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In Vitro Assessment on Designing Novel Antibiofilms of Pseudomonas aeruginosa Using a Computational Approach.

ABSTRACT: An anti-biofilm that can inhibit the matrix of biofilm formation is necessary to prevent recurrent and chronic Pseudomonas aeruginosa infection. This study aimed to design compounds with a new mechanism through competitive inhibitory activity against phosphomannomutase/phosphoglucomutase (PMM/PGM), using in vitro assessment and a computational (in silico) approach. The active site of PMM/PGM was assessed through molecular redocking using L-tartaric acid as the native ligand and other small molecules, such as glucaric acid, D-sorbitol, and ascorbic acid. The docking program set the small molecules to the active site, showing a stable complex formation. Analysis of structural similarity, bioavailability, absorption, distribution, metabolism, excretion, and toxicity properties proved the potential application of ligands as an anti-biofilm. In vitro assessment with crystal violet showed that the ligands could reach up to 95.87% inhibition at different concentrations. The nitrocellulose membrane and scanning electron microscopic visualization showed that the untreated P. aeruginosa biofilm was denser than the ligand-treated biofilm.

SUBMITTER: Rachmawati D

PROVIDER: S-EPMC9784811 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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In Vitro Assessment on Designing Novel Antibiofilms of <i>Pseudomonas aeruginosa</i> Using a Computational Approach.

Rachmawati Dian D Fahmi Mochammad Zakki MZ Abdjan Muhammad Ikhlas MI Wasito Eddy Bagus EB Siswanto Imam I Mazlan Nurzafirah N Rohmah Jazirotur J Baktir Afaf A

Molecules (Basel, Switzerland) 20221215 24

An anti-biofilm that can inhibit the matrix of biofilm formation is necessary to prevent recurrent and chronic <i>Pseudomonas aeruginosa</i> infection. This study aimed to design compounds with a new mechanism through competitive inhibitory activity against phosphomannomutase/phosphoglucomutase (PMM/PGM), using in vitro assessment and a computational (in silico) approach. The active site of PMM/PGM was assessed through molecular redocking using L-tartaric acid as the native ligand and other smal ...[more]

PMID: 36558064

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Project description:Multidrug-resistant Pseudomonas aeruginosa is one of the worldwide health problems involved in elevated mortality and morbidity. Therefore, it is important to find a therapeutic for this pathogen. In the present study, we have designed a chimeric vaccine against P. aeruginosa with the help of comparative proteomics and reverse vaccinology approaches. Using comparative subtractive proteomic analysis of 1,191 proteomes of P. aeruginosa, a total of twenty unique non-redundant proteomes were selected. In these proteomes, fifteen outer membrane proteins (OMPs) of P. aeruginosa were selected based on the basis of hydrophilicity, non-secretory nature, low transmembrane helix (<1), essentiality, virulence, pathway association, antigenic, and protein-protein network analysis. Reverse vaccinology approach was used to identify antigenic and immunogenic MHC class I, MHC class II and B cell epitopes present in the selected OMPs that can enhance T cell and B cell mediated immunogenicity. The selected epitopes were shortlisted based on their allergenicity, toxicity potentials, solubility, and hydrophilicity analysis. Immunogenic peptides were used to design a multi-epitope vaccine construct. Immune-modulating adjuvants and PADRE (Pan HLA-DR epitopes) sequence were added with epitopes sequence to enhance the immunogenicity. All the epitopes, adjuvants and PADRE sequence were joined by linkers. The designed vaccine constructs (VT1, VT2, VT3, and VT4) were analyzed by their physiochemical properties using different tools. Selected chimeric vaccine constructs (VT1, VT3, and VT4) were further shortlisted by their docking score with different HLA alleles. The final selected VT4 construct was docked with TLR4/MD2 complex and confirmed by molecular dynamics simulation studies. The final vaccine VT-4 construct was in-silico cloned in pET28a. Therefore, the designed construct VT4 may be studied to control the interaction of P. aeruginosa with host and infection caused by P. aeruginosa.

Dataset Information

In Vitro Assessment on Designing Novel Antibiofilms of Pseudomonas aeruginosa Using a Computational Approach.

Publications

In Vitro Assessment on Designing Novel Antibiofilms of <i>Pseudomonas aeruginosa</i> Using a Computational Approach.

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