A multi-method and structure-based in silico vaccine designing against Helicobacter pylori employing immuno-informatics approach

2020 ◽  
Vol 17 ◽  
Author(s):  
Anam Naz ◽  
Tahreem Zaheer ◽  
Hamza Arshad Dar ◽  
Faryal Mehwish Awan ◽  
Ayesha Obaid ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Vaccine Development ◽  
Amino Acid Sequences ◽  
The Body ◽  
New Drugs ◽  
Toll Like Receptor ◽  
Peptide Vaccines ◽  
Hla Alleles ◽  
Vaccine Candidates ◽  
H Pylori

Background: Helicobacter pylori infection and its treatment still remains a challenge to human health worldwide. A variety of antibiotics and combination therapies are currently used to treat H. pylori induced ulcers and carcinoma; however, no effective treatment is available to eliminate the pathogen from the body. Additionally, antibiotic resistance is also one of the main reasons for prolonged and persistent infection. Aim of the study: Until new drugs are available for this infection, vaccinology seems the only alternative opportunity to exploit against H. pylori induced diseases. Methods: Multiple epitopes prioritized in our previous study have been tested for their possible antigenic combinations, and results in 169-mer and 183-mer peptide vaccines containing the amino acid sequences of 3 and 4 epitopes respectively, along with adjuvant (Cholera Toxin Subunit B adjuvant at 5’ end) and linkers (GPGPG and EAAAK). Results: Poly-epitope proteins proposed as potential vaccine candidates against H. pylori include SabAHP0289-Omp16-VacA (SHOV), VacA-Omp16-HP0289-FecA (VOHF), VacA-Omp16-HP0289-SabA (VOHS), VacA-Omp16-HP0289-BabA (VOHB), VacA-Omp16-HP0289-SabA-FecA (VOHSF), VacAOmp16-HP0289-SabA-BabA (VOHSB) and VacA-Omp16-HP0289-BabA-SabA (VOHBS). Structures of these poly-epitope peptide vaccines have been modelled and checked for their affinity with HLA alleles and receptors. These proposed poly-epitope vaccine candidates bind efficiently with A2, A3, B7 and DR1 superfamilies of HLA alleles. They can also form stable and significant interactions with Toll-like receptor 2 and Toll-like receptor 4. Conclusion: Results suggest that these multi-epitopic vaccines can elicit a significant immune response against H. pylori and can be tested further for efficient vaccine development.

scholarly journals Association of toll-like receptor 4, 5 and 10 polymorphisms with Helicobacter pylori -positive peptic ulcer disease in a center in Jordan

2021 ◽  
Vol 41 (4) ◽  
pp. 206-215
Author(s):  
Laith AL-Eitan ◽  
Fouad Abdelaziz Almomani ◽  
Sohaib Mahmoud Al-Khatib ◽  
Hanan Abdulraheem Aljamal ◽  
Mohammed Nayef Al-Qusami ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Peptic Ulcer ◽  
Conflicts Of Interest ◽  
Care Center ◽  
Treatment Success ◽  
Tertiary Care ◽  
Genotype Distribution ◽  
Toll Like Receptor ◽  
Toll Like Receptor 4 ◽  
H Pylori

BACKGROUND: Helicobacter pylori infection is widespread, affecting about 50% of the global population. Polymorphisms in host genes such as the toll-like receptor 4 ( TLR4 ) might affect the susceptibility and severity of infection and treatment success. OBJECTIVE: Investigate the susceptibility and severity of H pylori infection with host TLR4 (rs11536889, rs4986790, rs200109652, rs10759932), TLR5 (rs5744174, rs2072493, rs746250566), TLR10 (rs559182335, rs10004195) polymorphisms. DESIGN: Analytical, cross-sectional. SETTING: Endoscopy clinic at tertiary care center. PATIENTS AND METHODS: Genomic DNA was extracted from formalin-fixed paraffin-embedded tissues collected from H pylori -infected patients and healthy individuals. The single nucleotide polymorphisms (SNPs) within the targeted TLR genes were genotyped to assess the genetic association of various SNPs with disease severity. MAIN OUTCOME MEASURES: Effect of genotype distribution on H pylori infection. SAMPLE SIZE: 250 peptic ulcer patients and 217 controls. RESULTS: The TLR10 genotype showed no significant association with H pylori infection except for rs10004195 (T>A) ( P =.002). The genotype frequency of Rs5744174 in TLR5 had a significant association with the presence of H pylori infection ( P =.046, OR=0.52). Except for gender (P=.022), there were no significant associations between clinical and demographic variables and SNPs relating to the severity of the H pylori infections. CONCLUSIONS: Our findings are consistent with differences in severity of H pylori infection due to TLR SNPs in different ethnic groups. Understanding differences in genetic susceptibility could help in classifying patients and matching patients with various treatment options on a genetic basis. LIMITATIONS: Lack of H pylori pathogenicity features assessment. CONFLICTS OF INTEREST: None.

scholarly journals Potential of FTIR-Spectroscopy for Drugs Screening against Helicobacter pylori

Antibiotics ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 897
Author(s):  
Pedro Sousa Sampaio ◽  
Cecília R. C. Calado
Keyword(s):  
Helicobacter Pylori ◽  
Ftir Spectroscopy ◽  
Partial Least Square ◽  
Least Square ◽  
New Drugs ◽  
Partial Least Square Regression ◽  
Dilution Method ◽  
Agar Dilution Method ◽  
Molecular Fingerprint ◽  
H Pylori

Helicobacter pylori colonizes the human stomach of half of the world’s population. The infection if not treated, persists through life, leading to chronic gastric inflammation, that may progress to severe diseases as peptic ulcer, gastric adenocarcinoma, and mucosa-associated lymphoid tissue lymphoma. The first line of treatment, based on 7 to 21 days of two antibiotics associated with a proton pump inhibitor, is, however, already failing most due to patient non-compliance that leads to antibiotic resistance. It is, therefore, urgent to screen for new and more efficient antimicrobials against this bacterium. In this work, Fourier Transform Infrared (FTIR) spectroscopy was evaluated to screen new drugs against H. pylori, in rapid (between 1 to 6 h), and high-throughput mode and based on a microliter volume processes in relation to the agar dilution method. The reference H. pylori strains 26,695 and J99, were evaluated against a peptide-based antimicrobial and the clinical antibiotic clarithromycin, respectively. After optimization of the assay conditions, as the composition of the incubation mixture, the time of incubation, and spectral pre-processing, it was possible to reproducibly observe the effect of the drug on the bacterial molecular fingerprint as pointed by the spectra principal component analysis. The spectra, obtained from both reference strains, after its incubation with drugs concentrations lower than the MIC, presented peak ratios statistically different (p < 0.05) in relation to the bacteria incubated with drugs concentrations equal or higher to the MIC. It was possible to develop a partial least square regression model, enabling to predict from spectra of both bacteria strains, the drug concentration on the assay, with a high correlation coefficient between predicted and experimental data (0.91) and root square error of 40% of the minimum inhibitory concentration. All this points to the high potential of the technique for drug screening against this fastidious growth bacterium.

scholarly journals Molecular Basis of Unexpected Specificity of ABC Transporter-Associated Substrate-Binding Protein DppA from Helicobacter pylori

2019 ◽  
Vol 201 (20) ◽  
Author(s):  
Mohammad M. Rahman ◽  
Mayra A. Machuca ◽  
Mohammad F. Khan ◽  
Christopher K. Barlow ◽  
Ralf B. Schittenhelm ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Abc Transporter ◽  
Binding Protein ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Amino Acid Sequences ◽  
Content Type ◽  
H Pylori ◽  
Substrate Binding Protein ◽  
Broad Specificity

ABSTRACT The gastric pathogen Helicobacter pylori has limited ability to use carbohydrates as a carbon source, relying instead on exogenous amino acids and peptides. Uptake of certain peptides by H. pylori requires an ATP binding cassette (ABC) transporter annotated dipeptide permease (Dpp). The transporter specificity is determined by its cognate substrate-binding protein DppA, which captures ligands in the periplasm and delivers them to the permease. Here, we show that, unlike previously characterized DppA proteins, H. pylori DppA binds, with micromolar affinity, peptides of diverse amino acid sequences ranging between two and eight residues in length. We present analysis of the 1.45-Å-resolution crystal structure of its complex with the tetrapeptide STSA, which provides a structural rationale for the observed broad specificity. Analysis of the molecular surface revealed a ligand-binding pocket that is large enough to accommodate peptides of up to nine residues in length. The structure suggests that H. pylori DppA is able to recognize a wide range of peptide sequences by forming interactions primarily with the peptide main chain atoms. The loop that terminates the peptide-binding pocket in DppAs from other bacteria is significantly shorter in the H. pylori protein, providing an explanation for its ability to bind longer peptides. The subsites accommodating the two N-terminal residues of the peptide ligand make the greatest contribution to the protein-ligand binding energy, in agreement with the observation that dipeptides bind with affinity close to that of longer peptides. IMPORTANCE The World Health Organization listed Helicobacter pylori as a high-priority pathogen for antibiotic development. The potential of using peptide transporters in drug design is well recognized. We discovered that the substrate-binding protein of the ABC transporter for peptides, termed dipeptide permease, is an unusual member of its family in that it directly binds peptides of diverse amino acid sequences, ranging between two and eight residues in length. We also provided a structural rationale for the observed broad specificity. Since the ability to import peptides as a source of carbon is critical for H. pylori, our findings will inform drug design strategies based on inhibition or fusion of membrane-impermeant antimicrobials with peptides.

scholarly journals Effects of vaccination by a recombinant antigen ureB138 (a segment of the β-subunit of urease) against Helicobacter pylori infection

2007 ◽  
Vol 56 (6) ◽  
pp. 847-853 ◽  
Author(s):  
Fumiko Morihara ◽  
Ryoji Fujii ◽  
Emi Hifumi ◽  
Akira Nishizono ◽  
Taizo Uda
Keyword(s):  
Helicobacter Pylori ◽  
Mononuclear Cells ◽  
Gel Filtration ◽  
Immunohistochemical Analysis ◽  
Inhibitory Effect ◽  
Enzymic Activity ◽  
Amino Acid Sequences ◽  
Glutathione S Transferase ◽  
Important Region ◽  
H Pylori

Helicobacter pylori has to counteract acidity during colonization in the stomach. The most important region for the enzymic activity of H. pylori urease, consisting of 138 aa (ureB138), was determined by a comparison of the homology of amino acid sequences, and a structural analysis, between urease of H. pylori and various other species. This region was expressed in Escherichia coli as a fusion protein with glutathione S-transferase (GST), which was cleaved by PreScission protease between the GST moiety and ureB138. The ureB138 protein was then purified by gel filtration. The polyclonal antibody (pAb) induced by immunization with the purified ureB138 could suppress urease activity by about 50 %, while the pAb against the H. pylori urease did not show any inhibitory effect at all. Immunohistochemical analysis indicated that the ureB138-specific pAb specifically recognized the H. pylori infecting human gastric tissues. The effects of vaccination of recombinant ureB138 against infection by this organism were also examined. Specific IgG and IgA antibodies against H. pylori urease were induced in the serum of mice immunized with ureB138. A reduction in the number of colonizing H. pylori was observed in mice treated with ureB138 compared to ones treated with BSA and infection control mice. In the protected mice, severe gastritis characterized by marked infiltration of mononuclear cells was noted compared with the gastritis observed in unprotected mice. Immunohistochemical staining for IgA in gastric mucosa showed that the number of mice positively stained with IgA was significantly higher in ureB138-vaccinated mice than in non-vaccinated mice. This indicates that local IgA antibody and severe post-immunization gastritis correlate well with the protection of mice against H. pylori infection.

Peroral immunization with Helicobacter pylori adhesin protein genetically linked to cholera toxin A2B subunits

2001 ◽  
Vol 100 (3) ◽  
pp. 291-298 ◽  
Author(s):  
Byung Oh KIM ◽  
Sung Seup SHIN ◽  
Young Hyo YOO ◽  
Suhkneung PYO
Keyword(s):  
Helicobacter Pylori ◽  
Cholera Toxin ◽  
Vaccine Development ◽  
Protective Antigen ◽  
Oral Immunization ◽  
Size Exclusion ◽  
Vaccine Antigen ◽  
Igg Antibodies ◽  
Serum Igg ◽  
H Pylori

Helicobacter pylori is a major cause of gastric-associated diseases. To evaluate the efficacy of a possible vaccine antigen against H. pylori infection, the chimaeric construct adhesin–CTXA2B, derived from H. pylori adhesin genetically coupled to cholera toxin (CTX) subunits A2 and B (CTXA2B), was expressed in Escherichia coli as an insoluble recombinant chimaeric protein. The protein was then purified by denaturation, renaturation and size-exclusion chromatography. The composition of purified adhesin–CTXA2B was verified by SDS/PAGE and Western blotting with antibodies to antigenic components of adhesin and CTXB, and confirmed as a chimaeric protein with GM1-ganglioside binding activity and adhesin epitopes by a GM1-ELISA developed using antibodies to adhesin. Oral immunization of mice with adhesin–CTXA2B induced higher levels of mucosal IgA and serum IgG antibodies to H. pylori adhesin and to CTXB than in mice immunized with adhesin or CTXA2B alone. Adhesin–CTXA2B was also demonstrated to be a potential protective antigen in a mouse model of H. pylori infection. The immunization of mice with adhesin–CTXA2B protected 62.5% of mice infected with H. pylori SS1 strain, whereas adhesin immunization was not able to confer protection to mice. This protection may be correlated with high levels of mucosal IgA and serum IgG antibodies against H. pylori adhesin. Taken together, the results indicate that the genetically linked CTXA2B acts as a useful mucosal adjuvant, and that the adhesin–CTXA2B chimaeric protein could be a potential component in future H. pylori vaccine development.

scholarly journals vacA Genotypes and Genetic Diversity in Clinical Isolates of Helicobacter pylori

1998 ◽  
Vol 5 (2) ◽  
pp. 139-145 ◽  
Author(s):  
Shan-Rui Han ◽  
Hans-Joachim Schreiber ◽  
Sucharit Bhakdi ◽  
Michael Loos ◽  
Markus J. Maeurer
Keyword(s):  
Genetic Diversity ◽  
Helicobacter Pylori ◽  
Virulence Factors ◽  
Signal Sequence ◽  
Genotypic Variation ◽  
Rflp Analysis ◽  
Amino Acid Sequences ◽  
Clinical Isolates ◽  
Gastric Ulcers ◽  
H Pylori

ABSTRACT Genetic diversity in Helicobacter pylori strains may affect the function and antigenicity of virulence factors associated with bacterial infection and, ultimately, disease outcome. In this study, DNA diversity of H. pylori isolates was examined by analysis of vacA genotypes and by restriction fragment length polymorphism (RFLP) analysis of H. pylori-associated genes (vacA, cagA, flaA,ureAB, and ureCD). Thirty-seven H. pylori isolates from 26 patients were successfully classified into distinct vacA allelic genotypes. The signal sequence allele s1 (31 of 37) predominated over the s2 allele (6 of 37) and was significantly associated with the occurrence (past or present) of gastric ulcers. A novel midregion allele, designated as m3, has been identified in two H. pylori isolates which could not be typed with midregion allele m1- or m2-specific primers. Additionally, significant nucleotide diversity yielding different amino acid sequences was demonstrated by DNA sequencing of vacAfragments from clinical isolates of H. pylori. Furthermore, RFLP analysis of 45 H. pylori isolates (including 15 paired isolates) obtained from antrum and corpus biopsy specimens from 30 individual patients showed remarkably high interhost diversity (one patient, one H. pylori strain) and intrahost identity in gene sequences coding for VacA, CagA, flagellin, and urease. Only in a single patient was a minor genotypic variation at different anatomic sites within the stomach identified. These data warrant the detailed analysis of the effect of genetic diversity on the function and antigenicity of H. pylori-associated virulence factors.

scholarly journals Identification of Potential Diagnostic and Vaccine Candidates ofHelicobacter pylori by Two-Dimensional Gel Electrophoresis, Sequence Analysis, and Serum Profiling

1998 ◽  
Vol 5 (4) ◽  
pp. 537-542 ◽  
Author(s):  
C. Patrick McAtee ◽  
Moon Young Lim ◽  
Kevin Fung ◽  
Mark Velligan ◽  
Kirk Fry ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gel Electrophoresis ◽  
Vaccine Development ◽  
Two Dimensional ◽  
Terminal Sequence ◽  
Two Dimensional Gel Electrophoresis ◽  
Western Blots ◽  
Vaccine Candidates ◽  
Serum Profiling ◽  
H Pylori

ABSTRACT There is great interest in characterizing the proteins of the gastric pathogen Helicobacter pylori, especially those to which humans respond immunologically, because of the potential importance of such proteins in diagnosis and vaccine development. Two-dimensional gel electrophoresis was used to separate and identify potential antigens of H. pylori ATCC 43504. Over 30 proteins were reactive in Western blots with pooled sera from 14 infected patients. These proteins were analyzed by N-terminal sequence analysis. Fourteen proteins were determined to be distinct from any proteins previously described from H. pylori; the others were previously isolated and characterized proteins. Analysis of eight distinct H. pylori strains showed that most of these antigens were produced by all of the strains. We propose that collection of new antigens such as those recognized here will be useful in serologic tests for detecting and monitoring H. pylori infection and may also serve as potential targets for antimicrobial agent or vaccine development.

scholarly journals Helicobacter pylori Infection, Virulence Genes’ Distribution and Accompanying Clinical Outcomes: The West Africa Situation

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
Eric Gyamerah Ofori ◽  
Cynthia Ayefoumi Adinortey ◽  
Ansumana Sandy Bockarie ◽  
Foster Kyei ◽  
Emmanuel Ayitey Tagoe ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
West Africa ◽  
Clinical Outcomes ◽  
Virulence Factors ◽  
Alcohol Exposure ◽  
The Body ◽  
African Countries ◽  
Genetic Characteristics ◽  
The Status ◽  
H Pylori

Data on Helicobacter pylori (H. pylori) infection and virulence factors in countries across West Africa are scattered. This systematic review seeks to present an update on the status of H. pylori infection focusing on prevalence rate, distribution of virulent genes, and their link to clinical outcomes across countries in the western part of Africa. This information is expected to broaden the knowledge base of clinicians and researchers regarding H. pylori infection and associated virulence factors in West African countries. Search Method. A comprehensive search of the scientific literature in PubMed and ScienceDirect was conducted using the search terms including “Helicobacter pylori infection in West Africa”. Databases were sourced from January 1988 to December 2018. Results. Data on the incidence of H. pylori infection and related pathological factors were found for some countries, whereas others had no information on it. Smoking, alcohol, exposure to high levels of carcinogens and diet were reported to be involved in the pathogenesis of gastroduodenal diseases and gastric cancer. Besides the environmental factors and genetic characteristics, there are important characteristics of H. pylori such as the ability to infect, replicate, and persist in a host that have been associated with the pathogenesis of various gastroduodenal diseases. Concluding Remarks. This systematic search has provided information so far available on H. pylori virulence factors and clinical outcomes in West Africa. Accordingly, this piece has identified gaps in the body of knowledge highlighting the need for more studies to clarify the role of H. pylori virulence factors and associated clinical outcomes in the burden of this bacterial infection in West Africa, as data from these countries do not give the needed direct relation.

scholarly journals Helicobacter pylori Activates Calpain via Toll-Like Receptor 2 To Disrupt Adherens Junctions in Human Gastric Epithelial Cells

2011 ◽  
Vol 79 (10) ◽  
pp. 3887-3894 ◽  
Author(s):  
Pamela M. O'Connor ◽  
Tamia K. Lapointe ◽  
Shannon Jackson ◽  
Paul L. Beck ◽  
Nicola L. Jones ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Adherens Junctions ◽  
Severe Disease ◽  
Elevated Serum ◽  
Toll Like Receptor ◽  
Content Type ◽  
Calpain Activation ◽  
Toll Like Receptor 2 ◽  
H Pylori ◽  
E Cadherin

ABSTRACTHelicobacter pyloriis a risk factor for the development of gastritis, gastroduodenal ulcers, and gastric adenocarcinoma.H. pylori-induced disruption of epithelial adherens junctions (AJs) is thought to promote the development of severe disease; however, the mechanisms wherebyH. pylorialters AJ structure remain incompletely understood. The present study demonstrates thatH. pyloriinfection in human patients is associated with elevated serum levels of an 80-kDa E-cadherin ectodomain, whose presence is independent of the presence of serum antibodies against CagA.In vitro, a heat-labileH. pylorisurface component activates the host protease calpain in human gastric MKN45 cells independently of the virulence factors CagA and VacA.H. pylori-induced calpain activation results in cleavage of E-cadherin to produce a 100-kDa truncated form and induce relocalization of E-cadherin and β-catenin. Stimulation of MKN45 cells with the toll-like receptor 2 (TLR2) ligand P3C activated calpain and disrupted E-cadherin and β-catenin in a pattern similar to that induced byH. pylori. Inhibition of TLR2 preventedH. pylori-induced calpain activation and AJ disassembly. Together, these findings identify a novel pathway wherebyH. pyloriactivates calpain via TLR2 to disrupt gastric epithelial AJ structure.

scholarly journals Ceramide and Toll-Like Receptor 4 Are Mobilized into Membrane Rafts in Response to Helicobacter pylori Infection in Gastric Epithelial Cells

2012 ◽  
Vol 80 (5) ◽  
pp. 1823-1833 ◽  
Author(s):  
Dah-Yuu Lu ◽  
Hui-Chen Chen ◽  
Mei-Shiang Yang ◽  
Yuan-Man Hsu ◽  
Hwai-Jeng Lin ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Epithelial Cells ◽  
Lipid Rafts ◽  
Gastric Epithelial Cells ◽  
Toll Like Receptor ◽  
Tlr4 Expression ◽  
Ags Cells ◽  
Content Type ◽  
Infected Cells ◽  
H Pylori

ABSTRACTHelicobacter pyloriinfection is thought to be involved in the development of several gastric diseases. TwoH. pylorivirulence factors (vacuolating cytotoxin A and cytotoxin-associated gene A) reportedly interact with lipid rafts in gastric epithelial cells. The role of Toll-like receptor (TLR)-mediated signaling in response toH. pyloriinfection has been investigated extensively in host cells. However, the receptor molecules in lipid rafts that are involved inH. pylori-induced innate sensing have not been well characterized. This study investigated whether lipid rafts play a role inH. pylori-induced ceramide secretion and TLR4 expression and thereby contribute to inflammation in gastric epithelial cells. We observed that both TLR4 and MD-2 mRNA and protein levels were significantly higher inH. pylori-infected AGS cells than in mock-infected cells. Moreover, significantly more TLR4 protein was detected in detergent-resistant membranes extracted fromH. pylori-infected AGS cells than in those extracted from mock-infected cells. However, this effect was attenuated by the treatment of cells with cholesterol-usurping agents, suggesting thatH. pylori-induced TLR4 signaling is dependent on cholesterol-rich microdomains. Similarly, the level of cellular ceramide was elevated and ceramide was translocated into lipid rafts afterH. pyloriinfection, leading to interleukin-8 (IL-8) production. Using the sphingomyelinase inhibitor imipramine, we observed thatH. pylori-induced TLR4 expression was ceramide dependent. These results indicate the mobilization of ceramide and TLR4 into lipid rafts byH. pyloriinfection in response to inflammation in gastric epithelial cells.

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