List of links used in this study.
<div><p>Significant progress has been made in <i>HIV-1</i> research; however, researchers have not yet achieved the objective of eradicating <i>HIV-1</i> infection. Accordingly, in this study, eucaryotic and procaryotic in silico vaccines were developed for <i&...
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2024
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| _version_ | 1852026315004182528 |
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| author | Ava Hashempour (11753878) |
| author2 | Nastaran Khodadad (17535416) Peyman Bemani (10651254) Younes Ghasemi (3125685) Shokufeh Akbarinia (17535419) Reza Bordbari (19751532) Amir Hossein Tabatabaei (19751535) Shahab Falahi (18301765) |
| author2_role | author author author author author author author |
| author_facet | Ava Hashempour (11753878) Nastaran Khodadad (17535416) Peyman Bemani (10651254) Younes Ghasemi (3125685) Shokufeh Akbarinia (17535419) Reza Bordbari (19751532) Amir Hossein Tabatabaei (19751535) Shahab Falahi (18301765) |
| author_role | author |
| dc.creator.none.fl_str_mv | Ava Hashempour (11753878) Nastaran Khodadad (17535416) Peyman Bemani (10651254) Younes Ghasemi (3125685) Shokufeh Akbarinia (17535419) Reza Bordbari (19751532) Amir Hossein Tabatabaei (19751535) Shahab Falahi (18301765) |
| dc.date.none.fl_str_mv | 2024-09-27T17:36:27Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pone.0306559.t001 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/List_of_links_used_in_this_study_/27121440 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Medicine Microbiology Molecular Biology Biotechnology Immunology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified molecular dynamic stimulation immunological simulation showed div >< p codon optimization ensured simulate immune responses strong binding affinities human vaccine model 1 gag </ strong binding gag </ 1 </ consistent responses human cells e </ coli </ γ induction yet achieved world ’ vaccine models vaccine formulated successful translation significant progress reverse vaccinology experimental verification epitopes located designed constructs conserved domains challenges faced bcl epitopes approximately 93 100 major |
| dc.title.none.fl_str_mv | List of links used in this study. |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <div><p>Significant progress has been made in <i>HIV-1</i> research; however, researchers have not yet achieved the objective of eradicating <i>HIV-1</i> infection. Accordingly, in this study, eucaryotic and procaryotic in silico vaccines were developed for <i>HIV-Gag</i> polyproteins from 100 major <i>HIV</i> subtypes and CRFs using immunoinformatic techniques to simulate immune responses in mice and humans. The epitopes located in the conserved domains of the <i>Gag</i> polyprotein were evaluated for allergenicity, antigenicity, immunogenicity, toxicity, homology, topology, and IFN-γ induction. Adjuvants, linkers, CTLs, HTLs, and BCL epitopes were incorporated into the vaccine models. Strong binding affinities were detected between HLA/MHC alleles, TLR-2, TLR-3, TLR-4, TLR-7, and TLR-9, and vaccine models. Immunological simulation showed that innate and adaptive immune cells elicited active and consistent responses. The human vaccine model was matched with approximately 93.91% of the human population. The strong binding of the vaccine to MHC/HLA and TLR molecules was confirmed through molecular dynamic stimulation. Codon optimization ensured the successful translation of the designed constructs into human cells and <i>E</i>. <i>coli</i> hosts. We believe that the <i>HIV-1 Gag</i> vaccine formulated in our research can reduce the challenges faced in developing an <i>HIV-1</i> vaccine. Nevertheless, experimental verification is necessary to confirm the effectiveness of these vaccines in these models.</p></div> |
| eu_rights_str_mv | openAccess |
| id | Manara_b2078b3eee7558df7e1760bd2362df0d |
| identifier_str_mv | 10.1371/journal.pone.0306559.t001 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/27121440 |
| publishDate | 2024 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | List of links used in this study.Ava Hashempour (11753878)Nastaran Khodadad (17535416)Peyman Bemani (10651254)Younes Ghasemi (3125685)Shokufeh Akbarinia (17535419)Reza Bordbari (19751532)Amir Hossein Tabatabaei (19751535)Shahab Falahi (18301765)MedicineMicrobiologyMolecular BiologyBiotechnologyImmunologyCancerInfectious DiseasesVirologyBiological Sciences not elsewhere classifiedmolecular dynamic stimulationimmunological simulation showeddiv >< pcodon optimization ensuredsimulate immune responsesstrong binding affinitieshuman vaccine model1 gag </strong bindinggag </1 </consistent responseshuman cellse </coli </γ inductionyet achievedworld ’vaccine modelsvaccine formulatedsuccessful translationsignificant progressreverse vaccinologyexperimental verificationepitopes locateddesigned constructsconserved domainschallenges facedbcl epitopesapproximately 93100 major<div><p>Significant progress has been made in <i>HIV-1</i> research; however, researchers have not yet achieved the objective of eradicating <i>HIV-1</i> infection. Accordingly, in this study, eucaryotic and procaryotic in silico vaccines were developed for <i>HIV-Gag</i> polyproteins from 100 major <i>HIV</i> subtypes and CRFs using immunoinformatic techniques to simulate immune responses in mice and humans. The epitopes located in the conserved domains of the <i>Gag</i> polyprotein were evaluated for allergenicity, antigenicity, immunogenicity, toxicity, homology, topology, and IFN-γ induction. Adjuvants, linkers, CTLs, HTLs, and BCL epitopes were incorporated into the vaccine models. Strong binding affinities were detected between HLA/MHC alleles, TLR-2, TLR-3, TLR-4, TLR-7, and TLR-9, and vaccine models. Immunological simulation showed that innate and adaptive immune cells elicited active and consistent responses. The human vaccine model was matched with approximately 93.91% of the human population. The strong binding of the vaccine to MHC/HLA and TLR molecules was confirmed through molecular dynamic stimulation. Codon optimization ensured the successful translation of the designed constructs into human cells and <i>E</i>. <i>coli</i> hosts. We believe that the <i>HIV-1 Gag</i> vaccine formulated in our research can reduce the challenges faced in developing an <i>HIV-1</i> vaccine. Nevertheless, experimental verification is necessary to confirm the effectiveness of these vaccines in these models.</p></div>2024-09-27T17:36:27ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.1371/journal.pone.0306559.t001https://figshare.com/articles/dataset/List_of_links_used_in_this_study_/27121440CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/271214402024-09-27T17:36:27Z |
| spellingShingle | List of links used in this study. Ava Hashempour (11753878) Medicine Microbiology Molecular Biology Biotechnology Immunology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified molecular dynamic stimulation immunological simulation showed div >< p codon optimization ensured simulate immune responses strong binding affinities human vaccine model 1 gag </ strong binding gag </ 1 </ consistent responses human cells e </ coli </ γ induction yet achieved world ’ vaccine models vaccine formulated successful translation significant progress reverse vaccinology experimental verification epitopes located designed constructs conserved domains challenges faced bcl epitopes approximately 93 100 major |
| status_str | publishedVersion |
| title | List of links used in this study. |
| title_full | List of links used in this study. |
| title_fullStr | List of links used in this study. |
| title_full_unstemmed | List of links used in this study. |
| title_short | List of links used in this study. |
| title_sort | List of links used in this study. |
| topic | Medicine Microbiology Molecular Biology Biotechnology Immunology Cancer Infectious Diseases Virology Biological Sciences not elsewhere classified molecular dynamic stimulation immunological simulation showed div >< p codon optimization ensured simulate immune responses strong binding affinities human vaccine model 1 gag </ strong binding gag </ 1 </ consistent responses human cells e </ coli </ γ induction yet achieved world ’ vaccine models vaccine formulated successful translation significant progress reverse vaccinology experimental verification epitopes located designed constructs conserved domains challenges faced bcl epitopes approximately 93 100 major |