Design of an epitope-based peptide vaccine against<i>Cryptococcus neoformans</i>

Khalil, I.; Omer, Itay; Iza, Farh; Ha, Mohamed; Ha, Elsharif; Aah, Mohamed; Ma, A.C.; Ma, Salih

doi:10.1101/434779

Cited by 6 publications

(7 citation statements)

References 56 publications

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“…T cell epitopes presented by MHC class I molecules are typically peptides between 8 and 11 amino acids in length, whereas MHC class II molecules present longer peptides, 13-17 amino acids in length [40,41]. The CD8 + T cell recognizes the antigen of a pathogen after its attachment with the MHC I molecules, therefore triggering a cytotoxic response against the pathogen [42][43][44][45]. Eight promising CD8 + T cell epitopes were predicted.…”

Section: Plos Onementioning

confidence: 99%

“…Prediction of peptide binding to MHC II molecules readily discriminate CD4 T-cell epitopes, but cannot tell their ability to activate the response of specific CD4 T-cell subsets (e.g., Th1, Th2, and Treg). However, there is evidence that some CD4 T-cell epitopes appear to stimulate specific subsets of Th cells [42,43]. The ability to distinguish the epitopes capable of inducing distinct responses is highly imperative in vaccine development.…”

Section: Plos Onementioning

confidence: 99%

“…The designed vaccine construct was predicted to be stable, soluble (i.e., hydrophilic) and with increased thermostability, as depicted in its physicochemical characteristics. The molecular weight of the vaccine and its high pI value signifies the efficacy as well as the stability of the vaccine construct since proteins having <110kD molecular weight are considered good vaccine candidates [43,44]. Apart from size, surface properties like surface charge and hydrophobicity can affect a designed vaccine candidate.…”

Section: Plos Onementioning

confidence: 99%

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Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein

et al. 2021

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Developing an efficacious vaccine for SARS-CoV-2 infection is critical to stemming COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in designing an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers and 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC I and II alleles, respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. With our In silico test, the vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was also characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We, therefore, propose that potential vaccine designs consider this approach.

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Section: Plos Onementioning

confidence: 99%

Section: Plos Onementioning

confidence: 99%

Section: Plos Onementioning

confidence: 99%

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Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein

et al. 2021

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“…This study used cholera toxin B subunit as an agent to increase the immunogenicity of the vaccine construct because the affinity of the adjuvant causes an increase in T-cell and B-cell responses via the innate immune system (McKee et al, 2007;McCartney et al, 2009;O'Hagan and De Gregorio, 2009). The engineered vaccine has a molecular weight (MW) of 40.82559 KDa, which is a significantly good candidate vaccine because the recommended MW for a good quality vaccine construct is <110 KDa (Khalil et al, 2018;Reche et al, 2014). The antigenicity of the suggested vaccine construct was determined to be 0.5558, which is comparable to the previously reported 0.5430 (Naveed et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach

Shehzad¹,

Sumartono²,

Nugraha³

et al. 2022

J Pharm Pharmacogn Res

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Context: The current COVID-19 pandemic has significantly impacted health and socio-economic status worldwide. The only way to combat this situation is to develop an effective vaccine and immunize people around the globe. Aims: To construct a multi-epitope spike glycoprotein-based vaccine from the SARS-CoV-2 Surabaya isolate using a bioinformatics approach. Methods: The spike protein was submitted to IEDB, VaxiJen, AllerTOP, and ToxinPred webservers to predict antigenic, non-allergic, non-toxic, B- and T-cell epitopes. To develop a multi-epitope vaccine, an adjuvant cholera toxin B subunit was linked to B-cell and B-cell with T-cell through EAAAK and GPGPG linkers, respectively. The designed vaccine 3D structure development, refinement, and validation were done through PHYRE2, Galaxy Refine, and RAMPAGE webservers. Moreover, the Cluspro-2.0 webserver was used for the molecular docking of the vaccine designed with TLR3. The vaccine+TLR3 complex was docked with Surfactant protein A as a control to validate the docking results. Finally, immune-simulation and in silico cloning of the vaccine were carried out by C-ImmSim webserver and SnapGene software, respectively. Results: A multi-epitopic vaccine containing B and T-cell was developed using 392 amino acids with a molecular weight of 40825.59 Da. The docking and immunogenicity results of the vaccine met all established parameters for constructing a quality vaccine. Furthermore, the optimized sequence of the vaccine was successfully cloned in expression vector pET 28 a (+) that yielded a colon of 2724 bp. Conclusions: The vaccine’s immunogenicity demonstrates its effectiveness against SARS-CoV-2 infection. Further confirmatory testing may therefore be performed as soon as possible in the public interest.

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“…Of those, TLQPVERVL and RIPKVMQLV were also recognized by CTL of HLA-A∗02:01 Chagas disease patients, indicating that these peptides are processed and displayed as MHC-I epitopes during the natural history of T. cruzi infection. Khalil's group [ 70 ] demonstrated the immunoreactive mannoprotein (MP88) of Cryptococcus neoformans var. grubii using an immunoinformatic approach and found three potential MHC-I and MHC-II epitopes for each (YMAADQFCL, VSYEEWMNY, and FQQRYTGTF) and (YARLLSLNA, ISYGTAMAV, and INQTSYARL) correspondingly and four promising B-cell epitopes (AYSTPA, AYSTPAS, PASSNCK, and DSAYPP).…”

Section: Discussionmentioning

confidence: 99%

Epitope-Based Immunoinformatic Approach on Heat Shock 70 kDa Protein Complex of Cryptococcus neoformans var. grubii

Elhassan

Alsony

Othman

et al. 2021

Journal of Immunology Research

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Introduction. Cryptococcosis is a ubiquitous opportunistic fungal disease caused by Cryptococcus neoformans var. grubii. It has high global morbidity and mortality among HIV patients and non-HIV carriers with 99% and 95%, respectively. Furthermore, the increasing prevalence of undesired toxicity profile of antifungal, multidrug-resistant organisms and the scarcity of FDA-authorized vaccines were the hallmark in the present days. This study was undertaken to design a reliable epitope-based peptide vaccine through targeting highly conserved immunodominant heat shock 70 kDa protein of Cryptococcus neoformans var. grubii that covers a considerable digit of the world population through implementing a computational vaccinology approach. Materials and Methods. A total of 38 sequences of Cryptococcus neoformans var. grubii’s heat shock 70 kDa protein were retrieved from the NCBI protein database. Different prediction tools were used to analyze the aforementioned protein at the Immune Epitope Database (IEDB) to discriminate the most promising T-cell and B-cell epitopes. The proposed T-cell epitopes were subjected to the population coverage analysis tool to compute the global population’s coverage. Finally, the T-cell projected epitopes were ranked based on their binding scores and modes using AutoDock Vina software. Results and Discussion. The epitopes (ANYVQASEK, QSEKPKNVNPVI, SEKPKNVNPVI, and EKPKNVNPVI) had shown very strong binding affinity and immunogenic properties to B-cell. (FTQLVAAYL, YVYDTRGKL) and (FFGGKVLNF, FINAQLVDV, and FDYALVQHF) exhibited a very strong binding affinity to MHC-I and MHC-II, respectively, with high population coverage for each, while FYRQGAFEL has shown promising results in terms of its binding profile to MHC-II and MHC-I alleles and good strength of binding when docked with HLA-C ∗ 12:03. In addition, there is massive global population coverage in the three coverage modes. Accordingly, our in silico vaccine is expected to be the future epitope-based peptide vaccine against Cryptococcus neoformans var. grubii that covers a significant figure of the entire world citizens.

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Design of an epitope-based peptide vaccine againstCryptococcus neoformans

Cited by 6 publications

References 56 publications

Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein

Immuno-informatics design of a multimeric epitope peptide based vaccine targeting SARS-CoV-2 spike glycoprotein

Development of a multi-epitope spike glycoprotein vaccine to combat SARS-CoV-2 using the bioinformatics approach

Epitope-Based Immunoinformatic Approach on Heat Shock 70 kDa Protein Complex of Cryptococcus neoformans var. grubii

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