In Silico Study on the Inhibition of UDP-N-Acetylglucosamine 1-Carboxy Vinyl Transferase from Salmonella typhimurium by the Lipopeptide Produced from Bacillus aryabhattai

Yaraguppi, Deepak A.; Bagewadi, Zabin K.; Deshpande, Sanjay H.; Chandramohan, Vivek

doi:10.1007/s10989-022-10388-z

Cited by 15 publications

(11 citation statements)

References 35 publications

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“…The binding space of the cocrystallized was analyzed, and the key residues were identified. A total of 103 water molecules were removed from the structure …”

Section: Resultsmentioning

confidence: 99%

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Investigation of the Fluorescence Turn-off Mechanism, Genome, Molecular Docking In Silico and In Vitro Studies of 2-Acetyl-3H-benzo[f]chromen-3-one

Koppal

Melavanki

Kusanur³

et al. 2022

ACS Omega

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The present study harnesses fluorescence quenching between a nonfluorescent aniline and fluorophore 2-acetyl-3 H -benzo[ f ]chromen-3-one [2AHBC] in binary solvent mixtures of acetonitrile and 1,4-dioxane at room temperature and explores the fluorophore as an antimicrobial material. Our findings throw light on the key performance of organic molecules in the medicinal and pharmaceutical fields, which are considered as the most leading drives in therapeutic applications. In view of that, fluorescence quenching data have been interpreted by various quenching models. This demonstrates that the sphere of action holds very well in the present work and also confirms the presence of static quenching reactions. Additionally, the fluorophore was first investigated for druglike activity with the help of in silico tools, and then it was investigated for antimicrobial activity through bioinformatics tools, which has shown promising insights.

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“…The binding space of the cocrystallized was analyzed, and the key residues were identified. A total of 103 water molecules were removed from the structure …”

Section: Resultsmentioning

confidence: 99%

“…A total of 103 water molecules were removed from the structure. 62 The grid box for the docking was considered based on the coordinates of the cocrystallized ligand. The coordinates were x = 27.37, y = 85.45, and z = 2.32, and the size of the grid box for the docking was 25 points for x, y, and z coordinates.…”

Section: = + [ ]mentioning

confidence: 99%

Investigation of the Fluorescence Turn-off Mechanism, Genome, Molecular Docking In Silico and In Vitro Studies of 2-Acetyl-3H-benzo[f]chromen-3-one

Koppal

Melavanki

Kusanur³

et al. 2022

ACS Omega

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“…A to the fungal cell membranes, as this approach has been recently used to identify potential protein targets of iturin A. 56,57…”

Section: Discussionmentioning

confidence: 99%

Total synthesis of antifungal lipopeptide iturin A analogues and evaluation of their bioactivity against F. graminearum

Karamanis,

Muldoon,

Murphy

et al. 2024

Journal of Peptide Science

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The pursuit of novel antifungal agents is imperative to tackle the threat of antifungal resistance, which poses major risks to both human health and to food security. Iturin A is a cyclic lipopeptide, produced by Bacillus sp., with pronounced antifungal properties against several pathogens. Its challenging synthesis, mainly due to the laborious synthesis of the β‐amino fatty acid present in its structure, has hindered the study of its mode of action and the development of more potent analogues. In this work, a facile synthesis of bioactive iturin A analogues containing an alkylated cysteine residue is presented. Two analogues with opposite configurations of the alkylated cysteine residue were synthesized, to evaluate the role of the stereochemistry of the newly introduced amino acid on the bioactivity. Antifungal assays, conducted against F. graminearum, showed that the novel analogues are bioactive and can be used as a synthetic model for the design of new analogues and in structure–activity relationship studies. The assays also highlight the importance of the β‐amino acid in the natural structure and the role of the stereochemistry of the amino fatty acid, as the analogue with the D configuration showed stronger antifungal properties than the one with the L configuration.

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“…The solvent-accessible surface area (SASA) was calculated using the “gmx sasa” command to determine the area accessible by water in the protein, in which the ligand can move around bound with the target protein. The hydrogen bond counts for the protein–ligand complex in both the target in complex with standard drug and the target in complex with the compound resulted from similarity indexing [ 47 ].…”

Section: Methodsmentioning

confidence: 99%

Exploring the Potential of Phytocompounds for Targeting Epigenetic Mechanisms in Rheumatoid Arthritis: An In Silico Study Using Similarity Indexing

et al. 2023

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Finding structurally similar compounds in compound databases is highly efficient and is widely used in present-day drug discovery methodology. The most-trusted and -followed similarity indexing method is Tanimoto similarity indexing. Epigenetic proteins like histone deacetylases (HDACs) inhibitors are traditionally used to target cancer, but have only been investigated very recently for their possible effectiveness against rheumatoid arthritis (RA). The synthetic drugs that have been identified and used for the inhibition of HDACs include SAHA, which is being used to inhibit the activity of HDACs of different classes. SAHA was chosen as a compound of high importance as it is reported to inhibit the activity of many HDAC types. Similarity searching using the UNPD database as a reference identified aglaithioduline from the Aglaia leptantha compound as having a ~70% similarity of molecular fingerprints with SAHA, based on the Tanimoto indexing method using ChemmineR. Aglaithioduline is abundantly present in the shell and fruits of A. leptantha. In silico studies with aglaithioduline were carried out against the HDAC8 protein target and showed a binding affinity of −8.5 kcal mol. The complex was further subjected to molecular dynamics simulation using Gromacs. The RMSD, RMSF, compactness and SASA plots of the target with aglaithioduline, in comparison with the co-crystallized ligand (SAHA) system, showed a very stable configuration. The results of the study are supportive of the usage of A. leptantha and A. edulis in Indian traditional medicine for the treatment of pain-related ailments similar to RA. Our study therefore calls for further investigation of A. leptantha and A. edulis for their potential use against RA by targeting epigenetic changes, using in vivo and in vitro studies.

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In Silico Study on the Inhibition of UDP-N-Acetylglucosamine 1-Carboxy Vinyl Transferase from Salmonella typhimurium by the Lipopeptide Produced from Bacillus aryabhattai

Cited by 15 publications

References 35 publications

Investigation of the Fluorescence Turn-off Mechanism, Genome, Molecular Docking In Silico and In Vitro Studies of 2-Acetyl-3H-benzo[f]chromen-3-one

Investigation of the Fluorescence Turn-off Mechanism, Genome, Molecular Docking In Silico and In Vitro Studies of 2-Acetyl-3H-benzo[f]chromen-3-one

Total synthesis of antifungal lipopeptide iturin A analogues and evaluation of their bioactivity against F. graminearum

Exploring the Potential of Phytocompounds for Targeting Epigenetic Mechanisms in Rheumatoid Arthritis: An In Silico Study Using Similarity Indexing

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