS2 in virus entry, thereby opening new avenues for therapeutic interventions. Complementing these efforts, advancements in structural biology have facilitated high-resolution mapping of virus–receptor interactions, offering a molecular blueprint for the development of targeted therapeutics.

As the field of coronavirus receptor recognition advances, it is confronted with a myriad of intricate challenges, each holding significant importance and necessitating a multifaceted approach for effective navigation. Among these challenges is the burgeoning exploration into the roles of alternative receptors and co-receptors, which highlights the complex virus–host dynamics that define these pathogens. This is exacerbated by the rapid mutation rates observed in the spike proteins of certain coronaviruses, a phenomenon that continually threatens to undermine the efficacy of existing vaccines and therapeutics. Adding to this complexity is the broad host range that coronaviruses exhibit, encompassing various animal species, which introduces additional layers of complexity to the study of receptor recognition mechanisms. As we navigate this critical juncture, it becomes increasingly clear that a comprehensive understanding of these dynamics is pivotal in crafting strategies that can effectively curb the spread and mitigate the impact of these viruses, marking significant strides in contemporary virological research. This evolving landscape sets the stage for future endeavors aimed at mitigating the repercussions of coronavirus outbreaks, underscoring the intricate and multifaceted nature of virus–host interactions.

This Special Issue invites contributions that offer a panoramic view of the current state of research in this field, encouraging submissions that not only delve into the molecular intricacies of receptor recognition across the diverse coronavirus family but also address the pressing challenges that impede progress in this critical area of study. We welcome original research articles, comprehensive reviews, and short communications that resonate with the evolving trends and prospective directions in this dynamic field.

We eagerly anticipate your invaluable contributions.

Sincerely,
Dr. Qibin Geng
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • coronavirus family (alpha, beta, gamma, delta)
  • receptor recognition mechanisms
  • spike protein mutations
  • host range diversity
  • emerging coronaviruses
  • vaccine and therapeutic challenges
  • molecular interaction complexity
  • viral evolution and zoonotic transmission
  • host–pathogen interactions
  • cellular entry factors

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Published Papers (5 papers)

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Research

11 pages, 831 KiB  
Article
Semi-Covariance Coefficient Analysis of Spike Proteins from SARS-CoV-2 and Its Variants Omicron, BA.5, EG.5, and JN.1 for Viral Infectivity, Virulence and Immune Escape
by Botao Zhu, Huancheng Lin, Jun Steed Huang and Wandong Zhang
Viruses 2024, 16(8), 1192; https://doi.org/10.3390/v16081192 - 25 Jul 2024
Viewed by 744
Abstract
Semi-covariance has attracted significant attention in recent years and is increasingly employed to elucidate statistical phenomena exhibiting fluctuations, such as the similarity or difference in charge patterns of spike proteins among coronaviruses. In this study, by examining values above and below the average/mean [...] Read more.
Semi-covariance has attracted significant attention in recent years and is increasingly employed to elucidate statistical phenomena exhibiting fluctuations, such as the similarity or difference in charge patterns of spike proteins among coronaviruses. In this study, by examining values above and below the average/mean based on the positive and negative charge patterns of amino acid residues in the spike proteins of SARS-CoV-2 and its current circulating variants, the proposed methods offer profound insights into the nonlinear evolving trends in those viral spike proteins. Our study indicates that the charge span value can predict the infectivity of the virus and the charge density can estimate the virulence of the virus, and both predicated infectivity and virulence appear to be associated with the capability of viral immune escape. This semi-covariance coefficient analysis may be used not only to predict the infectivity, virulence and capability of immune escape for coronaviruses but also to analyze the functionality of other viral proteins. This study improves our understanding of the trend of viral evolution in terms of viral infectivity, virulence or the capability of immune escape, which remains further validated by more future studies and statistical data. Full article
(This article belongs to the Special Issue Mechanism of Receptor Recognition in Coronavirus)
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13 pages, 4882 KiB  
Article
Impact of Missense Mutations on Spike Protein Stability and Binding Affinity in the Omicron Variant
by Vidhyanand Mahase, Adebiyi Sobitan, Qiaobin Yao, Xinghua Shi, Hong Qin, Dawit Kidane, Qiyi Tang and Shaolei Teng
Viruses 2024, 16(7), 1150; https://doi.org/10.3390/v16071150 - 17 Jul 2024
Viewed by 973
Abstract
The global effort to combat the COVID-19 pandemic faces ongoing uncertainty with the emergence of Variants of Concern featuring numerous mutations on the Spike (S) protein. In particular, the Omicron Variant is distinguished by 32 mutations, including 10 within its receptor-binding domain (RBD). [...] Read more.
The global effort to combat the COVID-19 pandemic faces ongoing uncertainty with the emergence of Variants of Concern featuring numerous mutations on the Spike (S) protein. In particular, the Omicron Variant is distinguished by 32 mutations, including 10 within its receptor-binding domain (RBD). These mutations significantly impact viral infectivity and the efficacy of vaccines and antibodies currently in use for therapeutic purposes. In our study, we employed structure-based computational saturation mutagenesis approaches to predict the effects of Omicron missense mutations on RBD stability and binding affinity, comparing them to the original Wuhan-Hu-1 strain. Our results predict that mutations such as G431W and P507W induce the most substantial destabilizations in the Wuhan-Hu-1-S/Omicron-S RBD. Notably, we postulate that mutations in the Omicron-S exhibit a higher percentage of enhancing binding affinity compared to Wuhan-S. We found that the mutations at residue positions G447, Y449, F456, F486, and S496 led to significant changes in binding affinity. In summary, our findings may shed light on the widespread prevalence of Omicron mutations in human populations. The Omicron mutations that potentially enhance their affinity for human receptors may facilitate increased viral binding and internalization in infected cells, thereby enhancing infectivity. This informs the development of new neutralizing antibodies capable of targeting Omicron’s immune-evading mutations, potentially aiding in the ongoing battle against the COVID-19 pandemic. Full article
(This article belongs to the Special Issue Mechanism of Receptor Recognition in Coronavirus)
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16 pages, 12030 KiB  
Article
Stabilization of the Metastable Pre-Fusion Conformation of the SARS-CoV-2 Spike Glycoprotein through N-Linked Glycosylation of the S2 Subunit
by Fuwen Zan, Yao Zhou, Ting Chen, Yahan Chen, Zhixia Mu, Zhaohui Qian and Xiuyuan Ou
Viruses 2024, 16(2), 223; https://doi.org/10.3390/v16020223 - 31 Jan 2024
Cited by 2 | Viewed by 2117
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic, represents a serious threat to public health. The spike (S) glycoprotein of SARS-CoV-2 mediates viral entry into host cells and is heavily glycosylated. In this [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic, represents a serious threat to public health. The spike (S) glycoprotein of SARS-CoV-2 mediates viral entry into host cells and is heavily glycosylated. In this study, we systemically analyzed the roles of 22 putative N-linked glycans in SARS-CoV-2 S protein expression, membrane fusion, viral entry, and stability. Using the α-glycosidase inhibitors castanospermine and NB-DNJ, we confirmed that disruption of N-linked glycosylation blocked the maturation of the S protein, leading to the impairment of S protein-mediated membrane fusion. Single-amino-acid substitution of each of the 22 N-linked glycosylation sites with glutamine revealed that 9 out of the 22 N-linked glycosylation sites were critical for S protein folding and maturation. Thus, substitution at these sites resulted in reduced S protein-mediated cell–cell fusion and viral entry. Notably, the N1074Q mutation markedly affected S protein stability and induced significant receptor-independent syncytium (RIS) formation in HEK293T/hACE2-KO cells. Additionally, the removal of the furin cleavage site partially compensated for the instability induced by the N1074Q mutation. Although the corresponding mutation in the SARS-CoV S protein (N1056Q) did not induce RIS in HEK293T cells, the N669Q and N1080Q mutants exhibited increased fusogenic activity and did induce syncytium formation in HEK293T cells. Therefore, N-glycans on the SARS-CoV and SARS-CoV-2 S2 subunits are highly important for maintaining the pre-fusion state of the S protein. This study revealed the critical roles of N-glycans in S protein maturation and stability, information that has implications for the design of vaccines and antiviral strategies. Full article
(This article belongs to the Special Issue Mechanism of Receptor Recognition in Coronavirus)
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20 pages, 6788 KiB  
Article
The Potential of Usnic-Acid-Based Thiazolo-Thiophenes as Inhibitors of the Main Protease of SARS-CoV-2 Viruses
by Olga I. Yarovaya, Aleksandr S. Filimonov, Dmitriy S. Baev, Sophia S. Borisevich, Anna V. Zaykovskaya, Varvara Yu. Chirkova, Mariya K. Marenina, Yulia V. Meshkova, Svetlana V. Belenkaya, Dmitriy N. Shcherbakov, Maxim A. Gureev, Olga A. Luzina, Oleg V. Pyankov, Nariman F. Salakhutdinov and Mikhail V. Khvostov
Viruses 2024, 16(2), 215; https://doi.org/10.3390/v16020215 - 31 Jan 2024
Viewed by 1635
Abstract
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on [...] Read more.
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (−)-usnic acid and studied their ability to inhibit the main protease of SARS-CoV-2. Substances containing unsubstituted thiophene groups or methyl- or bromo-substituted thiophene moieties showed moderate activity. Derivatives containing nitro substituents in the thiophene heterocycle—just as pure (+)- and (−)-usnic acids—showed no anti-3CLpro activity. Kinetic parameters of the most active compound, (+)-3e, were investigated, and molecular modeling of the possible interaction of the new thiazolo-thiophenes with the active site of the main protease was carried out. We evaluated the binding energies of the ligand and protein in a ligand–protein complex. Active compound (+)-3e was found to bind with minimum free energy; the binding of inactive compound (+)-3g is characterized by higher values of minimum free energy; the positioning of pure (+)-usnic acid proved to be unstable and is accompanied by the formation of intermolecular contacts with many amino acids of the catalytic binding site. Thus, the molecular dynamics results were consistent with the experimental data. In an in vitro antiviral assay against six strains (Wuhan, Delta, and four Omicron sublineages) of SARS-CoV-2, (+)-3e demonstrated pronounced antiviral activity against all the strains. Full article
(This article belongs to the Special Issue Mechanism of Receptor Recognition in Coronavirus)
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26 pages, 5876 KiB  
Article
Investigating the Potential Shared Molecular Mechanisms between COVID-19 and Alzheimer’s Disease via Transcriptomic Analysis
by Yixian Fan, Xiaozhao Liu, Fei Guan, Xiaoyi Hang, Ximiao He and Jing Jin
Viruses 2024, 16(1), 100; https://doi.org/10.3390/v16010100 - 9 Jan 2024
Cited by 1 | Viewed by 2213
Abstract
SARS-CoV-2 caused the COVID-19 pandemic. COVID-19 may elevate the risk of cognitive impairment and even cause dementia in infected individuals; it may accelerate cognitive decline in elderly patients with dementia, possibly in Alzheimer’s disease (AD) patients. However, the mechanisms underlying the interplay between [...] Read more.
SARS-CoV-2 caused the COVID-19 pandemic. COVID-19 may elevate the risk of cognitive impairment and even cause dementia in infected individuals; it may accelerate cognitive decline in elderly patients with dementia, possibly in Alzheimer’s disease (AD) patients. However, the mechanisms underlying the interplay between AD and COVID-19 are still unclear. To investigate the underlying mechanisms and associations between AD progression and SARS-CoV-2 infection, we conducted a series of bioinformatics research into SARS-CoV-2-infected cells, COVID-19 patients, AD patients, and SARS-CoV-2-infected AD patients. We identified the common differentially expressed genes (DEGs) in COVID-19 patients, AD patients, and SARS-CoV-2-infected cells, and these DEGs are enriched in certain pathways, such as immune responses and cytokine storms. We constructed the gene interaction network with the signaling transduction module in the center and identified IRF7, STAT1, STAT2, and OAS1 as the hub genes. We also checked the correlations between several key transcription factors and the SARS-CoV-2 and COVID-19 pathway-related genes. We observed that ACE2 expression is positively correlated with IRF7 expression in AD and coronavirus infections, and interestingly, IRF7 is significantly upregulated in response to different RNA virus infections. Further snRNA-seq analysis indicates that NRGN neurons or endothelial cells may be responsible for the increase in ACE2 and IRF7 expression after SARS-CoV-2 infection. The positive correlation between ACE2 and IRF7 expressions is confirmed in the hippocampal formation (HF) of SARS-CoV-2-infected AD patients. Our findings could contribute to the investigation of the molecular mechanisms underlying the interplay between AD and COVID-19 and to the development of effective therapeutic strategies for AD patients with COVID-19. Full article
(This article belongs to the Special Issue Mechanism of Receptor Recognition in Coronavirus)
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