scholarly journals Glycyrrhizic Acid Inhibits SARS-CoV-2 Infection by Blocking Spike Protein-Mediated Cell Attachment

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6090
Author(s):  
Jingjing Li ◽  
Dongge Xu ◽  
Lingling Wang ◽  
Mengyu Zhang ◽  
Guohai Zhang ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Glycyrrhizic Acid ◽  
Cell Attachment ◽  
Protein S ◽  
Host Cells ◽  
S Protein ◽  
Wide Range ◽  
Interaction Interface ◽  
Binding Pockets ◽  
Antiviral Activities

Glycyrrhizic acid (GA), also known as glycyrrhizin, is a triterpene glycoside isolated from plants of Glycyrrhiza species (licorice). GA possesses a wide range of pharmacological and antiviral activities against enveloped viruses including severe acute respiratory syndrome (SARS) virus. Since the S protein (S) mediates SARS coronavirus 2 (SARS-CoV-2) cell attachment and cell entry, we assayed the GA effect on SARS-CoV-2 infection using an S protein-pseudotyped lentivirus (Lenti-S). GA treatment dose-dependently blocked Lenti-S infection. We showed that incubation of Lenti-S virus, but not the host cells with GA prior to the infection, reduced Lenti-S infection, indicating that GA targeted the virus for infection. Surface plasmon resonance measurement showed that GA interacted with a recombinant S protein and blocked S protein binding to host cells. Autodocking analysis revealed that the S protein has several GA-binding pockets including one at the interaction interface to the receptor angiotensin-converting enzyme 2 (ACE2) and another at the inner side of the receptor-binding domain (RBD) which might impact the close-to-open conformation change of the S protein required for ACE2 interaction. In addition to identifying GA antiviral activity against SARS-CoV-2, the study linked GA antiviral activity to its effect on virus cell binding.

scholarly journals SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Palur V Raghuvamsi ◽  
Nikhil Kumar Tulsian ◽  
Firdaus Samsudin ◽  
Xinlei Qian ◽  
Kiren Purushotorman ◽  
...  
Keyword(s):  
Cleavage Site ◽  
Proteolytic Processing ◽  
Host Cells ◽  
Heptad Repeat ◽  
S Protein ◽  
Exchange Mass Spectrometry ◽  
Central Helix ◽  
Interaction Interface ◽  
Therapeutic Development ◽  
Dynamics Simulations

The Spike (S) protein is the main handle for SARS-CoV-2 to enter host cells via surface ACE2 receptors. How ACE2 binding activates proteolysis of S protein is unknown. Here, using amide hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations, we have mapped the S:ACE2 interaction interface and uncovered long-range allosteric propagation of ACE2 binding to sites necessary for host-mediated proteolysis of S protein, critical for viral host entry. Unexpectedly, ACE2 binding enhances dynamics at a distal S1/S2 cleavage site and flanking protease docking site ~27 Å away while dampening dynamics of the stalk hinge (central helix and heptad repeat) regions ~130 Å away. This highlights that the stalk and proteolysis sites of the S protein are dynamic hotspots in the pre-fusion state. Our findings provide a dynamics map of the S:ACE2 interface in solution and also offer mechanistic insights into how ACE2 binding is allosterically coupled to distal proteolytic processing sites and viral-host membrane fusion. Our findings highlight protease docking sites flanking the S1/S2 cleavage site, fusion peptide and heptad repeat 1 (HR1) as alternate allosteric hotspot targets for potential therapeutic development.

scholarly journals Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

2020 ◽  
Author(s):  
Micholas Smith ◽  
Jeremy C. Smith
Keyword(s):  
Small Molecules ◽  
High Throughput Screening ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
The Novel ◽  
S Protein ◽  
Host Virus Interactions ◽  
Virus Interactions ◽  
Ranked List

The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus shares substantial similarity with SARS-CoV. Here, using a computational model of the spike protein (S-protein) of SARS-CoV-2 interacting with the human ACE2 receptor, we make use of the world's most powerful supercomputer, SUMMIT, to enact an ensemble docking virtual high-throughput screening campaign and identify small-molecules which bind to either the isolated Viral S-protein at its host receptor region or to the S protein-human ACE2 interface. We hypothesize the identified small-molecules may be repurposed to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of compounds is given that can be tested experimentally.<br>

scholarly journals Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

2020 ◽  
Author(s):  
Micholas Smith ◽  
Jeremy C. Smith
Keyword(s):  
Small Molecules ◽  
High Throughput Screening ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
The Novel ◽  
S Protein ◽  
Host Virus Interactions ◽  
Virus Interactions ◽  
Ranked List

The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus shares substantial similarity with SARS-CoV. Here, using a computational model of the spike protein (S-protein) of SARS-CoV-2 interacting with the human ACE2 receptor, we make use of the world's most powerful supercomputer, SUMMIT, to enact an ensemble docking virtual high-throughput screening campaign and identify small-molecules which bind to either the isolated Viral S-protein at its host receptor region or to the S protein-human ACE2 interface. We hypothesize the identified small-molecules may be repurposed to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of compounds is given that can be tested experimentally.<br>

scholarly journals Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization

2021 ◽  
Author(s):  
Yunjeong Kim ◽  
Natasha N Gaudreault ◽  
David A Meekins ◽  
Krishani D Perera ◽  
Dashzeveg Bold ◽  
...  
Keyword(s):  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Animal Species ◽  
Virus Entry ◽  
Neutralizing Antibody ◽  
Protein S ◽  
Pseudotyped Virus ◽  
S Protein ◽  
Viral Neutralization ◽  
Wide Range

SARS-CoV-2 is a zoonotic agent capable of infecting humans and a wide range of animal species. Over the duration of the pandemic, mutations in the SARS-CoV-2 Spike protein (S) have arisen in circulating viral populations, culminating in the spread of several variants of concern (VOC) with varying degrees of altered virulence, transmissibility, and neutralizing antibody escape. In this study, we employed lentivirus-based pseudotyped viruses that express specific SARS-CoV-2 S protein substitutions and cell lines that stably express ACE2 from nine different animal species to gain insights into the effects of VOC mutations on viral entry and antibody neutralization capability. All animal ACE2 receptors tested, except mink, support viral cell entry for pseudoviruses expressing the parental (prototype Wuhan-1) S at levels comparable to human ACE2. Most single S substitutions (e.g., 452R, 478K, 501Y) did not significantly change virus entry, although 614G and 484K resulted in a decreased efficiency in viral entry.  Conversely, combinatorial VOC substitutions in the S protein were associated with significantly increased entry capacity of pseudotyped viruses compared to that of the parental Wuhan-1 pseudotyped virus. Similarly, infection studies using live ancestral (USA-WA1/2020), Alpha, and Beta SARS-CoV-2 viruses in hamsters revealed a higher replication potential for the Beta variant compared to the ancestral prototype virus. Moreover, neutralizing titers in sera from various animal species, including humans, were significantly reduced by single substitutions of 484K or 452R, double substitutions of 501Y-484K, 452R-484K and 452R-478K and the triple substitution of 501Y-484K-417N, suggesting that 484K and 452R are particularly important for evading neutralizing antibodies in human, cat, and rabbit sera. Cumulatively, this study reveals important insights into the host range of SARS-CoV-2 and the effect of recently emergent S protein substitutions on viral entry, virus replication and antibody-mediated viral neutralization.

scholarly journals Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

2020 ◽  
Author(s):  
Micholas Smith ◽  
Jeremy C. Smith
Keyword(s):  
Small Molecules ◽  
High Throughput Screening ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
The Novel ◽  
S Protein ◽  
Host Virus Interactions ◽  
Virus Interactions ◽  
Ranked List

The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus shares substantial similarity with SARS-CoV. Here, using a computational model of the spike protein (S-protein) of SARS-CoV-2 interacting with the human ACE2 receptor, we make use of the world's most powerful supercomputer, SUMMIT, to enact an ensemble docking virtual high-throughput screening campaign and identify small-molecules which bind to either the isolated Viral S-protein at its host receptor region or to the S protein-human ACE2 interface. We hypothesize the identified small-molecules may be repurposed to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of compounds is given that can be tested experimentally.<br>

scholarly journals Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 Interface

2020 ◽  
Author(s):  
Micholas Smith ◽  
Jeremy C. Smith
Keyword(s):  
Small Molecules ◽  
High Throughput Screening ◽  
Protein S ◽  
Host Cells ◽  
Spike Protein ◽  
The Novel ◽  
S Protein ◽  
Host Virus Interactions ◽  
Virus Interactions ◽  
Ranked List

The novel Wuhan coronavirus (SARS-CoV-2) has been sequenced, and the virus shares substantial similarity with SARS-CoV. Here, using a computational model of the spike protein (S-protein) of SARS-CoV-2 interacting with the human ACE2 receptor, we make use of the world's most powerful supercomputer, SUMMIT, to enact an ensemble docking virtual high-throughput screening campaign and identify small-molecules which bind to either the isolated Viral S-protein at its host receptor region or to the S protein-human ACE2 interface. We hypothesize the identified small-molecules may be repurposed to limit viral recognition of host cells and/or disrupt host-virus interactions. A ranked list of compounds is given that can be tested experimentally.<br>

scholarly journals Coronavirus Spike (S) Protein: A Brief Review on Structure-Function Relationship, Host Receptors, and Role in Cell Infection

2020 ◽  
pp. 116-124 ◽  
Author(s):  
Lidiane Pereira De Albuquerque ◽  
Leydianne Leite de Siqueira Patriota ◽  
Vitor Gonzatto ◽  
Emmanuel Viana Pontual ◽  
Patrícia Maria Guedes Paiva ◽  
...  
Keyword(s):  
Structure Function ◽  
Cell Attachment ◽  
Protein A ◽  
Host Cells ◽  
Cell Infection ◽  
S Protein ◽  
Host Tropism ◽  
Functional Aspects ◽  
Structure Function Relationship ◽  
Function Relationship

Coronaviruses (CoVs) are a broad group of spherical and enveloped viruses that cause diseases in humans and animals. CoVs have become a major threat to public health in the past two decades, exemplified by epidemics of acute respiratory syndromes and, most recently, the coronavirus disease 2019 pandemic. The envelope of CoVs contains spike (S) proteins, which are transmembrane proteins with a crown-like shape involved in cell attachment, cell‒cell fusion, host tropism, and pathogenesis. The receptors for spike proteins in host cells can be glycans and proteins. This review approaches the structural and functional aspects of the S protein of CoVs. Several issues are presented, including the structure‒function relationship, examples of host receptors, S protein-host cell connection, and its role in the entry of the virus into host cells. The S protein is one of the main targets of studies on the evolutionary relationships between CoVs, mapping of cross-host transmission events, changes in virulence, variations in disease severity level, and the development of therapeutic strategies and vaccines.

scholarly journals The Case for Re-Examining Glycosylation Inhibitors, Mimetics, Primers and Glycosylation Decoys as Antivirals and Anti-Inflammatories in COVID19.

2020 ◽  
Author(s):  
Roger A Laine
Keyword(s):  
Type 2 Diabetes ◽  
Side Effects ◽  
Antiviral Activity ◽  
Host Cells ◽  
Cellular Receptor ◽  
Infection Cycle ◽  
Short Term ◽  
Gaucher’S Disease ◽  
S Protein

Abstract: The SARS COV2 and other SARS viruses employ a heavily glycosylated spike S protein (1,2) to bind to the ACE2 cellular receptor, also heavily glycosylated (3), on host cells. Historically, there is abundant information of glycosylation inhibitors for antiviral activity to stimulate their investigation for COVID19 treatment. While there are certain to be side effects by interfering systematically with glycosylation, a short-term dose of primers, decoys or glycosylation inhibitors might be sufficient to stop or slow the COVID19 infection cycle with minimal or temporary side effects. For example, Castanospermine derivative Celgosivir (6-O-butanoylcastanospermine) (4) and Miglitol, Miglustat (N-butyl -1-deoxynojirimycin) (5,6) are already FDA approved for type 2 diabetes and Gaucher’s disease (7), passing safety and effectivity Phases. This article is to stimulate repurpose testing of these already-approved compounds and others for COVID19 therapeutics.

Discovery of Some Antiviral Natural products to fight against Novel Corona Virus (SARS-CoV-2) using Insilico approach

2020 ◽  
Vol 23 ◽  
Author(s):  
Ashish Shah ◽  
Vaishali Patel ◽  
Bhumika Parmar
Keyword(s):  
Binding Affinity ◽  
Protein S ◽  
Docking Studies ◽  
Spike Protein ◽  
Enveloped Viruses ◽  
Bioactivity Prediction ◽  
Corona Virus ◽  
Main Protease ◽  
Antiviral Activities ◽  
Deadly Disease

Background: Novel Corona virus is a type of enveloped viruses with a single stranded RNA enclosing helical nucleocapsid. The envelope consists of spikes on the surface which are made up of proteins through which virus enters into human cells. Until now there is no specific drug or vaccine available to treat COVID-19 infection. In this scenario, reposting of drug or active molecules may provide rapid solution to fight against this deadly disease. Objective: We had selected 30 phytoconstituents from the different plants which are reported for antiviral activities against corona virus (CoVs) and performed insilico screening to find out phytoconstituents which have potency to inhibit specific target of novel corona virus. Methods: We had perform molecular docking studies on three different proteins of novel corona virus namely COVID-19 main protease (3CL pro), papain-like protease (PL pro) and spike protein (S) attached to ACE2 binding domain. The screening of the phytoconstituents on the basis of binding affinity compared to standard drugs. The validations of screened compounds were done using ADMET and bioactivity prediction. Results: We had screened five compounds biscoclaurine, norreticuline, amentoflavone, licoricidin and myricetin using insilico approach. All compounds found safe in insilico toxicity studies. Bioactivity prediction reviles that these all compounds may act through protease or enzyme inhibition. Results of compound biscoclaurine norreticuline were more interesting as this biscoclaurine had higher binding affinity for the target 3CLpro and PLpro targets and norreticuline had higher binding affinity for the target PLpro and Spike protein. Conclusion: Our study concludes that these compounds could be further explored rapidly as it may have potential to fight against COVID-19.

Carbohydrate-Binding Agents: Potential of Repurposing for COVID-19 Therapy

2020 ◽  
Vol 21 (11) ◽  
pp. 1085-1096 ◽  
Author(s):  
Rajesh Kumar Gupta ◽  
Girish R. Apte ◽  
Kiran Bharat Lokhande ◽  
Satyendra Mishra ◽  
Jayanta K. Pal
Keyword(s):  
Vaccine Development ◽  
Host Cells ◽  
Carbohydrate Binding ◽  
Atypical Pneumonia ◽  
The Novel ◽  
High Infection ◽  
Binding Agents ◽  
Current Scenario ◽  
Antiviral Activities ◽  
Novel Drug

: With the emergence of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the whole world is suffering from atypical pneumonia, which resulted in more than 559,047 deaths worldwide. In this time of crisis and urgency, the only hope comes from new candidate vaccines and potential antivirals. However, formulating new vaccines and synthesizing new antivirals are a laborious task. Therefore, considering the high infection rate and mortality due to COVID-19, utilization of previous information, and repurposing of existing drugs against valid viral targets have emerged as a novel drug discovery approach in this challenging time. The transmembrane spike (S) glycoprotein of coronaviruses (CoVs), which facilitates the virus’s entry into the host cells, exists in a homotrimeric form and is covered with N-linked glycans. S glycoprotein is known as the main target of antibodies having neutralizing potency and is also considered as an attractive target for therapeutic or vaccine development. Similarly, targeting of N-linked glycans of S glycoprotein envelope of CoV via carbohydrate-binding agents (CBAs) could serve as an attractive therapeutic approach for developing novel antivirals. CBAs from natural sources like lectins from plants, marine algae and prokaryotes and lectin mimics like Pradimicin-A (PRM-A) have shown antiviral activities against CoV and other enveloped viruses. However, the potential use of CBAs specifically lectins was limited due to unfavorable responses like immunogenicity, mitogenicity, hemagglutination, inflammatory activity, cellular toxicity, etc. Here, we reviewed the current scenario of CBAs as antivirals against CoVs, presented strategies to improve the efficacy of CBAs against CoVs; and studied the molecular interactions between CBAs (lectins and PRM-A) with Man9 by molecular docking for potential repurposing against CoVs in general, and SARSCoV- 2, in particular.

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