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Last updated: 2021 Sep 7
Total hit(s): 399
Refining the N-Termini of the SARS-CoV-2 Spike Protein and Its Discrete Receptor-Binding Domain
SARS-CoV-2 spike protein receptor-binding domain (RBD) constructs were originally developed by Mt. Sinai or the Ragon Institute and later optimized in-house. Each construct was subjected to N-deglycosylation and subsequent intact mass analysis, revealing significant deviations from predicted theoretical mass for all five proteins.
J Proteome Res
2021 Sep 3
Analysis of SARS-CoV-2 nucleocapsid phosphoprotein N variations in the binding site to human 14-3-3 proteins
The SARS-CoV-2 N protein binds several cell host proteins including 14-3-3γ, a well-characterized regulatory protein. However, the biological function of this interaction is not completely understood. We studied how these mutations affect the binding energy and found that changes positively affecting the predicted interaction are the most successfully spread.
Biochem Biophys Res Commun
2021 Sep 10
A Novel Therapeutic Peptide Blocks SARS-CoV-2 Spike Protein Binding with Host Cell ACE2 Receptor
A critical step in the crosstalk between the virus and the host cell is the binding of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein to the peptidase domain of the angiotensin-converting enzyme 2 (ACE2) receptor present on the surface of host cells. There is an urgent need to develop effective therapeutics against coronavirus disease 2019.
Drugs R D
Interactions of Spike-RBD of SARS-CoV-2 and Platelet Factor 4: New Insights in the Etiopathogenesis of Thrombosis
Patients diagnosed with severe COVID-19 may develop a pro-thrombotic state with a much higher frequency. Anti-Spike antibodies do not recognize PF4, on the contrary, the anti-PF4 antibodies show some cross-reactivity for Spike-RBD.
Int J Mol Sci
2021 Aug 9
Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
Medicinal plants as rich sources of bioactive compounds are now being explored for drug development against COVID-19. 19 medicinal plants known to exhibit antiviral and anti-inflammatory effects were manually curated, procuring a library of 521 metabolites. Ochnaflavone and Licoflavone B, obtained from Lonicera japonica (Japanese Honeysuckle) and Glycyrrhiza glabra (Licorice), respectively, were identified to have the highest potential polypharmacological properties for the aforementioned targets.
J Biomol Struct Dyn
2021 Aug 9
A distinct ssDNA/RNA binding interface in the Nsp9 protein from SARS-CoV-2
SARS-CoV-2 is a novel, highly infectious RNA virus that belongs to the coronavirus family. Nsp9 protein 9 (Nsp9) is shown to be essential for virus replication through its ability to bind RNA in the closely related SARS CoV-1 strain. The binding affinity to RNA is very low which, until now, has prevented the determination of the structural details of this interaction.
2021 Aug 8
Potential therapeutic approaches for the early entry of SARS-CoV-2 by interrupting the interaction between the spike protein on SARS-CoV-2 and angiotensin-converting enzyme 2 (ACE2)
There is no precise and effective treatment for the patients with COVID-19, so rapid development of drugs is urgently needed in order to contain the highly infectious disease. The virus spike protein (S protein) can recognize the angiotensin-converting enzyme 2 (ACE2) receptor on the host cell membrane and undergo a series of conformational changes, protease cleavage and membrane fusion to complete the virus entry. This review offers valuable information for the discovery and development of potential antiviral agents in combating SARS-CoV-2.
2021 Aug 8
HD5 and LL-37 Inhibit SARS-CoV and SARS-CoV-2 Binding to Human ACE2 by Molecular Simulation
Angiotensin-converting enzyme-2 (ACE2) is a receptor of SARS-CoV-2 spike protein that initializes viral entry into host cells. The study proposes a human cathelicidin known as LL37 that strongly binds to the carboxypeptidase domain of human ACE2 compared to HD5.
2021 Aug 7
Contribution of Vitamin D-Binding Protein Polymorphism to Susceptibility and Outcome of COVID-19 Patients
Department of Nephrology at Ghent University Hospital, Ghent, Belgium.AD - Research Foundation-Flanders (FWO), Brussels, Belgium.AD - Department of Diagnostic Sciences. AD is a part of the Flanders Institute for Disease Prevention and Infection Control.
2021 Aug 7
Free Energy Landscapes from SARS-CoV-2 Spike Glycoprotein Simulations Suggest that RBD Opening Can Be Modulated via Interactions in an Allosteric Pocket
The SARS-CoV-2 coronavirus is an enveloped, positive-sense single-stranded RNA virus. The spike is a class I viral fusion glycoprotein that extends from the viral surface and is responsible for viral entry into the host cell. Using atomistic simulations of the glycosylated wild-type spike in the closed and 1-up RBD conformations, we map the free energy landscape for RBD opening and identify interactions in an allosteric pocket that influence RBD dynamics.
J Am Chem Soc
2021 Aug 4
Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins
Novel Coronavirus disease 2019 or COVID-19 has become a threat to human society due to fast spreading and increasing mortality. Life cycle and pathogenicity of SARS-CoV-2 have already been deciphered and possible drug target trials are on the way.
J Biol Res (Thessalon)
2021 Aug 4
RNA-Protein Interaction Analysis of SARS-CoV-2 5' and 3' Untranslated Regions Reveals a Role of Lysosome-Associated Membrane Protein-2a during Viral Infection
Using an RNA-protein interaction detection (RaPID) assay, we identified host interaction partners of SARS-CoV-2 5' and 3' UTRs. Lysosome-associated membrane protein-2a (Lamp2a), the receptor for chaperone-mediated autophagy, is one of the host proteins that interact with the 5'UTR. Analysis of the RPPI network revealed the enrichment of factors involved in translation initiation and RNA metabolism.
2021 Aug 31
Epigallocatechin gallate from green tea effectively blocks infection of SARS-CoV-2 and new variants by inhibiting spike binding to ACE2 receptor
Green tea beverage (GTB) or its major ingredient, epigallocatechin gallate (EGCG), were highly effective in inhibiting infection of live SARS-CoV-2 and human coronavirus (HCoV OC43) The highest inhibitory activity was observed when the viruses or the cells were pre-incubated with EGCG prior to the infection.
2021 Aug 30
Aromatic Cadinane Sesquiterpenoids from the Fruiting Bodies of Phellinus pini Block SARS-CoV-2 Spike-ACE2 Interaction
Chemical investigation on fruiting bodies of Phellinus pini led to the isolation of five aromatic cadinane sesquiterpenoids including four new ones. All of these inhibited the SARS-CoV-2 spike-ACE2 interaction, with IC(50) values ranging from 64.5 to 99.1 μM.
J Nat Prod
2021 Aug 27
Investigation of Interaction between the Spike Protein of SARS-CoV-2 and ACE2-Expressing Cells Using an In Vitro Cell Capturing System
Interaction between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with Angiotensin converting enzyme 2 (ACE2) on the host cells is a crucial step for the viral entry and infection. The study provides a new in vitro system for investigating the interaction between SARS-cov-2 and host cells and purifying ACE2-expressing cells.
Biol Proced Online
2021 Aug 26
Human Basigin (CD147) Does Not Directly Interact with SARS-CoV-2 Spike Glycoprotein
Basigin, or CD147, has been reported as a coreceptor used by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to invade host cells. It also has a well-established role in Plasmodium falciparum malaria infection of human erythrocytes. Here, we show that there is no direct interaction between the RBD and basigin casting doubt on its role as coreceptor and plausibility as a therapeutic target.
2021 Aug 25
Binding of boswellic acids to functional proteins of the SARS-CoV-2 virus: Bioinformatic studies
Boswellic acids (BAs) have been shown to possess antiviral activity. The binding effectiveness of BAs can be increased through phosphate esterification. Whether or not BAs are druggable against the SARS-CoV-2 disease remains to be established.
Arch Pharm (Weinheim)
2021 Aug 24
Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation
The spike protein of SARS-CoV-2 binds to the ACE2 receptor via its receptor-binding domain (RBD) RBD with Alpha and Beta variants has slightly different interacting AAs due to N501Y mutation. Electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs.
J Chem Inf Model
2021 Aug 24
Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity
Soluble ACE2 (sACE2) is a promising therapeutic candidate that neutralizes SARS CoV-2 infection by acting as a decoy. Using computational mutagenesis, we designed a number of sACE2 derivatives carrying three to four mutations. We show that computational methods have become sufficiently accurate for the design of therapeutics for current and future viral pandemics.
J Chem Inf Model
2021 Aug 24
Multiple Roles of SARS-CoV-2 N Protein Facilitated by Proteoform-Specific Interactions with RNA, Host Proteins, and Convalescent Antibodies
SARS-CoV-2 nucleocapsid (N) protein is a highly immunogenic viral protein that plays essential roles in replication and virion assembly. N protein binds RNA with a preference for GGG motifs, a common motif in coronavirus packaging signals. Unexpectedly, proteolytic processing of N protein resulted in the formation of additional proteoforms.
2021 Aug 23
SARS-CoV-2 Proteins Bind to Hemoglobin and Its Metabolites
We analyzed the recruitment of hemoglobin (Hb) and other metabolites (hemin and protoporphyrin IX-PpIX) by SARS-Cov2 proteins using different approaches. An inhibitory effect in vitro of Hb, hemin, and PpIX at different levels was observed. Strikingly, free Hb at 1mM suppressed viral replication (99%) and its interaction with Sars-CoV-2 was localized into the RBD region of the spike protein.
Int J Mol Sci
2021 Aug 21
Development and Evaluation of a Set of Spike and Receptor Binding Domain-Based Enzyme-Linked Immunosorbent Assays for SARS-CoV-2 Serological Testing
Anti-SARS-CoV-2 IgG serological assays are reported in this paper. S1 and RBD proteins were used to coat ELISA plates, and several secondary antibodies served as reporters. Assays were initially validated with 50 RT-PCR positive COVID-19 sera. Most of the sera were IgG positive at day 40, with seroconversion happening after 14-21 days. Given the robustness of this RBD/IgG assay, it received approval from the sanitary authority in Mexico (COFEPRIS) for production and commercialization under the name UDISTEST-V2G(®)
2021 Aug 20
Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant
The rapidly spreading B.1.617 lineage harbors two key mutations-L452R and E484Q-in the receptor binding domain (RBD) of its spike (S) protein. These mutations disrupts the conserved salt bridge formed between Lys31 of hACE2 and Glu484 of S protein. L452R introduces a charged patch near the binding surface that permits increased electrostatic attraction between the proteins. An improved network of intramolecular interactions observed is likely to increase the stability of the S protein and conformational changes may prevent the binding of neutralizing antibodies.
2021 Aug 20
An unexpected biomaterial against SARS-CoV-2: Bio-polyphosphate blocks binding of the viral spike to the cell receptor
The identification of effective agents/materials to prevent or treat COVID-19 caused by SARS-CoV-2 is an urgent global need. This review aims to survey novel strategies based on inorganic polyphosphate (polyP), a biologically formed but also synthetically available polyanionic polymeric material. PolyP blocks the binding of the virus to the host cell surface receptor ACE2 with its receptor binding domain (RBD)
Mater Today (Kidlington)
2021 Aug 2
Comparative study of the interaction of ivermectin with proteins of interest associated with SARS-CoV-2: A computational and biophysical approach
The mixture of homologs called ivermectin has shown antiviral activity against SARS-CoV-2 in vitro. We present the first comparative analysis of the potential theoretical inhibitory effect of both avermectins on biomolecules associated with COVID-19.
2021 Aug 19