Immunoinformatics designed T cell multi epitope dengue peptide vaccine derived from non structural proteome

G, Sunil Krishnan; Joshi, Amit; Akhtar, Nahid; Kaushik, Vikas

doi:10.1016/j.micpath.2020.104728

Cited by 43 publications

(28 citation statements)

References 54 publications

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“…Reverse vaccinology, an unconventional approach to the development of new vaccines that combines immunogenicity, immunogenicity, and bioinformatics, has attracted the attention of many researchers around the world 27 . This approach has been widely used to develop multi-epitope vaccines against a variety of organisms, including Helicobacter pylori 28 , Leishmania donovani 29 , Klebsiella pneumoniae 30 , hepatitis C virus 31 , Fasciola gigantica 32 , Tropheryma whipplei 33 , Elizabethkingia anopheles 34 , Candida auris 35 , dengue virus 36 , Zika virus 37 , and SARS-COV-2 38 – 40 . In recent years, several studies have been published focusing on the design of multi-epitope vaccines for HPV.…”

Section: Discussionmentioning

confidence: 99%

Design of a multi-epitope vaccine against cervical cancer using immunoinformatics approaches

Sanami

Azadegan‐Dehkordi

Rafieian-Kopaei

et al. 2021

Sci Rep

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Cervical cancer, caused by human papillomavirus (HPV), is the fourth most common type of cancer among women worldwide. While HPV prophylactic vaccines are available, they have no therapeutic effects and do not clear up existing infections. This study aims to design a therapeutic vaccine against cervical cancer using reverse vaccinology. In this study, the E6 and E7 oncoproteins from HPV16 were chosen as the target antigens for epitope prediction. Cytotoxic T lymphocytes (CTL) and helper T lymphocytes (HTL) epitopes were predicted, and the best epitopes were selected based on antigenicity, allergenicity, and toxicity. The final vaccine construct was composed of the selected epitopes, along with the appropriate adjuvant and linkers. The multi-epitope vaccine was evaluated in terms of physicochemical properties, antigenicity, and allergenicity. The tertiary structure of the vaccine construct was predicted. Furthermore, several analyses were also carried out, including molecular docking, molecular dynamics (MD) simulation, and in silico cloning of the vaccine construct. The results showed that the final proposed vaccine could be considered an effective therapeutic vaccine for HPV; however, in vitro and in vivo experiments are required to validate the efficacy of this vaccine candidate.

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Section: Discussionmentioning

confidence: 99%

Design of a multi-epitope vaccine against cervical cancer using immunoinformatics approaches

Sanami

Azadegan‐Dehkordi

Rafieian-Kopaei

et al. 2021

Sci Rep

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“…After the selection of the epitopes, they were linked by GGS linkers to adjuvants such as RS09 (APPHALS) and N and C terminal sequence of Salmonella dublin flagellin protein along with PADRE sequence to design the final vaccine construct. These linker and adjuvants have been previously used in multivalent epitopebased vaccine design of herpes simplex virus and human papillomavirus, Candida auris, human cytomegalovirus, and dengue virus [16,17,22,23,26,50]. PADRE (AKF-VAAWTLKAAA) sequence was added to enhance the stability and potency of the vaccine construct [50,51].…”

Section: Discussionmentioning

confidence: 99%

“…As, these proteins are highly conserved, are involved in viral pathogenesis, and can help to generate immune response, they can be a good target for identifying epitopes that could be used to design a vaccine construct which can help protect the dog population from potentially lethal canine circovirus infections [13][14][15]. Such in silico studies have been previously performed to design vaccine construct against dengue, Candida auris, human cytomegalovirus, SARS-CoV-2, Lassa virus, human papillomavirus, cervical cancer, and hepatitis C virus [16][17][18][19][20][21][22][23][24][25][26]. In our study, various immunoinformatic tools were used to design a potential vaccine construct against canine circovirus.…”

Section: Introductionmentioning

confidence: 99%

An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus

Jain

Joshi

Akhtar

et al. 2021

Journal of Genetic Engineering and Biotechnology

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Background Canine circovirus is a deadly pathogen of dogs and causes vasculitis and hemorrhagic enteritis. It causes lethal gastroenteritis in pigs, fox, and dogs. Canine circovirus genome contains two main (and opposite) transcription units which encode two open reading frames (ORFs), a replicase-associated protein (Rep) and the capsid (Cap) protein. The replicase protein and capsid protein consist of 303 amino acids and 270 amino acids respectively. Several immuno-informatics methods such as epitope screening, molecular docking, and molecular-dynamics simulations were used to craft peptide-based vaccine construct against canine circovirus. Results The vaccine construct was designed by joining the selected epitopes with adjuvants by suitable linker. The cloning and expression of the vaccine construct was also performed using in silico methods. Screening of epitopes was conducted by NetMHC server that uses ANN (Artificial neural networking) algorithm. These methods are fast and cost-effective for screening epitopes that can interact with dog leukocyte antigens (DLA) and initiate an immune response. Overall, 5 epitopes, YQHLPPFRF, YIRAKWINW, ALYRRLTLI, HLQGFVNLK, and GTMNFVARR, were selected and used to design a vaccine construct. The molecular docking and molecular dynamics simulation studies show that these epitopes can bind with DLA molecules with stability. The codon adaptation and in silico cloning studies show that the vaccine can be expressed by Escherichia coli K12 strain. Conclusion The results suggest that the vaccine construct can be useful in preventing the dogs from canine circovirus infections. However, the results need further validation by performing other in vitro and in vivo experiments.

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“…Such advancements of computer sciences in interdisciplinary fields make research more efficient, in a similar way our study is also very unique and shows in-depth application of computational biology in accessing pathogenic proteomic information and assisted us in designing peptide based vaccine against them. Latest in-silico vaccine developments assisted scientific community in identifying epitope-based vaccines against various human pathogens including SARS-CoV2 (Joshi et al 2020 ; Akhtar et al 2020 ), Tropheryma whipplei bacteria (Joshi et al 2020 ), Dengue virus (Krishnan et al 2020a , b ; Krishnan et al 2021 ), and Candida aurius fungus (Akhtar et al 2020 ). Such latest studies provide motivational support and opens doors to conduct research on other animal groups including fish species and its pathogens.…”

Section: Introductionmentioning

confidence: 99%

In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species

Joshi

Pathak

Mannan

et al. 2021

Netw Model Anal Health Inform Bioinforma

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Neural necrosis virus (NNV) of family Nodaviridae affect wide range of fish species with viral encephalopathy and retinopathy causing mass mortality up to 100%. Currently there is no effective treatment and depopulation is only suggested recommendation. New avenues and approach are required to control this harmful malady. In this study we developed an epitope-based vaccine (EBV), against NNV using computation approach. We have selected two conserved proteins RNA-dependent RNA polymerase (RdRP) and capsid proteins. Based on more than ~ 1000 epitopes we selected six antigenic epitopes. These were conjugated to adjuvant and linker peptides to generate a full-length vaccine candidate. Biochemical structural properties were analyzed by Phyre2 server. ProtParam, Molprobity. Ramachandran plot results indicate that 98.7% residues are in a favorable region and 93.4% residues in the favored region. The engineered EBV binds to toll like receptor-5 (TLR5) an important elicitor of immune response. Further molecular docking by PatchDock server reveals the atomic contact energy (i.e. − 267.08) for the best docked model of EBV and TLR5 receptor. The molecular simulation results suggest a stable interaction; the RMSD and RMSF values are 1–4 Ǻ and 1–12Ǻ, respectively. Further we have suggested the best possible codon optimized sequence for its cloning and subsequent purification of the protein. Overall, this is a first report to suggest an in-silico method for generation of an EBV candidate against NNV. We surmise that the method and approach suggested could be used as a promising cure for NNVs.

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Immunoinformatics designed T cell multi epitope dengue peptide vaccine derived from non structural proteome

Cited by 43 publications

References 54 publications

Design of a multi-epitope vaccine against cervical cancer using immunoinformatics approaches

Design of a multi-epitope vaccine against cervical cancer using immunoinformatics approaches

An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus

In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species

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