scholarly journals DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2

2020 ◽  
Author(s):  
Fabrizio Cleri ◽  
Marc F. Lensink ◽  
Ralf Blossey
Keyword(s):  
Host Cell ◽  
Low Cost ◽  
Protein A ◽  
Genetic Material ◽  
Dna Aptamers ◽  
Cell Binding ◽  
Host Cell Membrane ◽  
S Protein ◽  
Open Conformation ◽  
Viral Screening

<div> <div> <div> <p>DNA aptamers are versatile molecular species obtained by the folding of short single-stranded nucleotide sequences, with highly specific recognition capabilities against proteins. Here we test the ability of selected DNA aptamers in interacting with the spike (S-)protein of the SARS-CoV-2 viral capsid. The S-protein, a trimer made up of several subdomains, develops the crucial function of recognizing the ACE2 receptors on the surface of human cells, and sub- sequent fusioning of the virus membrane with the host cell membrane. In order to do this, the S1 domain of one protomer switches between a closed conformation, in which the binding site is inaccessible to the cell receptors, and an open conformation, in which ACE2 can bind, thereby initiating the entry process of the viral genetic material in the host cell. Here we show by means of state-of-the-art molecular simulations that small DNA aptamers can recognize the S-protein of SARS-CoV-2. Moreover, their interaction with different regions of the S-protein can effectively block, or at least considerably slow down the opening process of the S1 domain, thereby largely reducing the probability of virus-cell binding. We also provide evidence that binding of the human ACE2 receptor may be drastically affected under such conditions. Given the facility and low cost of fabrication of specific aptamers, the present findings could open the way to both an innovative viral screening technique with sub-nanomolar sensitivity, and to an effective and low impact curative strategy. </p> </div> </div> </div>

scholarly journals DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2

2021 ◽  
Vol 8 ◽  
Author(s):  
Fabrizio Cleri ◽  
Marc F. Lensink ◽  
Ralf Blossey
Keyword(s):  
Host Cell ◽  
Low Cost ◽  
Protein A ◽  
Genetic Material ◽  
Dna Aptamers ◽  
Cell Binding ◽  
Host Cell Membrane ◽  
S Protein ◽  
Open Conformation ◽  
Viral Screening

DNA aptamers are versatile molecular species obtained by the folding of short single-stranded nucleotide sequences, with highly specific recognition capabilities against proteins. Here we test the ability of DNA aptamers to interact with the spike (S-)protein of the SARS-CoV-2 viral capsid. The S-protein, a trimer made up of several subdomains, develops the crucial function of recognizing the ACE2 receptors on the surface of human cells, and subsequent fusioning of the virus membrane with the host cell membrane. In order to achieve this, the S1 domain of one protomer switches between a closed conformation, in which the binding site is inaccessible to the cell receptors, and an open conformation, in which ACE2 can bind, thereby initiating the entry process of the viral genetic material in the host cell. Here we show, by means of state-of-the-art molecular simulations, that small DNA aptamers experimentally identified can recognize the S-protein of SARS-CoV-2, and characterize the details of the binding process. We find that their interaction with different subdomains of the S-protein can effectively block, or at least considerably slow down the opening process of the S1 domain, thereby significantly reducing the probability of virus-cell binding. We provide evidence that, as a consequence, binding of the human ACE2 receptor may be crucially affected under such conditions. Given the facility and low cost of fabrication of specific aptamers, the present findings could open the way to both an innovative viral screening technique with sub-nanomolar sensitivity, and to an effective and low impact curative strategy.

scholarly journals DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2

2020 ◽  
Author(s):  
Fabrizio Cleri ◽  
Marc F. Lensink ◽  
Ralf Blossey
Keyword(s):  
Host Cell ◽  
Low Cost ◽  
Protein A ◽  
Genetic Material ◽  
Dna Aptamers ◽  
Cell Binding ◽  
Host Cell Membrane ◽  
S Protein ◽  
Open Conformation ◽  
Viral Screening

<div> <div> <div> <p>DNA aptamers are versatile molecular species obtained by the folding of short single-stranded nucleotide sequences, with highly specific recognition capabilities against proteins. Here we test the ability of selected DNA aptamers in interacting with the spike (S-)protein of the SARS-CoV-2 viral capsid. The S-protein, a trimer made up of several subdomains, develops the crucial function of recognizing the ACE2 receptors on the surface of human cells, and sub- sequent fusioning of the virus membrane with the host cell membrane. In order to do this, the S1 domain of one protomer switches between a closed conformation, in which the binding site is inaccessible to the cell receptors, and an open conformation, in which ACE2 can bind, thereby initiating the entry process of the viral genetic material in the host cell. Here we show by means of state-of-the-art molecular simulations that small DNA aptamers can recognize the S-protein of SARS-CoV-2. Moreover, their interaction with different regions of the S-protein can effectively block, or at least considerably slow down the opening process of the S1 domain, thereby largely reducing the probability of virus-cell binding. We also provide evidence that binding of the human ACE2 receptor may be drastically affected under such conditions. Given the facility and low cost of fabrication of specific aptamers, the present findings could open the way to both an innovative viral screening technique with sub-nanomolar sensitivity, and to an effective and low impact curative strategy. </p> </div> </div> </div>

scholarly journals The Fight against COVID-19 on the Multi-Protease Front and Surroundings: Could an Early Therapeutic Approach with Repositioning Drugs Prevent the Disease Severity?

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 710
Author(s):  
Annamaria Vianello ◽  
Serena Del Turco ◽  
Serena Babboni ◽  
Beatrice Silvestrini ◽  
Rosetta Ragusa ◽  
...  
Keyword(s):  
Host Cell ◽  
Serine Proteases ◽  
Time Window ◽  
Low Cost ◽  
Critical Role ◽  
Severe Infection ◽  
Viral Envelope ◽  
Host Cells ◽  
Host Cell Membrane ◽  
Inflammatory Conditions

The interaction between the membrane spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the transmembrane angiotensin-converting enzyme 2 (ACE2) receptor of the human epithelial host cell is the first step of infection, which has a critical role for viral pathogenesis of the current coronavirus disease-2019 (COVID-19) pandemic. Following the binding between S1 subunit and ACE2 receptor, different serine proteases, including TMPRSS2 and furin, trigger and participate in the fusion of the viral envelope with the host cell membrane. On the basis of the high virulence and pathogenicity of SARS-CoV-2, other receptors have been found involved for viral binding and invasiveness of host cells. This review comprehensively discusses the mechanisms underlying the binding of SARS-CoV2 to ACE2 and putative alternative receptors, and the role of potential co-receptors and proteases in the early stages of SARS-CoV-2 infection. Given the short therapeutic time window within which to act to avoid the devastating evolution of the disease, we focused on potential therapeutic treatments—selected mainly among repurposing drugs—able to counteract the invasive front of proteases and mild inflammatory conditions, in order to prevent severe infection. Using existing approved drugs has the advantage of rapidly proceeding to clinical trials, low cost and, consequently, immediate and worldwide availability.

scholarly journals Coronavirus S protein-induced fusion is blocked prior to hemifusion by Abl kinase inhibitors

2018 ◽  
Author(s):  
Jeanne M. Sisk ◽  
Matthew B. Frieman ◽  
Carolyn E. Machamer
Keyword(s):  
Host Cell ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Host Cells ◽  
Tissue Type ◽  
Host Cell Membrane ◽  
S Protein ◽  
Abl Kinase ◽  
Coronavirus Infection ◽  
Abl Kinase Inhibitors

ABSTRACTEnveloped viruses gain entry into host cells by fusing with cellular membranes, a step required for virus replication. Coronaviruses, including the severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and infectious bronchitis virus (IBV), fuse at the plasma membrane or use receptor-mediated endocytosis and fuse with endosomes depending on the cell or tissue type. The virus Spike (S) protein mediates fusion with the host cell membrane. We have shown previously that an Abl kinase inhibitor, imatinib, significantly reduces SARS-CoV and MERS-CoV viral titers and prevents endosomal entry by HIV SARS S and MERS S pseudotyped virions. SARS-CoV and MERS-CoV are classified as BSL-3 viruses, which can make experimentation into the cellular mechanisms involved in infection more challenging. Here, we use IBV, a BSL-2 virus, as a model for studying the role of Abl kinase activity during coronavirus infection. We found that imatinib and two specific Abl kinase inhibitors, GNF2 and GNF5, reduce IBV titers by blocking the first round of virus infection. Additionally, all three drugs prevented IBV S-induced syncytia formation prior to the hemifusion step. Our results indicate that membrane fusion (both virus-cell and cell-cell) is blocked in the presence of Abl kinase inhibitors. Studying the effects of Abl kinase inhibitors on IBV will be useful in identifying host cell pathways required for coronavirus infection. This will provide insight into possible therapeutic targets to treat infections by current as well as newly emerging coronaviruses.

scholarly journals The utility of native MS for understanding the mechanism of action of repurposed therapeutics in COVID-19: heparin as a disruptor of the SARS-CoV-2 interaction with its host cell receptor

2020 ◽  
Author(s):  
Yang Yang ◽  
Yi Du ◽  
Igor A. Kaltashov
Keyword(s):  
Host Cell ◽  
Gas Phase ◽  
Viral Entry ◽  
Protein A ◽  
Cell Receptor ◽  
Critical Element ◽  
S Protein ◽  
Host Cell Receptor ◽  
Native Ms ◽  
Gas Phase Ion

ABSTRACTThe emergence and rapid proliferation of the novel coronavirus (SARS-CoV-2) resulted in a global pandemic, with over six million cases and nearly four hundred thousand deaths reported world-wide by the end of May 2020. A rush to find the cures prompted re-evaluation of a range of existing therapeutics vis-à-vis their potential role in treating COVID-19, placing a premium on analytical tools capable of supporting such efforts. Native mass spectrometry (MS) has long been a tool of choice in supporting the mechanistic studies of drug/therapeutic target interactions, but its applications remain limited in the cases that involve systems with a high level of structural heterogeneity. Both SARS-CoV-2 spike protein (S-protein), a critical element of the viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively glycosylated, making them challenging targets for native MS. However, supplementing native MS with a gas-phase ion manipulation technique (limited charge reduction) allows meaningful information to be obtained on the non-covalent complexes formed by ACE2 and the receptor-binding domain (RBD) of the S-protein. Using this technique in combination with molecular modeling also allows the role of heparin in destabilizing the ACE2/RBD association to be studied, providing critical information for understanding the molecular mechanism of its interference with the virus docking to the host cell receptor. Both short (pentasaccharide) and relatively long (eicosasaccharide) heparin oligomers form 1:1 complexes with RBD, indicating the presence of a single binding site. This association alters the protein conformation (to maximize the contiguous patch of the positive charge on the RBD surface), resulting in a notable decrease of its ability to associate with ACE2. The destabilizing effect of heparin is more pronounced in the case of the longer chains due to the electrostatic repulsion between the low-pI ACE2 and the heparin segments not accommodated on the RBD surface. In addition to providing important mechanistic information on attenuation of the ACE2/RBD association by heparin, the study demonstrates the yet untapped potential of native MS coupled to gas-phase ion chemistry as a means of facilitating rational repurposing of the existing medicines for treating COVID-19.Abstract Figure

The Biology of Viruses

2019 ◽  
Author(s):  
Anna Jeffery-Smith ◽  
C. Y. William Tong
Keyword(s):  
Nucleic Acid ◽  
Host Cell ◽  
Genetic Material ◽  
Cell Types ◽  
Host Cells ◽  
Host Cell Membrane ◽  
Cell Receptors ◽  
A Cell ◽  
Independent Synthesis ◽  
Different Cell Types

In order to be classified as a virus, certain criteria have to be fulfilled. Viruses must ● Be only capable of growth and multiplication within living cells, i.e. obligate intracellular parasite. Host cells could include humans, animals, insects, plants, protozoa, or even bacteria. ● Have a nucleic acid genome (either RNA or DNA, but not both) surrounded by a protein coat (capsid). ● Have no semipermeable membrane, though some have an envelope formed of phospholipids and proteins. ● Be inert outside of the host cell. Enveloped viruses are susceptible to inactivation by organic solvents such as alcohol. ● Perform replication by independent synthesis of components followed by assembly (c.f. binary fission in bacteria). Viruses are considered as a bundle of genetic programmes encoded in nucleic acids and packaged with a capsid +/ - envelope protein, which can be activated on entry into a host cell (compare this with computer viruses packaged in an enticing way in order to infect and take over control of your PC). Although they share some similarities in their properties, mycoplasma and chlamydia are true bacteria. The virion (assembled infectious particle) consists of viral nucleic acid and capsid. The nucleic acid of a virus can either be ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), and the amount of genetic material varies widely, with some viruses able to encode a few proteins and others having genetic material that encodes hundreds of proteins. In association with the nucleic acid there may be non- structural viral proteins, such as a viral polymerase. The nucleic acid and non- structural proteins are protected by a surrounding layer of capsid proteins. The capsid includes proteins which can attach to host cell receptors. The proteins and the cell receptors to which they bind determine a virus’ tropism, i.e., the ability to bind to and enter different cell types. The term nucleocapsid refers to the nucleic acid core surrounded by capsid protein. Some viruses also have an envelope made up of phospholipids and proteins surrounding the nucleocapsid. This envelope can be formed by the host cell membrane during the process of a virus budding from a cell during replication.

scholarly journals The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicholas M. Negretti ◽  
Christopher R. Gourley ◽  
Prabhat K. Talukdar ◽  
Geremy Clair ◽  
Courtney M. Klappenbach ◽  
...  
Keyword(s):  
Host Cell ◽  
Campylobacter Jejuni ◽  
Foodborne Pathogen ◽  
Small Gtpase ◽  
Host Cells ◽  
Cell Protein ◽  
Host Cell Protein ◽  
Cell Binding ◽  
Actin Reorganization ◽  
Cell Cytosol

AbstractCampylobacter jejuni is a foodborne pathogen that binds to and invades the epithelial cells lining the human intestinal tract. Maximal invasion of host cells by C. jejuni requires cell binding as well as delivery of the Cia proteins (Campylobacter invasion antigens) to the host cell cytosol via the flagellum. Here, we show that CiaD binds to the host cell protein IQGAP1 (a Ras GTPase-activating-like protein), thus displacing RacGAP1 from the IQGAP1 complex. This, in turn, leads to the unconstrained activity of the small GTPase Rac1, which is known to have roles in actin reorganization and internalization of C. jejuni. Our results represent the identification of a host cell protein targeted by a flagellar secreted effector protein and demonstrate that C. jejuni-stimulated Rac signaling is dependent on IQGAP1.

scholarly journals 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 ◽  
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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