Investigation on Structural Prediction of Pectate Lyase Enzymes from Different Microbes and Comparative Docking Studies with Pectin: The Economical Waste from Food Industry

Panda, Swati Sudeshna; Dey, Jyotirmayee; Mahapatra, Soumya Ranjan; Kushwaha, G.S.; Misra, Namrata; Suar, Mrutyunjay; Ghosh, Mrinmoy

doi:10.1080/01490451.2021.1992042

Cited by 25 publications

(10 citation statements)

References 56 publications

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“…The efficiency of in silico vaccine development is increasing due to advancements in bioinformatics and immunoinformatic [ 21 ]. This phenomenon results in a decline in In vitro testing procedures.…”

Section: Discussionmentioning

confidence: 99%

A novel chimeric vaccine containing multiple epitopes for simulating robust immune activation against Klebsiella pneumoniae

Hakimian,

Doosti,

Sharifzadeh

2024

BMC Immunol

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Background Due to antibiotic resistance, the Klebsiella genus is linked to morbidity and death, necessitating the development of a universally protective vaccine against Klebsiella pathogens. Methods Core sequence analysis prioritized non-redundant host molecules and expected lipid bilayer peptides from fully sequenced Klebsiella genomes. These proteins were refined to identify epitopes, examining their immunogenicity, toxicity, solubility, and interaction with MHC alleles. Epitopes were linked to CPG ODN C274 via EAAAK, HEYGAEALERAG, and GGGS linkers to enhance immunological responses. The vaccine’s tertiary structure was modelled and docked with MHC-I and MHC-II. Results Fifty-five proteins were recognized in the Vaxign collection as having remarkable features. Twenty-three proteins with potential pathogenicity were then identified. Eight options for vaccines emerged after the immunogenicity of proteins was examined. The best antigens were three proteins: MrkD, Iron-regulated lipid membrane polypeptides, and RmpA. These compounds were selected for their sensitivity. The structural protein sequences of K. pneumoniae were utilized to identify seven CTL epitopes, seven HTL epitopes, and seven LBL epitopes, respectively. The produced immunization displayed a stable contact with the receptors, based on molecular dynamic simulations lasting 250 nanoseconds. Intermolecular binding free energies also indicated the dominance of the van der Waals and electrostatic energies. Conclusion In summary, the results of this study might help scientists develop a novel vaccine to prevent K. pneumoniae infections.

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Section: Discussionmentioning

confidence: 99%

A novel chimeric vaccine containing multiple epitopes for simulating robust immune activation against Klebsiella pneumoniae

Hakimian,

Doosti,

Sharifzadeh

2024

BMC Immunol

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“…This retrieved amino acid sequence is used to generate a novel vaccine construct. The NCBI and UniProt databases provide a huge amount of biological protein information (Narang et al 2021 ; Panda et al 2022 ). The amino acid sequence of the target protein can be extracted in FASTA format (Shawan et al 2014 , 2018 ).…”

Section: Methodsmentioning

confidence: 99%

“…The physicochemical properties, i.e., the number of amino acids, molecular weight (MW), theoretical pH (pI), amino acids composition, the total number of negatively charged residues, the total number of positively charged residues, atomic composition, formula, extinction coefficient, estimated half-life, instability index (II), aliphatic index (AI), and grand average of hydropathicity (GRAVY) of the formulated vaccine can be assessed using ProtParam tool within ExPASy proteomic server (Gasteiger 2003 ; Narang et al 2021 ; Panda et al 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…For a better understanding, another solubility prediction server, namely Protein-Sol, can be utilized, and a protein with a solubility score greater than 0.45 is considered highly soluble (Hebditch et al 2017 ). Next, the transmembrane helices and potential signal peptides within the vaccine construct can be determined using TMHMM v2.0 and SignalP 4.1 server (Krogh et al 2001 ; Nielsen 2017a ; Panda et al 2022 ).…”

Section: Methodsmentioning

confidence: 99%

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Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine

Shawan,

Sharma,

Halder

et al. 2023

Int J Pept Res Ther

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A vaccine is defined as a biologic preparation that trains the immune system, boosts immunity, and protects against a deadly microbial infection. They have been used for centuries to combat a variety of contagious illnesses by means of subsiding the disease burden as well as eradicating the disease. Since infectious disease pandemics are a recurring global threat, vaccination has emerged as one of the most promising tools to save millions of lives and reduce infection rates. The World Health Organization reports that immunization protects three million individuals annually. Currently, multi-epitope-based peptide vaccines are a unique concept in vaccine formulation. Epitope-based peptide vaccines utilize small fragments of proteins or peptides (parts of the pathogen), called epitopes, that trigger an adequate immune response against a particular pathogen. However, conventional vaccine designing and development techniques are too cumbersome, expensive, and time-consuming. With the recent advancement in bioinformatics, immunoinformatics, and vaccinomics discipline, vaccine science has entered a new era accompanying a modern, impressive, and more realistic paradigm in designing and developing next-generation strong immunogens. In silico designing and developing a safe and novel vaccine construct involves knowledge of reverse vaccinology, various vaccine databases, and high throughput techniques. The computational tools and techniques directly associated with vaccine research are extremely effective, economical, precise, robust, and safe for human use. Many vaccine candidates have entered clinical trials instantly and are available prior to schedule. In light of this, the present article provides researchers with up-to-date information on various approaches, protocols, and databases regarding the computational designing and development of potent multi-epitope-based peptide vaccines that can assist researchers in tailoring vaccines more rapidly and cost-effectively.

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“…There have been existing reports of exploiting putative drug targets of pathogenic organisms for vaccine development to elicit a robust immune response against the associated infections. Immunoinformatics approach has been previously employed to construct multi-epitope vaccines against Enterococcus faecium, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii and many other complications (Narang et al 2021 , 2022 ; Dey et al 2022a , b , c ; Sudeshna Panda et al 2022 ; Mahapatra et al 2022a , b ; Sahoo et al 2022 ). However, the current research article has focused on identifying therapeutic lead molecules against E. cloacae and evaluating their interaction profile with potent drug targets.…”

Section: Introductionmentioning

confidence: 99%

Translational protein RpsE as an alternative target for novel nucleoside analogues to treat MDR Enterobacter cloacae ATCC 13047: network analysis and molecular dynamics study

Debroy

Ramaiah

2023

World J Microbiol Biotechnol

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The pathogenic Enterobacter cloacae subsp. cloacae str. ATCC 13047 has contemporarily emerged as a multi-drug resistant strain. To formulate an effective treatment option, alternative therapeutic methods need to be explored. The present study focused on Gene Interaction Network study of 46 antimicrobial resistance genes to reveal the densely interconnecting and functional hub genes in E. cloacae ATCC 13047. The AMR genes were subjected to clustering, topological and functional enrichment analysis, revealing rpsE (RpsE), acrA (AcrA) and arnT (ArnT) as novel therapeutic drug targets for hindering drug resistance in the pathogenic strain. Network topology further indicated translational protein RpsE to be exploited as a promising drug-target candidate for which the structure was predicted, optimized and validated through molecular dynamics simulations (MDS). Absorption, distribution, metabolism and excretion screening recognized ZINC5441082 ( N -Isopentyladenosine) (Lead_1) and ZINC1319816 (cyclopentyl-aminopurinyl-hydroxymethyl-oxolanediol) (Lead_2) as orally bioavailable compounds against RpsE. Molecular docking and MDS confirmed the binding efficacy and protein−ligand complex stability. Furthermore, binding free energy (G bind ) calculations, principal component and free energy landscape analyses affirmed the predicted nucleoside analogues against RpsE protein to be comprehensively examined as a potential treatment strategy against E. cloacae ATCC 13047. Supplementary information The online version contains supplementary material available at 10.1007/s11274-023-03634-z.

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Investigation on Structural Prediction of Pectate Lyase Enzymes from Different Microbes and Comparative Docking Studies with Pectin: The Economical Waste from Food Industry

Cited by 25 publications

References 56 publications

A novel chimeric vaccine containing multiple epitopes for simulating robust immune activation against Klebsiella pneumoniae

A novel chimeric vaccine containing multiple epitopes for simulating robust immune activation against Klebsiella pneumoniae

Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine

Translational protein RpsE as an alternative target for novel nucleoside analogues to treat MDR Enterobacter cloacae ATCC 13047: network analysis and molecular dynamics study

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