scholarly journals Designing a Multi-Epitope Vaccine against Dracunculus medinensis by Employing Immuno-Informatics and In Silico Approaches

2021 ◽  
Author(s):  
Mian Talha Sarfraz ◽  
Marvah Mehmood Rana
Keyword(s):  
In Silico ◽  
Tertiary Structure ◽  
Coli Strain ◽  
Agricultural Field ◽  
Epitope Vaccine ◽  
E Coli ◽  
Guinea Worm ◽  
Field Worker ◽  
Cell Immunity ◽  
The Stability

Dracunculiasis (also known as Guinea worm disease) is caused by Dracunculus medinensis parasite and it spreads by drinking water containing Larvae of Guinea worm. The lack of safe water facilities, preventions and treatments resulted in highly dangerous consequences in its endemic regions. The economy of the affected regions totally falls down due to less production which is the result of agricultural field worker’s bad health. In this study, a multi epitope vaccine was designed against Dracunculus medinensis by using immune-informatics. The vaccine was designed by using T-Cell and B-Cell epitopes derived from Dracunculus medinensis proteins (Lactamase-B domain-containing protein, G-Domain containing protein and Ferrochelatase) in addition to Adjuvants and Linkers. The tertiary structure, physiochemical properties and immunogenic elements of vaccine were achieved. The validation of tertiary structure was accessed, and quality was achieved. In addition, the world coverage of parasite’s CTL and HTL epitopes is 95.61%. The stability of the chimeric vaccine was achieved through disulfide engineering. The molecular docking with Toll Like Receptor 4 (TLR-4) of vaccine showed its binding efficiency followed by Molecular Dynamic Simulation. The immune simulation suggested the mediated cell immunity and repeated antigen clearance. At the end, the optimized codon was used in in silico cloning to ensure vaccine’s higher exposure in bacterium E. coli strain K12. With further assessments, it is believed that the proposed multi epitope vaccine has strong immunogen to control Dracunculus medinensis which may result in better social and economic conditions of endemic regions.

scholarly journals Structural Analysis of Avian Encephalomyelitis Virus Polyprotein for Development of Multi Epitopes Vaccine Using Immunoinformatics Approach

2021 ◽  
Vol 15 (1) ◽  
pp. 262-278
Author(s):  
Fatima Khalid Elhassan ◽  
Yassir A. Almofti ◽  
Khoubieb Ali Abd-elrahman ◽  
Mashair AA Nouri ◽  
Elsideeq EM Eltilib
Keyword(s):  
T Cells ◽  
Disulfide Bonds ◽  
Tertiary Structure ◽  
High Mobility ◽  
Dynamics Simulation ◽  
High Morbidity ◽  
E Coli ◽  
Encephalomyelitis Virus ◽  
The Stability ◽  
Chimeric Vaccine

Avian Encephalomyelitis (AE) is the disease caused by avian encephalomyelitis virus (AEV). The disease mainly affects young birds nervous system worldwide causing high morbidity and variable mortality rate in chicks and noticed egg dropping and hatchability in mature hens. Vaccination is the only way to control AEV infection since there is no treatment yet to the avian encephalomyelitis. This study aimed to use immunoinformatics approaches to predict multi epitopes vaccine from the AEV polyprotein that could elicit both B and T cells. The vaccine construct comprises 482 amino acids obtained from epitopes predicted against B and T cells by IEDB server, adjuvant, linkers and 6-His-tag. The chimeric vaccine was potentially antigenic and nonallergic and demonstrated thermostability and hydrophilicity in protparam server. The solubility of the vaccine was measured in comparison to E. coli proteins. The stability was also assessed by disulfide bonds engineering to reduce the high mobility regions in the designed vaccine. Furthermore molecular dynamics simulation further strengthen stability of the predicted vaccine. Tertiary structure of the vaccine construct after prediction, refinement was used for molecular docking with chicken alleles BF2*2101 and BF2*0401 and the docking process demonstrated favourable binding energy score of -337.47 kcal/mol and -326.87 kcal/mol, respectively. Molecular cloning demonstrated the potential clonability of the chimeric vaccine in pET28a(+) vector. This could guarantee the efficient translation and expression of the vaccine within suitable expression vector.

scholarly journals Designing and Analyzing the Structure of DT-STXB Fusion Protein as an Anti-tumor Agent: An in Silico Approach

2019 ◽  
Vol 14 (4) ◽  
pp. 305-312 ◽  
Author(s):  
Zeynab Mohseni Moghadam ◽  
Raheleh Halabian ◽  
Hamid Sedighian ◽  
Elham Behzadi ◽  
Jafar Amani ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Fusion Protein ◽  
Shiga Toxin ◽  
In Silico ◽  
Tertiary Structure ◽  
Chimeric Protein ◽  
Human Tumors ◽  
Energy Calculation ◽  
Mrna Structure ◽  
The Stability

Background & Objective: A main contest in chemotherapy is to obtain regulator above the biodistribution of cytotoxic drugs. The utmost promising strategy comprises of drugs coupled with a tumor-targeting bearer that results in wide cytotoxic activity and particular delivery. The B-subunit of Shiga toxin (STxB) is nontoxic and possesses low immunogenicity that exactly binds to the globotriaosylceramide (Gb3/CD77). Gb3/CD77 extremely expresses on a number of human tumors such as pancreatic, colon, and breast cancer and acts as a functional receptor for Shiga toxin (STx). Then, this toxin can be applied to target Gb3-positive human tumors. In this study, we evaluated DT390-STXB chimeric protein as a new anti-tumor candidate via genetically fusing the DT390 fragment of DT538 (Native diphtheria toxin) to STxB. Methods: This study intended to investigate the DT390- STxB fusion protein structure in silico. Considering the Escherichia coli codon usage, the genomic construct was designed. The properties and the structure of the protein were determined by an in silico technique. The mRNA structure and the physicochemical characteristics, construction, and the stability of the designed chimeric protein were analyzed using computational and bioinformatics tools and servers. Hence, the GOR4 and I-TASSER online web servers were used to predict the secondary and tertiary structures of the designed protein. Results: The results demonstrated that codon adaptation index (CAI) of dt390-stxB chimeric gene raised from 0.6 in the wild type to 0.9 in the chimeric optimized gene. The mfold data revealed that the dt390-stxB mRNA was completely stable to be translated effectively in the novel host. The normal activity of the fusion protein determined by considering the secondary and tertiary structure of each construct. Energy calculation data indicated that the thermodynamic ensemble for mRNA structure was -427.40 kJ/mol. The stability index (SI) of DT390-STxB was 36.95, which is quite appropriate to preserve the stability of the construct. Ultimately, the DT390-STxB was classified as a steady fusion protein according to the Ramachandran plot. Conclusion: Our results showed that DT390-STXB was a stable chimeric protein and it can be recruited as a candidate of novel anti-tumor agents for the development of breast cancer treatment.

scholarly journals Synthesis and in Silico Modelling of the Potential Dual Mechanistic Activity of Small Cationic Peptides Potentiating the Antibiotic Novobiocin against Susceptible and Multi-Drug Resistant Escherichia coli

2020 ◽  
Vol 21 (23) ◽  
pp. 9134
Author(s):  
Ilaria Passarini ◽  
Pedro Ernesto de Resende ◽  
Sarah Soares ◽  
Tadeh Tahmasi ◽  
Paul Stapleton ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
In Silico ◽  
Mammalian Cells ◽  
Antimicrobial Agents ◽  
Efflux Pump ◽  
Coli Strain ◽  
Cell Permeability ◽  
Cationic Peptides ◽  
Drug Resistant ◽  
E Coli

Cationic antimicrobial peptides have attracted interest, both as antimicrobial agents and for their ability to increase cell permeability to potentiate other antibiotics. However, toxicity to mammalian cells and complexity have hindered development for clinical use. We present the design and synthesis of very short cationic peptides (3–9 residues) with potential dual bacterial membrane permeation and efflux pump inhibition functionality. Peptides were designed based upon in silico similarity to known active peptides and efflux pump inhibitors. A number of these peptides potentiate the activity of the antibiotic novobiocin against susceptible Escherichia coli and restore antibiotic activity against a multi-drug resistant E. coli strain, despite having minimal or no intrinsic antimicrobial activity. Molecular modelling studies, via docking studies and short molecular dynamics simulations, indicate two potential mechanisms of potentiating activity; increasing antibiotic cell permeation via complexation with novobiocin to enable self-promoted uptake, and binding the E. coli RND efflux pump. These peptides demonstrate potential for restoring the activity of hydrophobic drugs.

scholarly journals Investigation of Leish-111f Epitopes to Design a New Multi-epitope Vaccine Against Leishmania Major Using Immunoinformatics Approaches

2021 ◽  
Author(s):  
Mahsa Rabienia ◽  
Rasoul Daneshi ◽  
Nahid Mortazavidehkordi ◽  
Ali Ghanbariasad ◽  
Abbas Abdollahi ◽  
...  
Keyword(s):  
In Silico ◽  
Leishmania Major ◽  
Vaccine Antigen ◽  
Definitive Treatment ◽  
Epitope Vaccine ◽  
E Coli ◽  
High Prevalence ◽  
Malignant Lesions ◽  
Skin Vaccination ◽  
Adaptation Index

Abstract BackgroundSince the incidence of various types of leishmaniasis, no definitive treatment has been considered for the disease, and due to its high prevalence worldwide, this issue has caused many concerns. Cutaneous leishmaniasis is the most common form of the disease which, can cause malignant lesions on the skin. Vaccination for the prevention and treatment of leishmaniasis can be the most effective way to combat this disease. In this study, we designed a new multi-epitope vaccine using immunoinformatics tools, which confirmed its effectiveness in the in silico.MethodsSequences Leish-111f protein (TSA, Leif, and LMSTI1) of Leishmania major (L. major) were downloaded from GenBank and with the help of immunoinformatic tools, was designed a new multi-epitope vaccine antigen of L. major.ResultTh and Tc epitopes of the leish-111f protein were predicted using bioinformatics tools. The final multi epitope was consisted of 18 CTL epitopes that joined by AAY linker. There are also 9 HTL epitopes in the structure of the final vaccine that were joined by GPGPG linker. The profilin adjuvant was also added into the construct by AAY Linker. There were 613 residues in the structure of the final construct. The multi epitope was stable and non-allergic. the data obtained from the binding of final multi-epitope vaccine-TLR11 residues (band lengths and weighted scores) showed that the ligand and the receptor have a high affinity to bind to each other. Moreover, in silico cloning approach, was improved the expression of proposed vaccine in E. coli host. Codon adaptation index and GC percent were calculated 1.0 and 53.35, respectivelyConclusionBased on these results, we hope that the multi-epitope vaccine, which contains the most appropriate epitopes of a strong Leishmania major immunogen, along with an adjuvant capable of binding to TLR11, will further stimulate the immune system against the L.major.

scholarly journals In Silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike proteins

2020 ◽  
Author(s):  
Gunderao H Kathwate
Keyword(s):  
Humoral Immunity ◽  
In Silico ◽  
Tertiary Structure ◽  
E Coli ◽  
Interaction Prediction ◽  
Protein Protein Interaction ◽  
Protein Interaction Prediction ◽  
Cellular And Humoral Immunity ◽  
Interferon Gamma Response

AbstractCOVID 19 is disease caused by novel corona virus, SARS-CoV2 originated in China most probably of Bat origin. Till date, no specific vaccine or drug has been discovered to tackle the infections caused by SARS-CoV2. In response to this pandemic, we utilized bioinformatics knowledge to develop efficient vaccine candidate against SARS-CoV2. Designed vaccine was rich in effective BCR and TCR epitopes screened from the sequence of S-protein of SARS-CoV2. Predicted BCR and TCR epitopes were antigenic in nature non-toxic and probably non-allergen. Modelled and refined tertiary structure was predicted as valid for further use. Protein-Protein interaction prediction of TLR2/4 and designed vaccine indicates promising binding. Designed multiepitope vaccine has induced cell mediated and humoral immunity along with increased interferon gamma response. Macrophages and dendritic cells were also found increased over the vaccine exposure. In silico codon optimization and cloning in expression vector indicates that vaccine can be efficiently expressed in E. coli. In conclusion, predicted vaccine is a good antigen, probable no allergen and has potential to induce cellular and humoral immunity.

scholarly journals Anti-Tick Microbiota Vaccine Impacts Ixodes ricinus Performance during Feeding

Vaccines ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 702 ◽  
Author(s):  
Lourdes Mateos-Hernández ◽  
Dasiel Obregón ◽  
Jennifer Maye ◽  
Jeremie Borneres ◽  
Nicolas Versille ◽  
...  
Keyword(s):  
Wide Distribution ◽  
Experimental Manipulation ◽  
Coli Strain ◽  
E Coli ◽  
Promising Tool ◽  
The Family ◽  
Strain Bl21 ◽  
The Stability ◽  
Different Strains ◽  
In Silico Analyses

The tick microbiota is a highly complex ensemble of interacting microorganisms. Keystone taxa, with a central role in the microbial networks, support the stability and fitness of the microbial communities. The keystoneness of taxa in the tick microbiota can be inferred from microbial co-occurrence networks. Microbes with high centrality indexes are highly connected with other taxa of the microbiota and are expected to provide important resources to the microbial community and/or the tick. We reasoned that disturbance of vector microbiota by removal of ubiquitous and abundant keystone bacteria may disrupt the tick-microbiota homeostasis causing harm to the tick host. These observations and reasoning prompted us to test the hypothesis that antibodies targeting keystone bacteria may harm the ticks during feeding on immunized hosts. To this aim, in silico analyses were conducted to identify keystone bacteria in the microbiota of Ixodes nymphs. The family Enterobacteriaceae was among the top keystone taxa identified in Ixodes microbiota. Immunization of α-1,3-galactosyltransferase-deficient-C57BL/6 (α1,3GT KO) mice with a live vaccine containing the Enterobacteriaceae bacterium Escherichia coli strain BL21 revealed that the production of anti-E. coli and anti-α-Gal IgM and IgG was associated with high mortality of I. ricinus nymphs during feeding. However, this effect was absent in two different strains of wild type mice, BALB/c and C57BL/6. This result concurred with a wide distribution of α-1,3-galactosyltransferase genes, and possibly α-Gal, in Enterobacteriaceae and other bacteria of tick microbiota. Interestingly, the weight of I. ricinus nymphs that fed on E. coli-immunized C57BL/6 was significantly higher than the weight of ticks that fed on C57BL/6 immunized with a mock vaccine. Our results suggest that anti-tick microbiota vaccines are a promising tool for the experimental manipulation of vector microbiota, and potentially the control of ticks and tick-borne pathogens.

scholarly journals Human rhinovirus 2A proteinase mutant and its second-site revertants

1996 ◽  
Vol 318 (1) ◽  
pp. 213-218 ◽  
Author(s):  
Marion LUDERER-GMACH ◽  
Hans-Dieter LIEBIG ◽  
Wolfgang SOMMERGRUBER ◽  
Tilman VOSS ◽  
Frederike FESSL ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Three Dimensional ◽  
Temperature Stability ◽  
Coli Strain ◽  
Dimensional Structure ◽  
Peptide Substrate ◽  
E Coli ◽  
Overall Stability ◽  
The Stability ◽  
Inhibited Enzyme

The 2A proteinases of human rhinoviruses are cysteine proteinases with marked similarities to serine proteinases. In the absence of a three-dimensional structure, we developed a genetical screening system for proteolytic activity and identified Phe-130 as a key residue. The mutation Phe-130 → Tyr almost completely inhibited enzyme activity at 37 °C; activity was, however, partially restored by the following exchanges: Ser-27 → Pro, His-135 → Arg or His-137 → Arg. To investigate this phenotypic reversion, 2A proteinases with the mutations Phe-130 → Tyr, Phe-130 → Tyr/His-135 → Arg, Phe-130 → Tyr/His-137 → Arg, His-135 → Arg or His-137 → Arg were expressed in Escherichia coli and purified. None of these mutations affected the affinity of the enzyme for a peptide substrate. However, the temperature-dependence of enzyme activity, as assayed by cleavage of a peptide substrate and by monitoring the toxicity of the proteinases towards the E. coli strain BL21(DE3), and the structural stability, as monitored by 8-anilino-1-naphthalenesulphonic acid fluorescence and CD spectrometry, were affected. The thermal transition temperatures for both the activity and the stability of the Phe-130 → Tyr 2A proteinase were reduced by about 17 °C compared with the wild-type enzyme. The presence of the additional mutations His-135 → Arg or His-137 → Arg in the Phe-130 → Tyr mutant increased temperature stability by 3 °C and 6 °C respectively. Thus essential interactions exist within the C-terminal domain of human rhinoviral 2A proteinases which contribute to the overall stability and integrity of the enzyme.

Transport of escherichia coli through soil to groundwater traced by randomly amplified polymorphic DNA (RAPD)

1997 ◽  
Vol 35 (11-12) ◽  
pp. 351-357 ◽  
Author(s):  
R. Rothmaier ◽  
A. Weidenmann ◽  
K. Botzenhart
Keyword(s):  
Negative Impact ◽  
Random Amplified Polymorphic Dna ◽  
Coli Strain ◽  
Soil Samples ◽  
Test Field ◽  
Liquid Manure ◽  
E Coli ◽  
Rapd Pattern ◽  
Geological Situation ◽  
Different Strains

Isolates (50) of E. coli obtained from liquid manure (20 bovine, 20 porcine) were genotyped using random amplified polymorphic DNA (RAPD). Typing revealed 9 and 14 different strains in bovine and porcine liquid manure respectively with no strains in common. One porcine strain, showing a simple RAPD pattern, was subcultured and spread on a test field (1.5l/m2 at 1010 cfu/l) in a drinking water protection zone with loamy to sandy sediments in the Donauried area, Baden-Wurttemberg. Soil samples and groundwaters were collected at monthly intervals October 1994 – June 1995 during which 114 E. coli isolates were recovered. The first occurrence and maximum concentration of E. coli in soil samples taken from more than 20cm depth was in January 1995, declining rapidly with depth and time. All isolates from soil and only one from groundwater showed the RAPD pattern of the spread E. coli strain. The results could not demonstrate a severe negative impact of the spreading of liquid manure on the bacteriological quality of the groundwater in the given geological situation. The distinct strain patterns found in different kinds of liquid manure suggest that genotyping of E. coli by RAPD may be an adequate tool for tracing sources of faecal contamination.

Production and Preliminary In Vivo Evaluations of a Novel in silico-designed L2-based Potential HPV Vaccine

2020 ◽  
Vol 21 (4) ◽  
pp. 316-324
Author(s):  
Manica Negahdaripour ◽  
Navid Nezafat ◽  
Reza Heidari ◽  
Nasrollah Erfani ◽  
Nasim Hajighahramani ◽  
...  
Keyword(s):  
In Silico ◽  
Group Versus ◽  
Tlr Agonists ◽  
E Coli ◽  
Metal Affinity ◽  
Th1 And Th2 Cytokines ◽  
Ifn Γ ◽  
Humoral Responses ◽  
Future Work

Background: L2-based Human Papillomavirus (HPV) prophylactic vaccines, containing epitopes from HPV minor capsid proteins, are under investigation as second-generation HPV vaccines. No such vaccine has passed clinical trials yet, mainly due to the low immunogenicity of peptide vaccines; so efforts are being continued. A candidate vaccine composed of two HPV16 L2 epitopes, flagellin and a Toll-Like Receptor (TLR) 4 agonist (RS09) as adjuvants, and two universal T-helper epitopes was designed in silico in our previous researches. Methods: The designed vaccine construct was expressed in E. coli BL21 (DE3) and purified through metal affinity chromatography. Following mice vaccination, blood samples underwent ELISA and flow cytometry analyses for the detection of IgG and seven Th1 and Th2 cytokines. Results: Following immunization, Th1 (IFN-γ, IL-2) and Th2 (IL-4, IL-5, IL-10) type cytokines, as well as IgG, were induced significantly compared with the PBS group. Significant increases in IFN-γ, IL-2, and IL-5 levels were observed in the vaccinated group versus Freund’s adjuvant group. Conclusion: The obtained cytokine induction profile implied both cellular and humoral responses, with a more Th-1 favored trend. However, an analysis of specific antibodies against L2 is required to confirm humoral responses. No significant elevation in inflammatory cytokines, (IL-6 and TNF-α), suggested a lack of unwanted inflammatory side effects despite using a combination of two TLR agonists. The designed construct might be capable of inducing adaptive and innate immunity; nevertheless, comprehensive immune tests were not conducted at this stage and will be a matter of future work.

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