Multi-epitope based vaccine design against Sarcoptes scabiei paramyosin using immunoinformatics approach

Naz, Shumaila; Ahmad, Sajjad; Walton, Shelley F.; Abbasi, Sumra Wajid

doi:10.1016/j.molliq.2020.114105

Cited by 11 publications

(7 citation statements)

References 77 publications

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“…Epitopes that are similar to the B-cell receptor are not only important in vaccine development and antibody generation (Sanchez-Trincado et al 2017 ) but also responsible for the release of humoral or cellular immunity antibodies (Naz et al 2020 ). Thus, the ABCpred server was used to anticipate B-cell epitopes, and six epitopes for each of the six proteins with the highest score were chosen for the subunit vaccine design, along with appropriate linkers and an adjuvant (Table 5 ).…”

Section: Resultsmentioning

confidence: 99%

“…The vaccine sequence's tertiary structure was predicted using the Raptor X server and refined by using GalaxyWEB server ( http://galaxy.seoklab.org/ ) (Shin et al 2014 ). The best-refined model was then screened using Ramachandran plots analysis (Jaydari et al 2020 ); additionally, the ProSA-web server has been used to identify potential errors in the predicted 3-dimensional (3D) structures (Droppa-Almeida et al 2018 ; Naz et al 2020 ).…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, to protect from the disease, immunization or vaccine could be the best choice and advance technology makes the favorable amid to help with antigenic epitopes prediction, design protein structures, construct vaccine and provide insight into biological characteristics (Faisal et al 2017 ). The use of immune-informatics tools can save time, overcome cost hurdles, and improve the possibility of successful vaccine design (Naz et al 2020 ). In comparison vaccine design using traditional approaches requires huge time and investment along with probability of inducing allergenic responses (Khan et al 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach

Hasan

Mia

2022

Int J Pept Res Ther

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Cryptosporidiosis is the leading protozoan-induced cause of diarrheal illness in children, and it has been linked to childhood mortality, malnutrition, cognitive development, with retardation of growth. Cryptosporidium hominis , the anthroponotically transmitted species within the Cryptosporidium genus, contributes significantly to the global burden of infection, accounting for the majority of clinical cases in numerous nations, as well as its emergence in the last decade is largely due to detections obtained through noteworthy epidemiologic research. Nevertheless, there is no vaccine available, and the only licensed medication, nitazoxanide, has been demonstrated to have efficacy limitations in a number of patient groups recognized to be at high risk of complications. Therefore, current study delineates the computational vaccine design for Cryptosporidium hominis , the notable pathogen for enteric diarrhea. Firstly, a comprehensive literature search was conducted to identify six proteins based on their toxigenicity, allergenicity, antigenicity, and prediction of transmembrane helices to make up a multi-epitope-based subunit vaccine. Following that, antigenic non-toxic HTL epitope, CTL epitope with B cell epitope were predicted from the selected proteins and construct a vaccine candidate with adding an adjuvant and some linkers with immunologically superior epitopes. Afterwards, the constructed vaccine candidates and TLR2 receptor were put into the ClusPro server for molecular dynamic simulation to know the binding stability of the vaccine-TLR2 complex. Following that, Escherichia coli strain K12 was used as a cloning host for the chosen vaccine construct via the JCat server. As a result of the findings, it was resolute that the proposed chimeric peptide vaccine could improve the immune response to Cryptosporidium hominis .

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach

Hasan

Mia

2022

Int J Pept Res Ther

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“…GPGPG linkers were utilized to assemble the filtered epitopes into a multi-epitope peptide [ 61 ]. The 3D structure of the design was simulated using the 3Dpro of the SCRATCH protein predictor [ 62 ]. Galaxy Loop and Galaxy Refine of Galaxy Web were used to simulate the structure’s loops and optimize the structure further [ 63 , 64 ].…”

Section: Methodsmentioning

confidence: 99%

Immunoinformatics and Biophysics Approaches to Design a Novel Multi-Epitopes Vaccine Design against Staphylococcus auricularis

et al. 2022

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Due to the misuse of antibiotics in our daily lives, antimicrobial resistance (AMR) has become a major health problem. Penicillin, the first antibiotic, was used in the 1930s and led to the emergence of AMR. Due to alterations in the microbe’s genome and the evolution of new resistance mechanisms, antibiotics are losing efficacy against microbes. There are high rates of mortality and morbidity due to antibiotic resistance, so addressing this major health issue requires new approaches. Staphylococcus auricularis is a Gram-positive cocci and is capable of causing opportunistic infections and sepsis. S. auricularis is resistant to several antibiotics and does not currently have a licensed vaccine. In this study, we used bacterial pan-genome analysis (BPGA) to study S. auricularis pan-genome and applied a reverse immunology approach to prioritize vaccine targets against S. auricularis. A total of 15,444 core proteins were identified by BPGA analysis, which were then used to identify good vaccine candidates considering potential vaccine filters. Two vaccine candidates were evaluated for epitope prediction including the superoxide dismutase and gamma-glutamyl transferase protein. The epitope prediction phase involved the prediction of a variety of B-Cell and T-cell epitopes, and the epitopes that met certain criteria, such as antigenicity, immunogenicity, non-allergenicity, and non-toxicity were chosen. A multi-epitopes vaccine construct was then constructed from all the predicted epitopes, and a cholera toxin B-subunit adjuvant was also added to increase vaccine antigenicity. Three-dimensional models of the vaccine were used for downward analyses. Using the best-modeled structure, binding potency was tested with MHC-I, MHC-II and TLR-4 immune cells receptors, proving that the vaccine binds strongly with the receptors. Further, molecular dynamics simulations interpreted strong intermolecular binding between the vaccine and receptors and confirmed the vaccine epitopes exposed to the host immune system. The results support that the vaccine candidate may be capable of eliciting a protective immune response against S. auricularis and may be a promising candidate for experimental in vitro and in vivo studies.

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“…The system was then heated to 300K through the NVT ensemble supported via Langevin dynamics and SHAKE algorithm to limit hydrogen bonds. An equilibration for 100-ps was attained while sustaining pressure on the system via NPT ensemble letting restraint on Cα atoms of 5 kcal/mol -Å2 (Abbasi et al, 2016;Naz et al, 2020). The resulting trajectories, using the CPPTRAJ module, were examined, for the structural stability (Roe and Cheatham 2013).…”

Section: Molecular Dynamics (Md) Simulationsmentioning

confidence: 99%

Biological Evaluation and Computational Studies of Methoxy-flavones from Newly Isolated Radioresistant Micromonospora Aurantiaca Strain TMC-15

Sajjad

Nadeem

Alam

et al. 2022

Preprint

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This study aims to determine UV-B resistance and to investigate computational analysis and antioxidant potential of methoxy-flavones of Micromonospora aurantiaca TMC-15 isolated from Thal Desert, Pakistan. The cellular extract was purified through solid phase extraction and UV-Vis spectrum analysis indicated absorption peaks at λmax 250 nm, 343 nm, and 380 nm that revealed the presence of methoxy-flavones named eupatilin and 5-hydroxyauranetin. The flavones were evaluated for their antioxidant as well as protein and lipid peroxidation inhibition potential using di(phenyl)-(2,4,6-trinitrophenyl) iminoazanium (DPPH), 2,4-dinitrophenyl hydrazine (DNPH), and thiobarbituric acid reactive substances (TBARS) assays, respectively. The methoxy-flavones were further studied for their docking affinity and interaction dynamics to determine their structural and energetic properties at atomic level. The antioxidant potential, protein and lipid oxidation inhibition and DNA damage preventive abilities were correlated as predicted by computational analysis. The eupatilin and 5-hydroxyauranetin binding potential to their targeted proteins 1N8Q and 1OG5 is -4.1 and -7.5 kcal/mol, respectively. Moreover, the eupatiline and 5-hydroxyauranetin complexes illustrate van der Waals contacts and strong hydrogen bonds to their respective enzymes target. Both in-vitro studies and computational analysis results revealed that methoxy-flavones of Micromonospora aurantiaca TMC-15 can be used against radiation mediated oxidative damages due to its kosmotrophic nature. The demonstration of good antioxidant activities not only protect DNA but also protein and lipid oxidation and therefore could be a good candidate in radio-protective drugs and as sunscreen due to its kosmotropic nature.

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Multi-epitope based vaccine design against Sarcoptes scabiei paramyosin using immunoinformatics approach

Cited by 11 publications

References 77 publications

Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach

Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach

Immunoinformatics and Biophysics Approaches to Design a Novel Multi-Epitopes Vaccine Design against Staphylococcus auricularis

Biological Evaluation and Computational Studies of Methoxy-flavones from Newly Isolated Radioresistant Micromonospora Aurantiaca Strain TMC-15

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