In silico designing of a novel polyvalent multi-subunit peptide vaccine leveraging cross-immunity against human visceral and cutaneous leishmaniasis: an immunoinformatics-based approach

Bhattacharjee, Mainak; Banerjee, Monojit; Mukherjee, Arun

doi:10.1007/s00894-023-05503-w

Cited by 10 publications

(4 citation statements)

References 78 publications

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“…The approach was developed with auto cross-covariance (ACC), which indicated epitopes screened out as non-allergens with no allergenicity. According to FAO/WHO, any peptide comprising at least six contiguous amino acids can be considered allergic [ 30 ]. Because our selected epitopes were unable to meet the standards set for FAO/WHO evaluation method of allergenicity prediction, they were categorized as non-allergens by AllerTop v.2.0.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

Arshad,

Rehana,

Saleem

et al. 2024

Heliyon

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Section: Discussionmentioning

confidence: 99%

“…The Vaxigen 2.0 tool was used to estimate the antigenicity of the vaccine construct [ 30 ], while the AllerTOP web server was used to identify the allergenicity of the multi-epitope vaccine construct [ 31 ]. Moreover, ToxinPred ( http://crdd.osdd.net/raghava/toxinpred/ ) was used for toxicity analysis [ 32 ].…”

Section: Methodsmentioning

confidence: 99%

Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

Arshad,

Rehana,

Saleem

et al. 2024

Heliyon

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“…Red, white, and blue colors exhibit correlated, uncorrelated, and anticorrelated motions, respectively based on the covariance matrix analysis (Figure 13c). Additionally, rigidity and flexibility of springs between (Cα) atoms of docked protein molecule have been indicated as the darker and brighter colors (Figure 13d) [35]. For clarifying conformational change of CNT-1MWT complex, a snapshot at 0ns, 11ns, 22 ns, 33 ns, and 44 ns are illustrated in Figure 14a [36].…”

Section: The Normal Mode Analysismentioning

confidence: 98%

Interaction of carbon nanotube, capped carbon nanotube, C60 fullerene, and C70 fullerene with virulence factors of Gram-negative and Gram-positive bacteria: The potential application for 3D-printed scaffolds

Alavi¹,

Ashengroph²,

Mozafari³

2023

Preprint

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Antimicrobial application of carbon nanomaterials such as carbon nanotubes (CNTs), capped CNT, C60 fullerene, and C70 fullerene are increasing owing to their low cytotoxicity properties compared to other nanomaterials such as metallic nanoparticles. Enhanced mechanical property and antibacterial activity can be caused by incorporation of CNTs in 3-dimentional (3D) printed nanocomposites (NCs). Interruption of bacterial membrane resulting from cylindrical shape and high aspect ratio properties has been found as the prominent antibacterial mechanism of CNTs. However, unraveling interaction of CNT, capped CNT, C60 fullerene, and C70 fullerene with virulence factors of the main bacterial pathogenesis has not yet been known. Therefore, in the present study, interactions of CNT, capped CNT, C60, and C70 with the eight virulence factors including protein kinase A and ESX-secreted protein B of Mycobacterium tuberculosis, pseudomonas elastase and exotoxin A of Pseudomonas aeruginosa, alpha-hemolysin and penicillin binding protein 2a of Staphylococcus aureus and shiga toxin 2a and heat-labile enterotoxin of Escherichia coli have been evaluated by molecular docking method of AutoDock Vina. This study disclosed the binding strength followed the sequence CNT &gt; capped CNT &gt; C70 &gt; C60 towards alpha-hemolysin of S. aureus compared to other virulence factors with values of -19.6, -18.8, -13.6, and -12.8 kcal/mol, respectively. The lowest and highest binding affinity were found for CNT against 1TII and 1MWT by binding energy values of 97.4 and -20.1 kcal/mol. The stability of CNT-1MWT complex at the different times has resulted according to the normal mode analysis of elNémo and iMOD servers. Future studies should be focused on improving cellular uptake of CNTs, capped CNTs, C70, and C60 by surface functionalization for active targeting of bacteria.

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“…Red, white, and blue colors exhibit correlated, uncorrelated, and anti-correlated motions, respectively, based on the covariance matrix analysis (Figure 3c). Additionally, the rigidity and flexibility of springs between (Cα) atoms of docked protein molecules are indicated with darker and brighter colors (Figure 3d) [42]. To clarify the conformational change of the CNT 2-5 -7AHL complex, snapshots at frame 1, frame 5, and frame 11 are illustrated in Figure 4 [43].…”

Section: The Normal Mode Analysismentioning

confidence: 99%

Interaction of Carbon Nanotubes, Capped Carbon Nanotubes, CNT2–5, C60, C70, HO-C60, [C60]2, and [C60]3 Fullerenes with Virulence Factors of Gram-Negative and Gram-Positive Bacteria: Potential Applications for 3D-Printed Scaffolds

Alavi,

Ashengroph,

Mozafari

2024

Inorganics

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The antimicrobial application of carbon nanomaterials, such as carbon nanotubes (CNTs), capped CNTs, CNT2–5, C60, C70, HO-C60, [C60]2, and [C60]3 fullerenes, is increasing, owing to their low cytotoxicity properties compared to other nanomaterials such as metallic nanoparticles. Enhanced mechanical properties and antibacterial activity can be caused by the incorporation of CNTs in 3-dimensional (3D) printed nanocomposites (NCs). The interruption of the bacterial membrane resulting from the cylindrical shape and high aspect ratio properties has been found to be the most prominent antibacterial mechanism of CNTs. However, the unraveling interaction of CNTs, capped CNTs, CNT2–5, C60, C70, HO-C60, [C60]2, and [C60]3 fullerenes with virulence factors of the main bacterial pathogenesis has not yet been understood. Therefore, in the present study, interactions of these carbon-based nanomaterials with the eight virulence factors, including protein kinase A and (ESX)-secreted protein B of Mycobacterium tuberculosis, pseudomonas elastase and exotoxin A of Pseudomonas aeruginosa, alpha-hemolysin and penicillin-binding protein 2a of Staphylococcus aureus, and shiga toxin 2a and heat-labile enterotoxin of Escherichia coli, were evaluated with the molecular docking method of AutoDock Vina. This study disclosed that the binding affinity was highest for CNT2–5 and [C60]3 toward alpha-hemolysin, with binding energies of −32.7 and −26.6 kcal/mol, respectively. The stability of the CNT2–5–alpha-hemolysin complex at different times was obtained according to the normal mode analysis of ElNémo and iMOD servers.

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In silico designing of a novel polyvalent multi-subunit peptide vaccine leveraging cross-immunity against human visceral and cutaneous leishmaniasis: an immunoinformatics-based approach

Cited by 10 publications

References 78 publications

Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach

Interaction of carbon nanotube, capped carbon nanotube, C60 fullerene, and C70 fullerene with virulence factors of Gram-negative and Gram-positive bacteria: The potential application for 3D-printed scaffolds

Interaction of Carbon Nanotubes, Capped Carbon Nanotubes, CNT2–5, C60, C70, HO-C60, [C60]2, and [C60]3 Fullerenes with Virulence Factors of Gram-Negative and Gram-Positive Bacteria: Potential Applications for 3D-Printed Scaffolds

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