Immunoinformatics Study of gp120 of Human Immunodeficiency Virus Type 1 Subtype CRF35_AD Isolated from Iranian Patients

Keyvani, Hossein; Ahmadi, Nayeb Ali; Ranjbar, Malek Mohammad; Kachooei, Saeid Ataei; Ghorban, Khodayar; Dadmanesh, Maryam

doi:10.5812/archcid.36270

Cited by 7 publications

(3 citation statements)

References 36 publications

(32 reference statements)

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“…Predicting epitopes is highly important for the determination of an antigen's immunogenicity in vaccine development. So, bioinformatics tools and online resources can enable researchers to predict and recognize the potential epitopes of B-and T-cells [23][24][25][26]. Bioinformatics has recently become the preferred interdisciplinary new science for analyzing biological data using defined computer science, mathematics, statistics, physics, biology, medicine technologies and algorithms [23,26].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target

et al. 2021

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Objectives Toxoplasma gondii (T. gondii), an obligate intracellular apicomplexan parasite, could affect numerous warm-blooded animals, such as humans. Calcium-dependent protein kinases (CDPKs) are essential Ca2+ signaling mediators and participate in parasite host cell egress, outer membrane motility, invasion, and cell division. Results Several bioinformatics online servers were employed to analyze and predict the important properties of CDPK4 protein. The findings revealed that CDPK4 peptide has 1158 amino acid residues with average molecular weight (MW) of 126.331 KDa. The aliphatic index and GRAVY for this protein were estimated at 66.82 and – 0.650, respectively. The findings revealed that the CDPK4 protein comprised 30.14% and 34.97% alpha-helix, 59.84% and 53.54% random coils, and 10.02% and 11.49% extended strand with SOPMA and GOR4 tools, respectively. Ramachandran plot output showed 87.87%, 8.40%, and 3.73% of amino acid residues in the favored, allowed, and outlier regions, respectively. Also, several potential B and T-cell epitopes were predicted for CDPK4 protein through different bioinformatics tools. Also, antigenicity and allergenicity evaluation demonstrated that this protein has immunogenic and non-allergenic nature. This paper presents a basis for further studies, thereby provides a fundamental basis for the development of an effective vaccine against T. gondii infection.

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Section: Introductionmentioning

confidence: 99%

Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target

et al. 2021

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“…The implementation of proteomic technologies is helpful for studying biology, host-pathogen interaction, drug resistance, virulence and therapeutic targets in leishmania parasites [3,4]. Regarding the role of proteins in cellular systems in interactive state, as well as the significance of physical interactions between proteins in most biological processes, computational approaches such as analyzing protein-protein interaction (PPI) networks have been proposed to identify or predict the essential genes and novel drug targets in silico, which can help economize the time and cost [5][6][7][8]. Protein interaction networks present gene products, which physically interact with each other in cellular systems.…”

Section: Introductionmentioning

confidence: 99%

Prediction of Leishmania Major Key Proteins via Topological Analysis of Protein-Protein Interaction Network

Dashatan¹,

Tavirani²,

Zali³

et al. 2018

GMJ

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Background: Although leishmaniasis is regarded as a public health problem, no effective vaccine or decisive treatment has been introduced for this disease. Therefore, representing novel therapeutic proteins is essential. Protein-protein Interaction network analysis is a suitable tool to discover novel drug targets for leishmania major. To this aim, gene and protein expression data is used for instructing protein network and the key proteins are highlighted.Materials and Methods: In this computational and bioinformatics study, the protein/gene expression data related to leishmania major were studied, and 252 candidate proteins were extracted. Then, the protein networks of these proteins were explored and visualized by using String database and Cytoscape software. Finally, clustering and gene ontology were performed by MCODE and PANTHER databases, respectively.Results: Based on gene ontology analysis, most of the leishmania major proteins were located in cell compartments and membrane. Catalytic activity and binding were regarded as the relevant molecular functions and metabolic and cellular processes were the significant biological process. In this network analysis, UB-EP52, EF-2, chaperonin, Hsp70.4, Hsp60, tubulin alpha and beta chain, and ENOL and LACK were introduced as hub-bottleneck proteins. Based on clustering analysis, Lmjf.32.3270, ENOL and Lmjf.13.0290 were determined as seed proteins in each cluster.Conclusion: The results indicated that hub proteins play a significant role in pathogenesis and life cycle of leishmania major. Further studies of hubs will provide a better understanding of leishmaniasis mechanisms. Finally, these key hub proteins could be a suitable and helpful potential for drug targets and treating leishmaniasis by considering their validation. [GMJ.2018;7:e1129]

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Section: Introductionmentioning

confidence: 99%

Prediction of Leishmania Major Key Proteins via Topological Analysis of Protein-Protein Interaction Network

Amiri Dashatan,

Rezaie Tavirani,

Zali

et al. 2018

GMJ

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Background: Although leishmaniasis is regarded as a public health problem, no effective vaccine or decisive treatment has been introduced for this disease. Therefore, representing novel therapeutic proteins is essential. Protein-protein Interaction network analysis is a suitable tool to discover novel drug targets for leishmania major. To this aim, gene and protein expression data is used for instructing protein network and the key proteins are highlighted. Materials and Methods: In this computational and bioinformatics study, the protein/gene expression data related to leishmania major were studied, and 252 candidate proteins were extracted. Then, the protein networks of these proteins were explored and visualized by using String database and Cytoscape software. Finally, clustering and gene ontology were performed by MCODE and PANTHER databases, respectively. Results:Â Based on gene ontology analysis, most of the leishmania major proteins were located in cell compartments and membrane. Catalytic activity and binding were regarded as the relevant molecular functions and metabolic and cellular processes were the significant biological process. In this network analysis, UB-EP52, EF-2, chaperonin, Hsp70.4, Hsp60, tubulin alpha and beta chain, and ENOL and LACK were introduced as hub-bottleneck proteins. Based on clustering analysis, Lmjf.32.3270, ENOL and Lmjf.13.0290 were determined as seed proteins in each cluster. Conclusion: The results indicated that hub proteins play a significant role in pathogenesis and life cycle of leishmania major. Further studies of hubs will provide a better understanding of leishmaniasis mechanisms. Finally, these key hub proteins could be a suitable and helpful potential for drug targets and treating leishmaniasis by considering their validation. [GMJ.2018;7:e1129]

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Immunoinformatics Study of gp120 of Human Immunodeficiency Virus Type 1 Subtype CRF35_AD Isolated from Iranian Patients

Cited by 7 publications

References 36 publications

Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target

Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target

Prediction of Leishmania Major Key Proteins via Topological Analysis of Protein-Protein Interaction Network

Prediction of Leishmania Major Key Proteins via Topological Analysis of Protein-Protein Interaction Network

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