Computational design of peptide ligands to target the intermolecular interaction between viral envelope protein and pediatric receptor

Xu, Darong; Bian, Hongliang; Cai, Jinlan; Bao, Daocheng; Jin, Qinian; Zhu, Min; Cui-feng, Zhang; Tao, Tingting

doi:10.1016/j.compbiolchem.2017.06.001

Cited by 6 publications

(2 citation statements)

References 26 publications

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“…The peptide targets are more superior than traditional ligandbased drugs including less toxicity, fewer side-effects, and their ultrafast action. Immunoinformatics methodologies are helping researchers by reducing the workload of laboratory trials; additionally, these approaches are less timeconsuming and cost-efficient than traditional approaches [99][100][101]. Since the last decade, there has been much progress in in silico drug designing [102].…”

Section: Discussionmentioning

confidence: 99%

Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening

Waqas

Ali

Rehman

et al. 2021

BioMed Research International

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Background. Coronaviruses (CoVs) are enveloped positive-strand RNA viruses which have club-like spikes at the surface with a unique replication process. Coronaviruses are categorized as major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Nowadays, a new strain of coronaviruses is identified and named as SARS-CoV-2. Multiple cases of SARS-CoV-2 attacks are being reported all over the world. SARS-CoV-2 showed high death rate; however, no specific treatment is available against SARS-CoV-2. Methods. In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against SARS-CoV-2 for the development of the coronavirus vaccine. Cytotoxic T-lymphocyte and B-cell epitopes were predicted for SARS-CoV-2 coronavirus protein. Multiple sequence alignment of three genomes (SARS-CoV, MERS-CoV, and SARS-CoV-2) was used to conserved binding domain analysis. Results. The docking complexes of 4 CTL epitopes with antigenic sites were analyzed followed by binding affinity and binding interaction analyses of top-ranked predicted peptides with MHC-I HLA molecule. The molecular docking (Food and Drug Regulatory Authority library) was performed, and four compounds exhibiting least binding energy were identified. The designed epitopes lead to the molecular docking against MHC-I, and interactional analyses of the selected docked complexes were investigated. In conclusion, four CTL epitopes (GTDLEGNFY, TVNVLAWLY, GSVGFNIDY, and QTFSVLACY) and four FDA-scrutinized compounds exhibited potential targets as peptide vaccines and potential biomolecules against deadly SARS-CoV-2, respectively. A multiepitope vaccine was also designed from different epitopes of coronavirus proteins joined by linkers and led by an adjuvant. Conclusion. Our investigations predicted epitopes and the reported molecules that may have the potential to inhibit the SARS-CoV-2 virus. These findings can be a step towards the development of a peptide-based vaccine or natural compound drug target against SARS-CoV-2.

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Section: Discussionmentioning

confidence: 99%

Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening

Waqas

Ali

Rehman

et al. 2021

BioMed Research International

View full text Add to dashboard Cite

show abstract

“…The peptide targets are more preferable than traditional ligand-based drugs and vaccines due to different aspects including less toxic, fewer side-effects and their ultrafast action. Immunoinformatics approaches help by reducing the work-load of laboratory trials, additionally these approaches are less time consuming and cost efficient than traditional approaches (Vanhee et al, 2011;Heurich et al, 2013;Xu et al, 2017). In the last 10 years, there has been much progress in in silico drug designing (Sehgal, 2017).…”

Section: Discussionmentioning

confidence: 99%

Determine the Potential Epitope Based Peptide Vaccine Against Novel SARS-CoV-2 Targeting Structural Proteins Using Immunoinformatics Approaches

Waqas

Ali

Sufyan

et al. 2020

Front. Mol. Biosci.

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Coronaviruses (CoVs) belong to the Coronaviridae-family. The genus Betacoronaviruses, are enveloped positive strand RNA viruses with club-like spikes at the surface with a unique replication process and a large RNA genome (∼25 kb). CoVs are known as one of the major pathogenic viruses causing a variety of diseases in birds and mammals including humans (lethal respiratory dysfunctions). Recently, a new strain of coronavirus has been identified and named as SARS-CoV-2. A large number of COVID-19 (disease caused by SARS-CoV-2) cases are being diagnosed all over the World especially in China (Wuhan). COVID-19 showed high mortality rate exponentially, however, not even a single effective cure is being introduced yet against COVID-19. In the current study, immunoinformatics approaches were employed to predict the antigenic epitopes against COVID-19 for the development of a coronavirus peptide vaccine. Cytotoxic T-lymphocyte (CTL) and B-cell epitopes were predicted for SARS-CoV-2 coronavirus structural proteins (Spikes, Membrane, Envelope, and Nucleocapsid). The docking complexes of the top 10 epitopes having antigenic sites were analyzed led by binding affinity and binding interactional analyses of top ranked predicted peptides with the MHC-I HLA molecule. The predicted peptides may have potential to be used as peptide vaccine against COVID-19.

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Structure-based rational design of peptide inhibitors to disrupt the recognition and interaction between hepatitis B virus large envelope protein and human hepatocyte receptor γ2-adaptin

et al. 2017

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Computational design of peptide ligands to target the intermolecular interaction between viral envelope protein and pediatric receptor

Cited by 6 publications

References 26 publications

Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening

Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening

Determine the Potential Epitope Based Peptide Vaccine Against Novel SARS-CoV-2 Targeting Structural Proteins Using Immunoinformatics Approaches

Structure-based rational design of peptide inhibitors to disrupt the recognition and interaction between hepatitis B virus large envelope protein and human hepatocyte receptor γ2-adaptin

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