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Open AccessJournal ArticleDOI

Identification of potential riboflavin synthase inhibitors by virtual screening and molecular dynamics simulation studies

TLDR
Insights from this study provide promising starting points for the rational designs of new effective and safe anti-leptospirosis drugs.
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This article is published in Journal of King Saud University - Science.The article was published on 2021-03-01 and is currently open access. It has received 5 citations till now. The article focuses on the topics: Riboflavin synthase & Virtual screening.

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Identification of Severe Acute Respiratory Syndrome Coronavirus-2 inhibitors through in silico structure-based virtual screening and molecular interaction studies.

TL;DR: In this article, 2,96 365 natural and synthetic derivatives (ligands) belonging to 102 classes of compounds were obtained from PubChem and assessed on Lipinski's parameters for their potential bioavailability.
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Mining therapeutic targets from the antibiotic-resistant Campylobacter coli and virtual screening of natural product inhibitors against its riboflavin synthase

TL;DR: G genomes of 89 antibiotic-resistant strains of C. coli were downloaded from the PATRIC database and compounds identified appear safe for targeting this pathogen and can be further validated by experimental analysis before clinical trials.
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Identification of Therapeutic Targets in an Emerging Gastrointestinal Pathogen Campylobacter ureolyticus and Possible Intervention through Natural Products

TL;DR: The findings of this report may serve as baseline information for laboratory studies leading to the discovery of drugs for use against C. ureolyticus infections and help identify potential risks associated with the selected compounds.
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Unraveling the crystal structure of Leptospira kmetyi riboflavin synthase and computational analyses for potential development of new antibacterials

TL;DR: In this article , the crystal structure of riboflavin synthase from leptospira kmetyi was determined at 3.2 Å and belonged to the orthorhombic space group P212121, with an R-factor of 21.8%.
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Subtractive sequence-mediated therapeutic targets from the conserved gene clusters of Campylobacter hyointestinalis and computational inhibition assessment.

TL;DR: Sarma et al. as discussed by the authors used subtractive computational screening of the C. hyointestinalis genome for the purpose of identifying the therapeutic targets and reported no therapeutic targets have been identified and reported in this bacterium.
References
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Journal ArticleDOI

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

TL;DR: The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities.
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Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes

TL;DR: Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.
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ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.

TL;DR: The quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer in the ProSA-web service.
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Lead- and drug-like compounds: the rule-of-five revolution.

TL;DR: This topic is explored in terms ofDrug-like physicochemical features, drug-like structural features, a comparison of drug- like and non-drug-like in drug discovery and a discussion of how drug-Like features relate to clinical success.
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Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field.

TL;DR: An all‐atom force field aimed at protein and nucleotide optimization in vacuo (NOVA), which has been specifically designed to avoid this problem and can be applied to modeling applications as well as X‐ray and NMR structure refinement.
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