Targeting Lipid Rafts as a Strategy Against Coronavirus

Lipid rafts are functional membrane microdomains containing sphingolipids, including gangliosides, and cholesterol. These regions are characterized by highly ordered and tightly packed lipid molecules. Several studies revealed that lipid rafts are involved in life cycle of different viruses, including coronaviruses. Among these recently emerged the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The main receptor for SARS-CoV-2 is represented by the angiotensin-converting enzyme-2 (ACE-2), although it also binds to sialic acids linked to host cell surface gangliosides. A new type of ganglioside-binding domain within the N-terminal portion of the SARS-CoV-2 spike protein was identified. Lipid rafts provide a suitable platform able to concentrate ACE-2 receptor on host cell membranes where they may interact with the spike protein on viral envelope. This review is focused on selective targeting lipid rafts components as a strategy against coronavirus. Indeed, cholesterol-binding agents, including statins or methyl-β-cyclodextrin (MβCD), can affect cholesterol, causing disruption of lipid rafts, consequently impairing coronavirus adhesion and binding. Moreover, these compounds can block downstream key molecules in virus infectivity, reducing the levels of proinflammatory molecules [tumor necrosis factor alpha (TNF-α), interleukin (IL)-6], and/or affecting the autophagic process involved in both viral replication and clearance. Furthermore, cyclodextrins can assemble into complexes with various drugs to form host–guest inclusions and may be used as pharmaceutical excipients of antiviral compounds, such as lopinavir and remdesivir, by improving bioavailability and solubility. In conclusion, the role of lipid rafts-affecting drugs in the process of coronavirus entry into the host cells prompts to introduce a new potential task in the pharmacological approach against coronavirus.

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Retrovirus Entry by Endocytosis and Cathepsin Proteases

Advances in Virology ◽

10.1155/2012/640894 ◽

2012 ◽

Vol 2012 ◽

pp. 1-14 ◽

Cited By ~ 12

Author(s):

Yoshinao Kubo ◽

Hideki Hayashi ◽

Toshifumi Matsuyama ◽

Hironori Sato ◽

Naoki Yamamoto

Keyword(s):

Host Cell ◽

Leukemia Virus ◽

Retroviral Vectors ◽

Viral Envelope ◽

Host Cells ◽

Target Cells ◽

Cellular Mechanisms ◽

Cathepsin Proteases ◽

Transfer Genes ◽

Host Cell Membranes

Retroviruses include infectious agents inducing severe diseases in humans and animals. In addition, retroviruses are widely used as tools to transfer genes of interest to target cells. Understanding the entry mechanism of retroviruses contributes to developments of novel therapeutic approaches against retrovirus-induced diseases and efficient exploitation of retroviral vectors. Entry of enveloped viruses into host cell cytoplasm is achieved by fusion between the viral envelope and host cell membranes at either the cell surface or intracellular vesicles. Many animal retroviruses enter host cells through endosomes and require endosome acidification. Ecotropic murine leukemia virus entry requires cathepsin proteases activated by the endosome acidification. CD4-dependent human immunodeficiency virus (HIV) infection is thought to occur via endosomes, but endosome acidification is not necessary for the entry whereas entry of CD4-independent HIVs, which are thought to be prototypes of CD4-dependent viruses, is low pH dependent. There are several controversial results on the retroviral entry pathways. Because endocytosis and endosome acidification are complicatedly controlled by cellular mechanisms, the retrovirus entry pathways may be different in different cell lines.

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The Extended Intermediate of the SARS-CoV-2 Spike Protein uses Extreme Reach and Flexibility to Capture Host Cell Membranes

Biophysical Journal ◽

10.1016/j.bpj.2020.11.2027 ◽

2021 ◽

Vol 120 (3) ◽

pp. 321a

Author(s):

Rui Su ◽

Jin Zeng ◽

Sathish Thiyagarajan ◽

Ben O'Shaughnessy

Keyword(s):

Host Cell ◽

Cell Membranes ◽

Spike Protein ◽

Host Cell Membranes

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Exaptation of Retroviral Syncytin for Development of Syncytialized Placenta, Its Limited Homology to the SARS-CoV-2 Spike Protein and Arguments against Disturbing Narrative in the Context of COVID-19 Vaccination

Biology ◽

10.3390/biology10030238 ◽

2021 ◽

Vol 10 (3) ◽

pp. 238

Author(s):

Malgorzata Kloc ◽

Ahmed Uosef ◽

Jacek Z. Kubiak ◽

Rafik M. Ghobrial

Keyword(s):

Cell Membrane ◽

Host Cell ◽

Envelope Glycoprotein ◽

Mammalian Species ◽

Viral Envelope ◽

Spike Protein ◽

Mammalian Evolution ◽

Trophoblast Cells ◽

Host Cell Membrane ◽

Uterine Endometrium

Human placenta formation relies on the interaction between fused trophoblast cells of the embryo with uterine endometrium. The fusion between trophoblast cells, first into cytotrophoblast and then into syncytiotrophoblast, is facilitated by the fusogenic protein syncytin. Syncytin derives from an envelope glycoprotein (ENV) of retroviral origin. In exogenous retroviruses, the envelope glycoproteins coded by env genes allow fusion of the viral envelope with the host cell membrane and entry of the virus into a host cell. During mammalian evolution, the env genes have been repeatedly, and independently, captured by various mammalian species to facilitate the formation of the placenta. Such a shift in the function of a gene, or a trait, for a different purpose during evolution is called an exaptation (co-option). We discuss the structure and origin of the placenta, the fusogenic and non-fusogenic functions of syncytin, and the mechanism of cell fusion. We also comment on an alleged danger of the COVID-19 vaccine based on the presupposed similarity between syncytin and the SARS-CoV-2 spike protein.

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Heparan Sulfate Facilitates Spike Protein-Mediated SARS-CoV-2 Host Cell Invasion and Contributes to Increased Infection of SARS-CoV-2 G614 Mutant and in Lung Cancer

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.649575 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jingwen Yue ◽

Weihua Jin ◽

Hua Yang ◽

John Faulkner ◽

Xuehong Song ◽

...

Keyword(s):

Lung Cancer ◽

Cell Surface ◽

Heparan Sulfate ◽

Host Cell ◽

Host Cells ◽

Cell Surface Receptor ◽

Spike Protein ◽

Effective Prevention ◽

Heparin Derivatives ◽

Host Cell Surface

The severe acute respiratory syndrome (SARS)-like coronavirus disease (COVID-19) is caused by SARS-CoV-2 and has been a serious threat to global public health with limited treatment. Cellular heparan sulfate (HS) has been found to bind SARS-CoV-2 spike protein (SV2-S) and co-operate with cell surface receptor angiotensin-converting enzyme 2 (ACE2) to mediate SARS-CoV-2 infection of host cells. In this study, we determined that host cell surface SV2-S binding depends on and correlates with host cell surface HS expression. This binding is required for SARS-Cov-2 virus to infect host cells and can be blocked by heparin lyase, HS antagonist surfen, heparin, and heparin derivatives. The binding of heparin/HS to SV2-S is mainly determined by its overall sulfation with potential, minor contribution of specific SV2-S binding motifs. The higher binding affinity of SV2-S G614 mutant to heparin and upregulated HS expression may be one of the mechanisms underlying the higher infectivity of the SARS-CoV-2 G614 variant and the high vulnerability of lung cancer patients to SARS-CoV-2 infection, respectively. The higher host cell infection by SARS-CoV-2 G614 variant pseudovirus and the increased infection caused by upregulated HS expression both can be effectively blocked by heparin lyase and heparin, and possibly surfen and heparin derivatives too. Our findings support blocking HS-SV2-S interaction may provide one addition to achieve effective prevention and/treatment of COVID-19.

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Disruption of Lipid Rafts Interferes with the Interaction ofToxoplasma gondiiwith Macrophages and Epithelial Cells

BioMed Research International ◽

10.1155/2014/687835 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 5

Author(s):

Karla Dias Cruz ◽

Thayana Araújo Cruz ◽

Gabriela Veras de Moraes ◽

Tatiana Christina Paredes-Santos ◽

Marcia Attias ◽

...

Keyword(s):

Epithelial Cells ◽

Host Cell ◽

Lipid Rafts ◽

Tyrosine Kinases ◽

Plasma Membranes ◽

Animal Cell ◽

Cell Lineage ◽

Cell Types ◽

Peritoneal Macrophages ◽

Membrane Microdomains

The intracellular parasiteToxoplasma gondiican penetrate any warm-blooded animal cell. Conserved molecular assemblies of host cell plasma membranes should be involved in the parasite-host cell recognition. Lipid rafts are well-conserved membrane microdomains that contain high concentrations of cholesterol, sphingolipids, glycosylphosphatidylinositol, GPI-anchored proteins, and dually acylated proteins such as members of the Src family of tyrosine kinases. Disturbing lipid rafts of mouse peritoneal macrophages and epithelial cells of the lineage LLC-MK2 with methyl-beta cyclodextrin (MβCD) and filipin, which interfere with cholesterol or lidocaine, significantly inhibited internalization ofT. gondiiin both cell types, although adhesion remained unaffected in macrophages and decreased only in LLC-MK2 cells. Scanning and transmission electron microscopy confirmed these observations. Results are discussed in terms of the original role of macrophages as professional phagocytes versus the LLC-MK2 cell lineage originated from kidney epithelial cells.

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A modular molecular framework for quickly estimating the binding affinity of the spike protein of SARS-CoV-2 variants for ACE2, in presence of mutations at the spike receptor binding domain.

10.1101/2021.05.26.445422 ◽

2021 ◽

Author(s):

Vincenzo Tragni ◽

Francesca Preziusi ◽

Luna Laera ◽

Angelo Onofrio ◽

Simona Todisco ◽

...

Keyword(s):

Host Cell ◽

Receptor Binding ◽

Conformational Changes ◽

Binding Domain ◽

Host Cells ◽

Spike Protein ◽

Binding Affinities ◽

Receptor Binding Domain ◽

Rapid Spread ◽

Related Proteins

The rapid spread of new SARS-CoV-2 variants needs the development of rapid tools for predicting the affinity of the mutated proteins responsible for the infection, i.e., the SARS-CoV-2 spike protein, for the human ACE2 receptor, aiming to understand if a variant can be more efficient in invading host cells. Here we show how our computational pipeline, previously used for studying SARS-CoV-2 spike receptor-binding domain (RBD)/ACE2 interactions and pre-/post-fusion conformational changes, can be used for predicting binding affinities of the human ACE2 receptor for the spike protein RBD of the characterized infectious variants of concern/interest B.1.1.7-UK (carrying the mutations N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417N/T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 variant (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Furthermore, we searched for ACE2 structurally related proteins that might be involved in interactions with the SARS-CoV-2 spike protein, in those tissues showing low ACE2 expression, revealing two new proteins, THOP1 and NLN, deserving to be investigated for their possible inclusion in the group of host-cell entry factors responsible for host-cell SARS-CoV-2 invasion and immunity response.

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Genetic variability in the expression of the SARS-CoV-2 host cell entry factors across populations

10.1101/2020.04.06.027698 ◽

2020 ◽

Cited By ~ 2

Author(s):

Lourdes Ortiz-Fernández ◽

Amr H Sawalha

Keyword(s):

Host Cell ◽

Viral Entry ◽

Quantitative Measure ◽

Individual Variability ◽

Host Cells ◽

Genetic Determinants ◽

Angiotensin Converting Enzyme 2 ◽

African Populations ◽

Host Cell Entry ◽

Host Cell Membranes

AbstractThe entry of SARS-CoV-2 into host cells is dependent upon angiotensin-converting enzyme 2 (ACE2), which serves as a functional attachment receptor for the viral spike glycoprotein, and the serine protease TMPRSS2 which allows fusion of the viral and host cell membranes. We devised a quantitative measure to estimate genetic determinants of ACE2 and TMPRSS2 expression and applied this measure to >2,500 individuals. Our data show significant variability in genetic determinants of ACE2 and TMPRSS2 expression among individuals and between populations, and demonstrate a genetic predisposition for lower expression levels of both key viral entry genes in African populations. These data suggest that genetic factors might lead to lower susceptibility for SARS-CoV-2 infection in African populations and that host genetics might help explain inter-individual variability in disease susceptibility and severity of COVID-19.

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SARS-CoV2 genome analysis of Indian isolates and molecular modelling of D614G mutated spike protein with TMPRSS2 depicted its enhanced interaction and virus infectivity

10.1101/2020.07.23.217430 ◽

2020 ◽

Cited By ~ 3

Author(s):

Sunil Raghav ◽

Arup Ghosh ◽

Jyotirmayee Turuk ◽

Sugandh Kumar ◽

Atimukta Jha ◽

...

Keyword(s):

Molecular Modelling ◽

Genome Analysis ◽

Disease Transmission ◽

Amplicon Sequencing ◽

Virus Genome ◽

Host Cells ◽

Spike Protein ◽

Disease Spread ◽

Clinical Samples ◽

Virus Infectivity

AbstractCOVID-19 that emerged as a global pandemic is caused by SARS-CoV-2 virus. The virus genome analysis during disease spread reveals about its evolution and transmission. We did whole genome sequencing of 225 clinical strains from the state of Odisha in eastern India using ARTIC protocol-based amplicon sequencing. Phylogenetic analysis identified the presence of all five reported clades 19A, 19B, 20A, 20B and 20C in the population. The analyses revealed two major routes for the introduction of the disease in India i.e. Europe and South-east Asia followed by local transmission. Interestingly, 19B clade was found to be much more prevalent in our sequenced genomes (17%) as compared to other genomes reported so far from India. The haplogroup analysis for clades showed evolution of 19A and 19B in parallel whereas the 20B and 20C appeared to evolve from 20A. Majority of the 19A and 19B clades were present in cases that migrated from Gujarat state in India suggesting it to be one of the major initial points of disease transmission in India during month of March and April. We found that with the time 20A and 20B clades evolved drastically that originated from central Europe. At the same time, it has been observed that 20A and 20B clades depicted selection of four common mutations i.e. 241 C>T (5’UTR), P323L in RdRP, F942F in NSP3 and D614G in the spike protein. We found an increase in the concordance of G614 mutation evolution with the viral load in clinical samples as evident from decreased Ct value of spike and Orf1ab gene in qPCR. Molecular modelling and docking analysis identified that D614G mutation enhanced interaction of spike with TMPRSS2 protease, which could impact the shedding of S1 domain and infectivity of the virus in host cells.

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Elucidating Interactions Between SARS-CoV-2 Trimeric Spike Protein and ACE2 Using Homology Modeling and Molecular Dynamics Simulations

Frontiers in Chemistry ◽

10.3389/fchem.2020.622632 ◽

2021 ◽

Vol 8 ◽

Author(s):

Sugunadevi Sakkiah ◽

Wenjing Guo ◽

Bohu Pan ◽

Zuowei Ji ◽

Gokhan Yavas ◽

...

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Host Cell ◽

Tertiary Structure ◽

Cell Receptor ◽

Host Cells ◽

Spike Protein ◽

Receptor Protein ◽

Dynamics Simulations

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). As of October 21, 2020, more than 41.4 million confirmed cases and 1.1 million deaths have been reported. Thus, it is immensely important to develop drugs and vaccines to combat COVID-19. The spike protein present on the outer surface of the virion plays a major role in viral infection by binding to receptor proteins present on the outer membrane of host cells, triggering membrane fusion and internalization, which enables release of viral ssRNA into the host cell. Understanding the interactions between the SARS-CoV-2 trimeric spike protein and its host cell receptor protein, angiotensin converting enzyme 2 (ACE2), is important for developing drugs and vaccines to prevent and treat COVID-19. Several crystal structures of partial and mutant SARS-CoV-2 spike proteins have been reported; however, an atomistic structure of the wild-type SARS-CoV-2 trimeric spike protein complexed with ACE2 is not yet available. Therefore, in our study, homology modeling was used to build the trimeric form of the spike protein complexed with human ACE2, followed by all-atom molecular dynamics simulations to elucidate interactions at the interface between the spike protein and ACE2. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) and in silico alanine scanning were employed to characterize the interacting residues at the interface. Twenty interacting residues in the spike protein were identified that are likely to be responsible for tightly binding to ACE2, of which five residues (Val445, Thr478, Gly485, Phe490, and Ser494) were not reported in the crystal structure of the truncated spike protein receptor binding domain (RBD) complexed with ACE2. These data indicate that the interactions between ACE2 and the tertiary structure of the full-length spike protein trimer are different from those between ACE2 and the truncated monomer of the spike protein RBD. These findings could facilitate the development of drugs and vaccines to prevent SARS-CoV-2 infection and combat COVID-19.

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Host cell glutamine metabolism as a potential antiviral target

Clinical Science ◽

10.1042/cs20201042 ◽

2021 ◽

Vol 135 (2) ◽

pp. 305-325

Author(s):

Sandro Massao Hirabara ◽

Renata Gorjao ◽

Adriana Cristina Levada-Pires ◽

Laureane Nunes Masi ◽

Elaine Hatanaka ◽

...

Keyword(s):

Host Cell ◽

Immune Cell ◽

Antiviral Drugs ◽

Viral Envelope ◽

Host Cells ◽

Glutamine Metabolism ◽

Infected Host ◽

Potential Candidate ◽

Cell Functions ◽

Glutamine Transport

Abstract A virus minimally contains a nucleic acid genome packaged by a protein coat. The genome and capsid together are known as the nucleocapsid, which has an envelope containing a lipid bilayer (mainly phospholipids) originating from host cell membranes. The viral envelope has transmembrane proteins that are usually glycoproteins. The proteins in the envelope bind to host cell receptors, promoting membrane fusion and viral entry into the cell. Virus-infected host cells exhibit marked increases in glutamine utilization and metabolism. Glutamine metabolism generates ATP and precursors for the synthesis of macromolecules to assemble progeny viruses. Some compounds derived from glutamine are used in the synthesis of purines and pyrimidines. These latter compounds are precursors for the synthesis of nucleotides. Inhibitors of glutamine transport and metabolism are potential candidate antiviral drugs. Glutamine is also an essential nutrient for the functions of leukocytes (lymphocyte, macrophage, and neutrophil), including those in virus-infected patients. The increased glutamine requirement for immune cell functions occurs concomitantly with the high glutamine utilization by host cells in virus-infected patients. The development of antiviral drugs that target glutamine metabolism must then be specifically directed at virus-infected host cells to avoid negative effects on immune functions. Therefore, the aim of this review was to describe the landscape of cellular glutamine metabolism to search for potential candidates to inhibit glutamine transport or glutamine metabolism.

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