Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach

Kharisma, Viol Dhea; Ansori, Arif Nur Muhammad; Posa, Gabrielle Ann Villar; Rizky, Wahyu Choirur; Permana, Sofy; Parikesit, Arli Aditya

doi:10.29238/teknolabjournal.v10i1.274

Cited by 9 publications

(8 citation statements)

References 27 publications

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“…Correspondingly, several publications on the multiepitope vaccine-based computational design that represents potential docking with TLR receptors could induce antibody production after in vivo immunization 54 , 55 . Moreover, the RMSF profiles of the CMEV-TLR4 complexes with an average score of ≤ 4 Å might define their complex stability resulting in stimulating receptor response by fluctuating residues 11 , 14 – 56 .…”

Section: Discussionmentioning

confidence: 99%

Computational design of novel chimeric multiepitope vaccine against bacterial and viral disease in tilapia (Oreochromis sp.)

Pumchan,

Proespraiwong,

Sawatdichaikul

et al. 2024

Sci Rep

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Regarding several infectious diseases in fish, multiple vaccinations are not favorable. The chimeric multiepitope vaccine (CMEV) harboring several antigens for multi-disease prevention would enhance vaccine efficiency in terms of multiple disease prevention. Herein, the immunogens of tilapia’s seven pathogens including E. tarda, F. columnare, F. noatunensis, S. iniae, S. agalactiae, A. hydrophila, and TiLV were used for CMEV design. After shuffling and annotating the B-cell epitopes, 5,040 CMEV primary protein structures were obtained. Secondary and tertiary protein structures were predicted by AlphaFold2 creating 25,200 CMEV. Proper amino acid alignment in the secondary structures was achieved by the Ramachandran plot. In silico determination of physiochemical and other properties including allergenicity, antigenicity, glycosylation, and conformational B-cell epitopes were determined. The selected CMEV (OSLM0467, OSLM2629, and OSLM4294) showed a predicted molecular weight (MW) of 70 kDa, with feasible sites of N- and O-glycosylation, and a number of potentially conformational B-cell epitope residues. Molecular docking, codon optimization, and in-silico cloning were tested to evaluate the possibility of protein expression. Those CMEVs will further elucidate in vitro and in vivo to evaluate the efficacy and specific immune response. This research will highlight the new era of vaccines designed based on in silico structural vaccine design.

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Section: Discussionmentioning

confidence: 99%

Computational design of novel chimeric multiepitope vaccine against bacterial and viral disease in tilapia (Oreochromis sp.)

Pumchan,

Proespraiwong,

Sawatdichaikul

et al. 2024

Sci Rep

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“…PubChem (https://pubchem.ncbi.nlm.nih.gov/) is used to retrieve data on ligands such as CID, molecular weight (g/mol), formula, and 3D structure with structure data format (sdf) files. Minimization of ligands and conversion to protein databank (pdb) format were done through OpenBabel software to increase ligand flexibility 21,22 .…”

Section: Methods Compound Retrievalmentioning

confidence: 99%

Triple Inhibitor Mechanism of Antiretroviral from Sambucus nigra Phytochemical through Screening Docking

et al. 2023

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Human immunodeficiency virus type 1 (HIV-1) has a higher infectious nature than HIV-2 because of the genetic drift mechanism. Several HIV-1 strains such as A, B, C, D, E, F, G, H, & J were obtained from Africa, Asia, Europe, Australia, and America. Endemic cases of HIV-1 are often found and HIV-2 is very rare, therefore the development of antiretroviral drugs is currently focused on treating HIV-1 infection5. Research on HIV-1 vaccines is still in the research phase and some patients are only taking antiretrovirals to survive. Sambucus nigra L. is used by the community for traditional medicine such as influenza A, B, C and SARS-CoV-2 infectious diseases. There are no research reports related to the potential of Sambucus nigra L. as an antiretroviral in the treatment of HIV-1 infection and the specific molecular mechanisms that explain it, therefore this research is important for the discovery of alternative antiretroviral drugs from natural materials. The in silico method used in this study consists of Sambucus nigra L. compounds retrieval, HIV-1 protein preparation, molecular docking, and 3D visualization. Sambucus nigra L. can have inhibitory activity on three enzymes of HIV-1 such as protease (PR), reverse transcriptase (RT), integrase (INT) through naringenin and Cyanidin-3,5-diglucoside compounds. Both compounds have more negative binding energy, form stable binding interactions in the target domain, and trigger inhibitory activity.

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“…The results of the recommended analysis are the results of the analysis with a low similarity value to the human body cell protein, especially at the cell surface receptor itself 31 . This is done to avoid any autoimmune response from the patient's body that will receive the vaccine 32 . In the results of BLAST need to be considered for the score above 70%, because there must be sequences have similarities to human surfaces receptor, especially those on the cell surface 33 .…”

Section: Similarity Analysismentioning

confidence: 99%

B-cell Epitope Mapping of Capsid L1 from Human Papillomavirus to Development Cervical Cancer Vaccine Through In Silico Study

Rasyadan Taufiq Probojati,

Utami,

Turista

et al. 2022

SAISNTEK

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Human papillomavirus (HPV) is a virus that plays an important role in the occurrence of cervical cancer. The HPV gene is composed of two parts: early and late gene. The L1 protein has a conserved region composed of cysteine and lysine residues, both of which have involved in the binding process between virions and host receptors. Previous research has shown that vaccines can be developed based on epitopes that have conserved areas. This study is important to identify conserved protein sequences in L1 of HPV capsid, predict epitope mapping of B cells and antigenicity in the conserved region of L1 HPV capsid, as well as the similarity of amino acid residues of epitope composers with surface receptors of human body cells. The conserved areas were identified in L1 HPV as a potential epitope of B cells based on epitope mapping analysis of positions 23-46 and 97-119 with EGRGQPLGGSGHPNDDE DRDKQ and RHNGGPGPSGSSQFNKPYWAQGN peptides and each had a peptide length of 22-mer and 23-mer. The 97-119 epitope has a high antigenicity score and the similarity of the low amino acid residue sequence to the cell surface receptor of the human body, the 23-mer RHNGGPGPSGSSQFNKPYWAQGN peptide can be used as a reference for the development of cervical cancer prevention vaccine.

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Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach

Cited by 9 publications

References 27 publications

Computational design of novel chimeric multiepitope vaccine against bacterial and viral disease in tilapia (Oreochromis sp.)

Computational design of novel chimeric multiepitope vaccine against bacterial and viral disease in tilapia (Oreochromis sp.)

Triple Inhibitor Mechanism of Antiretroviral from Sambucus nigra Phytochemical through Screening Docking

B-cell Epitope Mapping of Capsid L1 from Human Papillomavirus to Development Cervical Cancer Vaccine Through In Silico Study

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