Immunoinformatics and molecular dynamics studies to predict T-cell-specific epitopes of four <i>Klebsiella pneumoniae</i> fimbriae antigens

Rostamian, Mosayeb; Farasat, Alireza; Lorestani, Roya Chegene; Zargaran, Fatemeh Nemati; Ghadiri, Keyghobad; Akya, Alisha

doi:10.1080/07391102.2020.1810126

Cited by 15 publications

(14 citation statements)

References 59 publications

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“…Therefore, defining the HLA alleles is required for the epitope prediction. Here, 10 HLA-I alleles with high frequency in the world that have been determined in our previous study (Rostamian et al 2020 ) were applied.…”

Section: Methodsmentioning

confidence: 99%

“…The epitope prediction was performed as previously report (Akya et al 2019 ; Rostamian et al 2020 ). Briefly, based on the highly frequent HLA-I alleles, FepA sequence was screened by three epitope prediction tools, namely IEDB ( http://tools.iedb.org , (Fleri et al 2017 ), ProPred-I ( http://crdd.osdd.net/raghava/propred1/ , (Singh and Raghava 2003 ) and SYFPEITHI ( http://www.syfpeithi.de/bin/MHCServer.dll/EpitopePrediction.htm , (Schuler et al 2007 )).…”

Section: Methodsmentioning

confidence: 99%

“…These HLA-II alleles should be defined for epitope prediction tools. Here, eight previously determined highly frequent HLA-II alleles (Rostamian et al 2020 ) were used as entries to three epitope prediction tools, IEDB, ProPred-II ( http://crdd.osdd.net/raghava/propred/ ), and SYFPEITHI. The percentile rank ≤ 10 for IEDB and the score of ≥ 10 for ProPred-II and SYFPEITHI were used as the thresholds and 15-mer epitopes were chosen to be predicted.…”

Section: Methodsmentioning

confidence: 99%

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Detecting the Dominant T and B Epitopes of Klebsiella pneumoniae Ferric Enterobactin Protein (FepA) and Introducing a Single Epitopic Peptide as Vaccine Candidate

Zargaran

Akya

Ghadiri

et al. 2021

Int J Pept Res Ther

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Klebsiella pneumoniae causes various human infections. Ferric enterobactin protein (FepA) is a conserved protein of K. pneumoniae with high immunogenicity. In the present study, using comprehensive in silico approaches the T and B cell-specific epitopes of K. pneumoniae FepA were identified. The T (both class I and class II) and B (both linear and conformational) epitopes of FepA were predicted using prediction tools. The predicted epitopes were screened for human similarity, immunogenicity, antigenicity, allergenicity, toxicity, conservancy, structural and physicochemical suitability, and in case of T epitopes binding to HLA alleles, using numerous immune-informatics, homology modeling, and molecular docking approaches. These analyses led to introduce the most dominant FepA epitopes that are appropriate for vaccine development. Furthermore, we introduced an antigenic peptide containing both T and B epitopes which comprises suitable structural and physiochemical properties needed for vaccine development and it is conserved in many bacteria. Altogether, here the highly immunogenic T and B epitopes of FepA as well as a final epitopic peptide containing both T and B epitopes were found and introduced for future vaccine development studies. It is suggested that the actual efficiency and efficacy of our final epitopic peptide be investigated by in vitro/in vivo testing. Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10247-3.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Detecting the Dominant T and B Epitopes of Klebsiella pneumoniae Ferric Enterobactin Protein (FepA) and Introducing a Single Epitopic Peptide as Vaccine Candidate

Zargaran

Akya

Ghadiri

et al. 2021

Int J Pept Res Ther

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“…Vaccines built on recombinant proteins have also been developed against S. aureus using extracellular bacterial vesicles coating mesoporous silica nanoparticles [ 329 , 331 , 332 ]. In K. pneumoniae , the in vivo studies in mice model infection and non-human primate model of severe lower respiratory tract infection revealed the unique immunogenic properties of T cell-specific epitopes [ 333 ], recombinant protein vaccine [ 334 ], and polysaccharide capsule type 2 vaccine [ 335 ].…”

Section: Alternative Approaches To Combat Eskape Pathogensmentioning

confidence: 99%

Emerging Strategies to Combat β-Lactamase Producing ESKAPE Pathogens

Vrâncianu

Gheorghe

Dobre

et al. 2020

IJMS

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Since the discovery of penicillin by Alexander Fleming in 1929 as a therapeutic agent against staphylococci, β-lactam antibiotics (BLAs) remained the most successful antibiotic classes against the majority of bacterial strains, reaching a percentage of 65% of all medical prescriptions. Unfortunately, the emergence and diversification of β-lactamases pose indefinite health issues, limiting the clinical effectiveness of all current BLAs. One solution is to develop β-lactamase inhibitors (BLIs) capable of restoring the activity of β-lactam drugs. In this review, we will briefly present the older and new BLAs classes, their mechanisms of action, and an update of the BLIs capable of restoring the activity of β-lactam drugs against ESKAPE (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens. Subsequently, we will discuss several promising alternative approaches such as bacteriophages, antimicrobial peptides, nanoparticles, CRISPR (clustered regularly interspaced short palindromic repeats) cas technology, or vaccination developed to limit antimicrobial resistance in this endless fight against Gram-negative pathogens.

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“…In our previous work, we predicted T cell epitopes of four type 1 fimbriae antigens namely FimA, FimF, FimG, and FimH using immunoinformatic, docking and molecular dynamics (Rostamian et al 2020). Due to the importance of humoral immune responses against K. pneumoniae, here we performed an in silico study on these four Fim antigens as vaccine candidates and tried to find and characterize B-cell epitopes of these antigens.…”

Section: Introductionmentioning

confidence: 99%

B Cell Epitopes of Four Fimbriae Antigens of Klebsiella pneumoniae: A Comprehensive In Silico Study for Vaccine Development

Zargaran

Akya

Rezaeian

et al. 2020

Int J Pept Res Ther

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Klebsiella pneumoniae is one of the major causes of nosocomial infections worldwide which can cause several diseases in children and adults. The globally dissemination of hyper-virulent strains of K. pneumoniae and the emergence of antibioticsresistant isolates of this pathogen narrows down the treatment options and has renewed interest in its vaccines. Vaccine candidates of Klebsiella pneumoniae have not been adequately protective, safe and globally available yet. In K. pneumoniae infection, it is well known that B cells that induce robust humoral immunity are necessary for the host complete protection. Identifying the B cell epitopes of antigens is valuable to design novel vaccine candidates. In the present study using immunoinformatics approaches we found B cell epitopes of four K. pneumoniae type 1 fimbriae antigens namely FimA, FimF, FimG, and FimH. Linear and conformational B cell epitopes of each antigen were predicted using different programs. Subsequently, many bioinformatics assays were applied to choose the best epitopes including prediction antigenicity, toxicity, human similarity and investigation on experimental records. These assays resulted in final four epitopes (each for one Fim protein). These final epitopes were modeled and their physiochemical properties were estimated to be used as potential vaccine candidates. Altogether, we found four B cell epitopes of K. pneumoniae Fim antigens that are immunogen, antigenic, not similar to human peptides, not allergen and not toxic. Also, they have suitable physiochemical properties to administrate as vaccine, although their complete efficacy should be also shown in vitro and in vivo.

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Immunoinformatics and molecular dynamics studies to predict T-cell-specific epitopes of four Klebsiella pneumoniae fimbriae antigens

Cited by 15 publications

References 59 publications

Detecting the Dominant T and B Epitopes of Klebsiella pneumoniae Ferric Enterobactin Protein (FepA) and Introducing a Single Epitopic Peptide as Vaccine Candidate

Detecting the Dominant T and B Epitopes of Klebsiella pneumoniae Ferric Enterobactin Protein (FepA) and Introducing a Single Epitopic Peptide as Vaccine Candidate

Emerging Strategies to Combat β-Lactamase Producing ESKAPE Pathogens

B Cell Epitopes of Four Fimbriae Antigens of Klebsiella pneumoniae: A Comprehensive In Silico Study for Vaccine Development

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