scholarly journals Targeting the ENV spike protein of HIV with naturally occurring compounds: an in-silico study for drug designing

2021 ◽  
Author(s):  
S. Sreeram ◽  
R. Sathishkumar ◽  
P. S. Amritha
Keyword(s):  
In Silico ◽  
Spike Protein ◽  
Naturally Occurring ◽  
In Silico Study ◽  
Drug Designing

scholarly journals Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development

2020 ◽  
pp. 1-11 ◽  
Author(s):  
Preeti Pandey ◽  
Jitendra Subhash Rane ◽  
Aroni Chatterjee ◽  
Abhijeet Kumar ◽  
Rajni Khan ◽  
...  
Keyword(s):  
Drug Development ◽  
In Silico ◽  
Spike Protein ◽  
Naturally Occurring ◽  
In Silico Study

scholarly journals In Silico Study of Polyunsaturated Fatty Acids as Potential SARS-CoV-2 Spike Protein Closed Conformation Stabilizers: Epidemiological and Computational Approaches

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 711
Author(s):  
Alonso Vivar-Sierra ◽  
María José Araiza-Macías ◽  
José Patricio Hernández-Contreras ◽  
Arely Vergara-Castañeda ◽  
Gabriela Ramírez-Vélez ◽  
...  
Keyword(s):  
Linoleic Acid ◽  
In Silico ◽  
Cell Types ◽  
Host Cells ◽  
Spike Protein ◽  
Omega 3 ◽  
Angiotensin Converting Enzyme 2 ◽  
Closed Conformation ◽  
In Silico Study ◽  
Omega 6

SARS-CoV-2 infects host cells by interacting its spike protein with surface angiotensin-converting enzyme 2 (ACE2) receptors, expressed in lung and other cell types. Although several risk factors could explain why some countries have lower incidence and fatality rates than others, environmental factors such as diet should be considered. It has been described that countries with high polyunsaturated fatty acid (PUFA) intake have a lower number of COVID-19 victims and a higher rate of recovery from the disease. Moreover, it was found that linoleic acid, an omega-6 PUFA, could stabilize the spike protein in a closed conformation, blocking its interaction with ACE2. These facts prompted us to perform in silico simulations to determine if other PUFA could also stabilize the closed conformation of spike protein and potentially lead to a reduction in SARS-CoV-2 infection. We found that: (a) countries whose source of omega-3 is from marine origin have lower fatality rates; and (b) like linoleic acid, omega-3 PUFA could also bind to the closed conformation of spike protein and therefore, could help reduce COVID-19 complications by reducing viral entrance to cells, in addition to their known anti-inflammatory effects.

scholarly journals In Silico Study on Spice-Derived Antiviral Phytochemicals Against SARS-CoV-2 TMPRSS2 Target

2020 ◽  
Author(s):  
Pradeep Kumar Yadav ◽  
Amit Jaiswal ◽  
Rajiv Kumar Singh
Keyword(s):  
Molecular Simulation ◽  
In Silico ◽  
Catalytic Domain ◽  
Host Protein ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Potential Inhibitor ◽  
In Silico Study

We predicted the structure of TMPRSS2 (transmembrane protease serine 2), a host protein that truncates spike protein of SARS-CoV-2. Then we docked 18 anti-viral compounds found in Indian spices against the catalytic domain of TMPRSS2. We then performed rigorous molecular simulation dynamics simulation to screen the best natural phytochemical which could act as a potential inhibitor of TMPRSS2 activation. <br>

scholarly journals Functional and Structural Characterization of SARS-Cov-2 Spike Protein: An In Silico Study

2021 ◽  
Vol 31 (2) ◽  
Author(s):  
Hadi Sedigh Ebrahim-Saraie ◽  
Behzad Dehghani ◽  
Ali Mojtahedi ◽  
Mohammad Shenagari ◽  
Meysam Hasannejad-Bibalan
Keyword(s):  
B Cell ◽  
In Silico ◽  
Disulfide Bonds ◽  
Deep Understanding ◽  
Structural Features ◽  
Spike Protein ◽  
Tertiary Structures ◽  
In Silico Study ◽  
High Prevalence

BACKGROUND፡ Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of coronavirus disease 2019 (Covid-19), which has been considered as a pandemic by WHO. SARS-CoV-2 encodes four major structural proteins, among which spike protein has always been a main target for new vaccine studies. This in silico study aimed to investigate some physicochemical, functional, immunological, and structural features of spike protein using several bioinformatics tools.METHOD: We retrieved all SARS-CoV-2 spike protein sequences from different countries registered in NCBI GenBank. CLC Sequence Viewer was employed to translate and align the sequences, and several programs were utilized to predict B-cell epitopes. Modification sites such as phosphorylation, glycosylation, and disulfide bonds were defined. Secondary and tertiary structures of all sequences were further computed.RESULTS: Some mutations were determined, where only one (D614G) had a high prevalence. The mutations did not impact the B-cell and physicochemical properties of the spike protein. Seven disulfide bonds were specified and also predicted in several N-link glycosylation and phosphorylation sites. The results also indicated that spike protein is a non-allergen.CONCLUSION: In summary, our findings provided a deep understanding of spike protein, which can be valuable for future studies on SARS CoV-2 infections and design of new vaccines.

scholarly journals Drug Repurposing to Identify Therapeutics Against COVID 19 with SARS-Cov-2 Spike Glycoprotein and Main Protease as Targets: An in Silico Study

2020 ◽  
Author(s):  
arun kumar ◽  
Sharanya C.S ◽  
Abhithaj J ◽  
Sadasivan C
Keyword(s):  
In Silico ◽  
Drug Repurposing ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Drug Candidates ◽  
Protein Receptor ◽  
Main Protease ◽  
In Silico Study ◽  
Molecular Modeling And Docking ◽  
Different Parts

<p>The total cases of novel corona virus (SARS-CoV-2) infections is more than one million and total deaths recorded is more than fifty thousand. The research for developing vaccines and drugs against SARS-CoV-2 is going on in different parts of the world. Aim of the present study was to identify potential drug candidates against SARS-CoV-2 from existing drugs using <i>in silico</i> molecular modeling and docking. The targets for the present study was the spike protein and the main protease of SARS-CoV-2. The study was able to identify some drugs that can either bind to the spike protein receptor binding domain or the main protease of SARS-CoV-2. These include some of the antiviral drugs. These drugs might have the potential to inhibit the infection and viral replication.</p>

scholarly journals Cutting epitopes to survive: the case of lambda variant

2021 ◽  
Author(s):  
Stefano Pascarella ◽  
Massimo Ciccozzi ◽  
Martina Bianchi ◽  
Domenico Benvenuto ◽  
Roberto Cauda ◽  
...  
Keyword(s):  
In Silico ◽  
Adaptation Strategy ◽  
Host Immunity ◽  
Spike Protein ◽  
Viral Variant ◽  
Glycosylation Sites ◽  
Immunogenic Epitope ◽  
In Silico Study ◽  
Potential Impact ◽  
Protein Mutations

This manuscript concisely reports an in-silico study on the potential impact of the Spike protein mutations on immuno-escape ability of SARS-CoV-2 lambda variant. Biophysical and bioinformatics data suggest that a combination of shortening immunogenic epitope loops and generation of potential N-glycosylation sites may be a viable adaptation strategy potentially allowing this emerging viral variant escaping host immunity.

scholarly journals Phospholipids dock SARS-CoV-2 spike protein via hydrophobic interactions: a minimal in-silico study of lecithin nasal spray therapy

2021 ◽  
Vol 44 (11) ◽  
Author(s):  
Muhammad Nawaz Qaisrani ◽  
Roman Belousov ◽  
Jawad Ur Rehman ◽  
Elham Moharramzadeh Goliaei ◽  
Ivan Girotto ◽  
...  
Keyword(s):  
Nasal Spray ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Spike Protein ◽  
In Silico Study

scholarly journals In Silico Study on Spice-Derived Antiviral Phytochemicals Against SARS-CoV-2 TMPRSS2 Target

2020 ◽  
Author(s):  
Pradeep Kumar Yadav ◽  
Amit Jaiswal ◽  
Rajiv Kumar Singh
Keyword(s):  
Molecular Simulation ◽  
In Silico ◽  
Catalytic Domain ◽  
Host Protein ◽  
Dynamics Simulation ◽  
Spike Protein ◽  
Potential Inhibitor ◽  
In Silico Study

We predicted the structure of TMPRSS2 (transmembrane protease serine 2), a host protein that truncates spike protein of SARS-CoV-2. Then we docked 18 anti-viral compounds found in Indian spices against the catalytic domain of TMPRSS2. We then performed rigorous molecular simulation dynamics simulation to screen the best natural phytochemical which could act as a potential inhibitor of TMPRSS2 activation. <br>

scholarly journals Structural Deviation and Identification of Novel Inhibitor of SARS-CoV-2 Spike Protein Through Molecular Docking: An In Silico Study

2020 ◽  
Author(s):  
Anindya Panja ◽  
Aniket Sarkar
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Half Life ◽  
Attachment Site ◽  
Spike Protein ◽  
Structural Comparison ◽  
Docking Result ◽  
In Silico Study ◽  
Novel Coronavirus ◽  
Bat Coronavirus

Purpose: Pandemic Novel Coronavirus (SARS-CoV-2) has emerger centered from wuhan, China. Structurally homologous spike protein of SARS-CoV-2 receptor is taxonomically homologous with SARS-Cov and SARS associated bat coronavirus. Still now scientists are trying to find out proper vaccine and treatments for this disease. Methods: Systematically we modeled and compared the structure of SARS-CoV-2 spike protein along with Bat Cov, Bat SARS Cov and SARS Cov Urbani. S1 and S2 unit of the coronavirus (SARS-CoV-2) are attached with ACE2 and furin, here we docked 5 Ca+ chelating drugs with these two proteins. Results: Structural comparison with all these spike proteins revealed that less significant but not negligible difference exists among them. Inserted stable nucleotide sequences and corresponding surface exposed peptidal region may be considered as epitope. Docking result with Toxicokinetics and half life of Penicillamine can effectly inhibit the attachment site of spike protein of coronavirus (SARS-CoV-2). Conclusions: Docking summery and the pharmacokinetics with toxicokinetics index recommend that Penicillamine can able to inhibit the infection of SARS-CoV-2.

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