Immunoinformatics-guided designing of epitope-based subunit vaccine from Pilus assembly protein of Acinetobacter baumannii bacteria

Mahapatra, Soumya Ranjan; Dey, Jyotirmayee; Jaiswal, Aryan; Roy, Riya; Misra, Namrata; Suar, Mrutyunjay

doi:10.1016/j.jim.2022.113325

Cited by 50 publications

(19 citation statements)

References 65 publications

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“…The population coverage was observed to exhibit 99.51% across worldwide. These outcomes indicate the applicability and potency of the designed vaccine construct for large geographical populations 62,63 . ProtParam classified the vaccine as stable (Instability index <40).…”

Section: Discussionmentioning

confidence: 99%

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An immunoinformatics and structural vaccinology study to design a multi‐epitope vaccine against Staphylococcus aureus infection

Chatterjee

Mahapatra

Dey

et al. 2023

J of Molecular Recognition

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Staphylococcus aureus has been widely reported to be majorly responsible for causing nosocomial infections worldwide. Due to an increase in antibiotic‐resistant strains, the development of an effective vaccine against the bacteria is the most viable alternative. Therefore, in the current work, an effort has been undertaken to develop a novel peptide‐based vaccine construct against S aureus that can potentially evoke the B and T cell immune responses. The fibronectin‐binding proteins are an attractive target as they play a prominent role in bacterial adherence and host cell invasion and are also well conserved among rapidly mutating pathogens. Therefore, highly immunogenic linear B lymphocytes (LBL), cytotoxic T lymphocytes (CTL), and helper T lymphocytes (HTL) epitopes were identified from the antigenic fibronectin‐binding proteins A and B (FnBPA and FnBPB) of S aureus using immunoinformatics approaches. The selected peptides were confirmed to be non‐allergenic, non‐toxic, and with a high binding affinity to the majority of human leukocyte antigens (HLA) alleles. Consequently, the multi‐peptide vaccine construct was developed by fusing the screened epitopes (three LBL, five CTL, and two HTL) together with the suitable adjuvant and linkers. In addition, the tertiary conformation of the peptide construct was modeled and later docked to the Toll‐like receptor 2. Subsequently, a molecular dynamics simulation of 100 ns was employed to corroborate the stability of the designed vaccine‐receptor complex. Besides exhibiting high immunogenicity and conformational stability, the developed vaccine was observed to possess wide population coverage of 99.51% worldwide. Additional in vivo and in vitro validation studies would certainly corroborate the designed vaccine construct to have improved prophylactic efficacy against S aureus.

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Section: Discussionmentioning

confidence: 99%

“…These outcomes indicate the applicability and potency of the designed vaccine construct for large geographical populations. 62,63 ProtParam classified the vaccine as stable (Instability index <40). The negative GRAVY value shows its hydrophilic nature.…”

Section: Discussionmentioning

confidence: 99%

An immunoinformatics and structural vaccinology study to design a multi‐epitope vaccine against Staphylococcus aureus infection

Chatterjee

Mahapatra

Dey

et al. 2023

J of Molecular Recognition

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“…In fact, synthetic vaccines are more reliable than conventional [ 56 ]. This approach has been used against various pathogens such as Klebsiella pneumonia , Acinetobacter baumannii , SARS-CoV-2, microalgae, and Staphylococcus aureus [ [57] , [58] , [59] , [60] ]. In this scientific approach, based on the scientific evidence from the literature, we selected four candidate proteins that are reportedly involved in S. gordonii Infection.…”

Section: Discussionmentioning

confidence: 99%

Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

Nasir,

Iftikhar,

Zubair

et al. 2023

Heliyon

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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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Immunoinformatics-guided designing of epitope-based subunit vaccine from Pilus assembly protein of Acinetobacter baumannii bacteria

Cited by 50 publications

References 65 publications

An immunoinformatics and structural vaccinology study to design a multi‐epitope vaccine against Staphylococcus aureus infection

An immunoinformatics and structural vaccinology study to design a multi‐epitope vaccine against Staphylococcus aureus infection

Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

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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