Short Communication: Association of HLA-A*1101 with Resistance and B*4006 with Susceptibility to HIV and HIV-TB: An in Silico Analysis of Promiscuous T Cell Epitopes

2009 ◽  
Vol 25 (10) ◽  
pp. 1023-1028 ◽  
Author(s):  
S. Raghavan ◽  
P. Selvaraj ◽  
S. Swaminathan ◽  
G. Narendran
Keyword(s):  
T Cell ◽  
In Silico ◽  
Short Communication ◽  
In Silico Analysis ◽  
T Cell Epitopes ◽  
Silico Analysis

scholarly journals In silico analysis and modeling of putative T cell epitopes for vaccine design of Toscana virus

3 Biotech ◽  
2014 ◽  
Vol 5 (4) ◽  
pp. 497-503 ◽  
Author(s):  
Amisha Jain ◽  
Pranav Tripathi ◽  
Aniket Shrotriya ◽  
Ritu Chaudhary ◽  
Ajeet Singh
Keyword(s):  
T Cell ◽  
In Silico ◽  
In Silico Analysis ◽  
Vaccine Design ◽  
T Cell Epitopes ◽  
Toscana Virus ◽  
Silico Analysis

In silico analysis of four structural proteins of aphthovirus serotypes revealed significant B and T cell epitopes

2019 ◽  
Vol 128 ◽  
pp. 254-262 ◽  
Author(s):  
Sohail Raza ◽  
Kalsoom Siddique ◽  
Masood Rabbani ◽  
Tahir Yaqub ◽  
Aftab Ahmad Anjum ◽  
...  
Keyword(s):  
T Cell ◽  
In Silico ◽  
In Silico Analysis ◽  
Structural Proteins ◽  
T Cell Epitopes ◽  
Silico Analysis

scholarly journals Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In Silico Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-17
Author(s):  
Onyeka S. Chukwudozie ◽  
Rebecca C. Chukwuanukwu ◽  
Onyekachi O. Iroanya ◽  
Daniel M. Eze ◽  
Vincent C. Duru ◽  
...  
Keyword(s):  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Rna Binding ◽  
Peptide Vaccine ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Translation Efficiency ◽  
T Cell Epitopes

The novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has previously never been identified with humans, thereby creating devastation in public health. The need for an effective vaccine to curb this pandemic cannot be overemphasized. In view of this, we designed a subcomponent antigenic peptide vaccine targeting the N-terminal (NT) and C-terminal (CT) RNA binding domains of the nucleocapsid protein that aid in viral replication. Promising antigenic B cell and T cell epitopes were predicted using computational pipelines. The peptides “RIRGGDGKMKDL” and “AFGRRGPEQTQGNFG” were the B cell linear epitopes with good antigenic index and nonallergenic property. Two CD8+ and Three CD4+ T cell epitopes were also selected considering their safe immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity, and putative restrictions to a number of MHC-I and MHC-II alleles. With these selected epitopes, a nonallergenic chimeric peptide vaccine incapable of inducing a type II hypersensitivity reaction was constructed. The molecular interaction between the Toll-like receptor-5 (TLR5) which was triggered by the vaccine was analyzed by molecular docking and scrutinized using dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing the pET-28a vector. This research, therefore, provides a guide for experimental investigation and validation.

scholarly journals 910 Overexpression of miR-155–5p can upregulate antigen processing and presentation pathway via targeting tapasin

2021 ◽  
Vol 9 (Suppl 3) ◽  
pp. A956-A956
Author(s):  
Yuan Wang ◽  
Maria-Filothei Lazaridou ◽  
Chiara Massa ◽  
Barbara Seliger
Keyword(s):  
T Cell ◽  
Mhc Class I ◽  
In Silico ◽  
Posttranscriptional Regulation ◽  
Antigen Processing ◽  
In Silico Analysis ◽  
Surface Expression ◽  
Class I ◽  
Antigen Processing And Presentation ◽  
Silico Analysis

BackgroundDysregulation of major histocompatibility complex (MHC) class I antigen processing and presentation machinery (APM) components in the tumor as one main molecular mechanism of immune escape leading to deactivation of T cell immune surveillance could be due to post-transcriptional regulation via immune-modulatory microRNAs (miRNA). It is now well established from a variety of studies that several miRNAs could effectively modulate the expression of some MHC class I APM components in tumors. Tapasin is an important APM molecule involved in the association of MHC class I with transporter associated with antigen processing (TAP) and peptide loading. Since so far no detailed investigation of the posttranscriptional regulation of tapasin exists, the aim of this study is to identify and functionally characterize miRNAs targeting tapasin in melanoma.MethodsUsing miRNA trapping by RNA in vitro affinity purification (miTRAP) and in silico as well as small RNA sequencing, miRNAs will be identified, which bind to the 3’untranslated region (3’ UTR) of tapasin. Dual-luciferase assays will be performed to determine to bind of the miRNA. In silico analysis was performed to predict the effect of miRNAs on the survival of melanoma patients in correlation to tapasin. RT-qPCR, Western blot, flow cytometry, and other functional assays were performed after transfecting miRNA mimics in three melanoma cell lines.ResultsUsing the combination strategy of miTRAP and RNA seq we identified miR-155-5p to bind to the 3’UTR of tapasin, which was further confirmed by in silico analysis and dual-luciferase reporter assay. Transfection of miR-155-5p mimics demonstrated that miR-155-5p upregulate tapasin protein level, which was accompanied by an upregulation of the MHC class I (HLA-ABC) surface expression. Simultaneously, in several different types of cancer, including melanoma, the expression of miR-155-5p is significantly positively correlated with the patient‘s survival and HLA-A protein.ConclusionsOur data revealed for the first time a positive role of miR-155-5p in the posttranscriptional regulation of tapasin in melanoma and provide further insights into the miR-155-5p-mediated induction of HLA-ABC surface expression. This might lead to a better T cell response, avoidance tumor cell escape, improvement of patients‘ survival and thus might be a potential therapeutic target.AcknowledgementsThe work was supported by a grant from the DKH (BS).

scholarly journals Attenuated Subcomponent Vaccine Design Targeting the SARS-CoV-2 Nucleocapsid Phosphoprotein RNA Binding Domain: In silico analysis

2020 ◽  
Author(s):  
Onyeka S. Chukwudozie ◽  
Rebecca C. Chukwuanukwu ◽  
Iroanya O. Onyekachi ◽  
Eze M. Daniel ◽  
Duru C. Vincent ◽  
...  
Keyword(s):  
T Cell ◽  
In Silico ◽  
Rna Binding ◽  
Peptide Vaccine ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Effective Vaccine ◽  
Translation Efficiency ◽  
T Cell Epitopes ◽  
Mhc I

ABSTRACTThe novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has previously never been identified with humans, thereby creating devastation in public health. The need for an effective vaccine to curb this pandemic cannot be overemphasized. In view of this, we, therefore, designed a subcomponent antigenic peptide vaccine targeting the N-terminal (NT) and C-terminal (CT) RNA binding domains of nucleocapsid protein that aid in viral replication. Promising antigenic B-cells and T cell epitopes were predicted using computational pipelines. The peptides “RIRGGDGKMKDL” and “AFGRRGPEQTQGNFG” were the B cell linear epitopes with good antigenic index and non-allergenic property. Two CD8+ and Three CD4+ T-cell epitopes were also selected considering their safe immunogenic profiling such as allergenicity, antigen level conservancy, antigenicity, peptide toxicity, and putative restrictions to a number of MHC-I and II alleles. With these selected epitopes, a non-allergenic chimeric peptide vaccine incapable of inducing a Type II hypersensitivity reaction was constructed. The molecular interaction between the toll-like receptor-5 (TLR5) which was triggered by the vaccine was analyzed by molecular docking and scrutinized using dynamics simulation. Finally, in silico cloning was performed to ensure the expression and translation efficiency of the vaccine, utilizing pET-28a vector. This research, therefore, provides a guide for experimental investigation and validation.

scholarly journals A Bioinformatics Approach for the Prediction of Immunogenic Properties and Structure of the SARS-COV-2 B.1.617.1 Variant Spike Protein

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Vijay Kumar Srivastava ◽  
Sanket Kaushik ◽  
Gazal Bhargava ◽  
Ajay Jain ◽  
Juhi Saxena ◽  
...  
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
B Cell ◽  
In Silico ◽  
Tertiary Structure ◽  
In Silico Analysis ◽  
Respiratory Illness ◽  
T Cell Epitopes ◽  
S Protein ◽  
Immunogenic Properties

Background. B.1.617.1, a variant of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causing respiratory illness is responsible for the second wave of COVID-19 and associated with a high incidence of infectivity and mortality. To mitigate the B.1.617.1 variant of SARS-CoV-2, deciphering the protein structure and immunological responses by employing bioinformatics tools for data mining and analysis is pivotal. Objectives. Here, an in silico approach was employed for deciphering the structure and immune function of the subunit of spike (S) protein of SARS-CoV-2 B.1.617.1 variant. Methods. The partial amino acid sequence of SARS-CoV-2 B.1.617.1 variant S protein was analyzed, and its putative secondary and tertiary structure was predicted. Immunogenic analyses including B- and T-cell epitopes, interferon-gamma (IFN-γ) response, chemokine, and protective antigens for SARS-CoV 2 S proteins were predicted using appropriate tools. Results. B.1.617.1 variant S protein sequence was found to be highly stable and amphipathic. ABCpred and CTLpred analyses led to the identification of two potential antigenic B cell and T cell epitopes with starting amino acid positions at 60 and 82 (for B cell epitopes) and 54 and 98 (for T cell epitopes) having prediction scores > 0.8 . Further, RAMPAGE tool was used for determining the allowed and disallowed regions of the three-dimensional predicted structure of SARS-CoV-2 B.1.617.1 variant S protein. Conclusion. Together, the in silico analysis revealed the predicted structure of partial S protein, immunogenic properties, and possible regions for S protein of SARS-CoV-2 and provides a valuable prelude for engineering the targeted vaccine or drug against B.1.617.1 variant of SARS-CoV-2.

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