Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus)

Azim, Kazi Faizul; Hasan, Mahmudul; Hossain, Nazmul; Somana, Saneya Risa; Hoque, Syeda Farjana; Bappy, Md. Nazmul Islam; Chowdhury, Anjum Taiebah; Lasker, Tahera

doi:10.1016/j.meegid.2019.103936

Cited by 52 publications

(32 citation statements)

References 95 publications

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“…Ver097 and the result is provided in Table 7. Development of vaccine candidates against these membrane proteins can contribute to the control and eradication of infectious diseases of human which type of studies have already been reported [56,57].…”

Section: Resultsmentioning

confidence: 99%

Subtractive Genomic Analysis for Identification of Novel Drug Targets and Vaccine Candidates against Bartonella bacilliformis subsp. Ver097

Khan

Mahmud

Iqbal

et al. 2019

Preprint

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Bartonella bacilliformis is the causative agent of Carrión’s disease, one of the truly neglected tropical diseases found in Peru, Colombia and Ecuador. Recent evidence predicts that Bartonella bacilliformis subsp. ver097 can emerge as an antibacterial resistant strain and hence identification of novel drug targets is a crying need. Subtractive genome analysis of B. bacilliformis subsp. ver097 was successfully done in order to address the challenges. Various computational tools and online based servers were used to screen out human homologous proteins of pathogen and proteins involved in common metabolic pathways of host and pathogen. Only 7 proteins involved in pathogen specific pathways were further analyzed to identify membrane proteins. ‘Flagellar biosynthesis protein FlhA’ and ‘ABC transporter permease’ were found to be novel as targets according to DrugBank database. To avoid side effects in human while administering drugs, human ‘anti-targets’ analysis was performed to confirm non-homology of selected novel drug targets. Both predicted proteins also showed probability of antigenicity prediction through VaxiJen, however, ‘Flagellar biosynthesis protein FlhA’ showed broad spectrum conservancy with Bartonella strains. Therefore, Flagellar biosynthesis protein FlhAcould facilitate the development of novel drugs and therapeutic compounds along with vaccines for efficient treatment of infections caused by Bartonella bacilliformis subsp. ver097.

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Section: Resultsmentioning

confidence: 99%

Subtractive Genomic Analysis for Identification of Novel Drug Targets and Vaccine Candidates against Bartonella bacilliformis subsp. Ver097

Khan

Mahmud

Iqbal

et al. 2019

Preprint

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“…The confidence of each model is quantitatively measured by C-score (38). To enhance the accuracy of the predicted structures, refinement was performed using ModRefiner (39) followed by FG-MD refinement server (40, 41). Finally, the refined structures were also validated using Verified 3D (42, 43), ERRAT (44) and Ramachandran Plot Assessment server (RAMPAGE) (45, 46).…”

Section: Methodsmentioning

confidence: 99%

Antimicrobial Resistance Profile andmcr-1Gene Detection inSalmonellaIsolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization

Uddin

Smb

Hasan

et al. 2020

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Antimicrobial resistance gene mcr-1 has been disseminated globally since its first discovery in Southern China in late 2015. However, the mcr-1 gene had not been identified previously in Salmonella isolates from poultry in Bangladesh. Here, we aimed to explore antimicrobial resistance gene mcr-1 in Salmonella isolates. Eighty two Salmonella isolates were isolated and characterized from suspected poultry specimens received from different zones of the country. A phenotypic disc diffusion assay with 15 antimicrobial agents was performed following CLSI standard. The disk diffusion assay showed that, all of the isolates presented high resistance to colistin (92.68%), oxytetracycline (86.59%), co-trimoxazole (76.83%), ciprofloxacin (73.17%) and enrofloxacin (65.85%). Further, randomly selected 10 Salmonella isolates were analyzed by polymerase chain reaction (PCR) targeting genus-specific invA and antimicrobial (colistin) resistance mcr-1 genes. Five were confirmed for the presence of the mcr-1 gene belonging to Salmonella spp. Further, sequencing followed by phylogenetic analysis revealed divergent evolutionary relation between the LptA and MCR proteins rendering them resistant to colistin. Three-dimensional homology structures of MCR-1 proteins were constructed and verified using different bioinformatics tools. Moreover, molecular docking interactions suggested that, MCR-1 and LptA share a similar substrate binding cavity which could be validated for the functional analysis. The results represent here is the first molecular and in silico analysis of colistin resistance mcr-1 gene of Salmonella in poultry in Bangladesh, which may emphasize the importance of the study on antibiotic resistance genes requiring for national monitoring and strategic surveillance in the country.

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“…The disease-based approach of the traditional method of drug discovery is both expensive, and time-consuming since significant time and devoted researchers are required to identify potential ligands. In recent years, computational aided drug targets discovery methods reduce consumption of time by eliminating compounds in this process that have limited chance of success [20,21,22,23]. Among various computational methods and strategies, subtractive genomic analysis can be regarded worthy since data regarding genome and proteome are available in various online based databases.…”

Section: Introductionmentioning

confidence: 99%

Proteome Exploration of Legionella pneumophila for Identifying Novel Therapeutics: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

Khan

Mahmud

Hasan

et al. 2020

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Legionella pneumophila, the causative agent of a serious type of pneumonia (lung infection) called Legionnaires' disease. It is emerging as an antibacterial resistant strain day by day.Hence, identification of novel drug targets and vaccine candidates is essential to fight against this pathogen. Herein attempts were taken through subtractive genomics approach on complete proteome of L. pneumophila to address the challenges of multidrug resistance. A total 2930 proteins from L. pneumophila proteome were investigated through diverse subtractive proteomics approaches, e.g., identification of human non homologous and pathogen specific essential proteins, druggability and 'anti-target' analysis, prediction of subcellular localization, human microbiome non-homology screening, protein-protein interactions studies in order to find out effective drug and vaccine targets. Only 3 were identified that fulfilled all these criteria and proposed as novel drug targets against L. pneumophila. Furthermore, outer membrane protein TolB was identified as potential vaccine target with better antigenicity score and allowed for further in silico analysis to design a unique multiepitope subunit vaccine against it. Antigenicity and transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were adopted to generate the most potent epitopes. The final vaccine was constructed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. The designed vaccine construct showed higher binding interaction with different MHC molecules and human immune TLR2 receptor with minimum deformability at molecular level. The translational potency and microbial expression of the vaccine protein was also analyzed using pET28a(+) vector. The present study aids in the development of novel therapeutics and vaccine candidates for efficient treatment of the infections caused by Legionella pneumophila. However, further wet lab based investigations and in vivo trials are highly recommended to experimentally validate our prediction.

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Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus)

Cited by 52 publications

References 95 publications

Subtractive Genomic Analysis for Identification of Novel Drug Targets and Vaccine Candidates against Bartonella bacilliformis subsp. Ver097

Subtractive Genomic Analysis for Identification of Novel Drug Targets and Vaccine Candidates against Bartonella bacilliformis subsp. Ver097

Antimicrobial Resistance Profile andmcr-1Gene Detection inSalmonellaIsolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization

Proteome Exploration of Legionella pneumophila for Identifying Novel Therapeutics: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

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