“…5 b) to allow for some degree of flexibility in the binding pocket of the receptor, which is essential for its function and to correct for vaccine matching but is not present in the crude docking procedure Sousa et al, 2006 , de Medeiros et al, 2016 , Harmalkar and Gray, 2021 . The efficacy of this procedure has already been validated in the development of improved schizophrenia drugs Zanatta et al (2014) and multiepitope peptide vaccines against Mayaro virus Silva et al, 2021 , daSilva et al, 2022 . Fig.…”
Section: Resultsmentioning
confidence: 99%
“…1 . Recently, our research group validated similar immunoinformatics and molecular modeling approaches in the construction of a multiepitope vaccine against Mayaro virus Silva et al, 2021 , daSilva et al, 2022 . Fig.…”
“…5 b) to allow for some degree of flexibility in the binding pocket of the receptor, which is essential for its function and to correct for vaccine matching but is not present in the crude docking procedure Sousa et al, 2006 , de Medeiros et al, 2016 , Harmalkar and Gray, 2021 . The efficacy of this procedure has already been validated in the development of improved schizophrenia drugs Zanatta et al (2014) and multiepitope peptide vaccines against Mayaro virus Silva et al, 2021 , daSilva et al, 2022 . Fig.…”
Section: Resultsmentioning
confidence: 99%
“…1 . Recently, our research group validated similar immunoinformatics and molecular modeling approaches in the construction of a multiepitope vaccine against Mayaro virus Silva et al, 2021 , daSilva et al, 2022 . Fig.…”
“…This approach combines quantum mechanics for the ligand-receptor interactions with molecular mechanics for the surrounding environment, allowing for a more accurate representation of the system's behavior. QM/MM methods have solidified their position as advanced computational tools for studying biomolecular systems, as evidenced by the increasing number of publications utilizing these methods 20 , 26 , 53 , 54 . this procedure consists of taking an input sequence in FASTA format and implementing three techniques: single and multiple template threading, along with prediction of alignment quality 7 .…”
Section: Methodsmentioning
confidence: 99%
“…Furthermore, in silico gene cloning was conducted using the pET-28a( +) vector. This is a consolidated approach that has been used in several studies with pathogenic microorganisms such as SARS-CoV-2 20 , Streptococcus pneumoniae 21 , and Alkhurma hemorrhagic fever virus 22 as well as with other arboviruses such as dengue 23 , chikungunya 24 , and Mayaro virus 25 , 26 .…”
Yellow fever outbreaks are prevalent, particularly in endemic regions. Given the lack of an established treatment for this disease, significant attention has been directed toward managing this arbovirus. In response, we developed a multiepitope vaccine designed to elicit an immune response, utilizing advanced immunoinformatic and molecular modeling techniques. To achieve this, we predicted B- and T-cell epitopes using the sequences from all structural (E, prM, and C) and nonstructural proteins of 196 YFV strains. Through comprehensive analysis, we identified 10 cytotoxic T-lymphocyte (CTL) and 5T-helper (Th) epitopes that exhibited overlap with B-lymphocyte epitopes. These epitopes were further evaluated for their affinity to a wide range of human leukocyte antigen system alleles and were rigorously tested for antigenicity, immunogenicity, allergenicity, toxicity, and conservation. These epitopes were linked to an adjuvant ($$\beta$$
β
-defensin) and to each other using ligands, resulting in a vaccine sequence with appropriate physicochemical properties. The 3D structure of this sequence was created, improved, and quality checked; then it was anchored to the Toll-like receptor. Molecular Dynamics and Quantum Mechanics/Molecular Mechanics simulations were employed to enhance the accuracy of docking calculations, with the QM portion of the simulations carried out utilizing the density functional theory formalism. Moreover, the inoculation model was able to provide an optimal codon sequence that was inserted into the pET-28a( +) vector for in silico cloning and could even stimulate highly relevant humoral and cellular immunological responses. Overall, these results suggest that the designed multi-epitope vaccine can serve as prophylaxis against the yellow fever virus.
“… 20 on the comparative efficacy of chimeric porcine circovirus vaccines illuminates potential avenues for mitigating the impact of circoviruses. Furthermore, the vaccine development models for virus-induced diseases provide critical insights for creating effective strategies against circoviruses 9 – 12 .…”
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