PyFepRestr: Plugin to PyMOL Molecular Graphics System for Calculating the Free Energy of Ligand‒Receptor Binding

Lashkov, A.A.; Толмачев, И. В.; Eistrikh-Heller, P. A.; Rubinsky, S. V.

doi:10.1134/s1063774521050126

Cited by 7 publications

(2 citation statements)

References 19 publications

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“…The molecular dynamics analysis was performed using the Simulation Interaction Diagram from Desmond. Pymol 1.8.6 was used for the visualization of the complexes (Lashkov et al, 2021 ). Furthermore, the top 20 ranked compounds were selected for further property evaluation.…”

Section: Methodsmentioning

confidence: 99%

Identification of TonB-dependent siderophore receptor inhibitors against Flavobacterium columnare using a structure-based high-throughput virtual screening method

Li,

Chen,

et al. 2024

Front. Microbiol.

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TonB-dependent siderophore receptors play a critical transport role for Flavobacterium columnare virulence formation and growth, and have become valuable targets for the development of novel antimicrobial agents. Traditional Chinese medicine has demonstrated notable efficacy in the treatment of fish diseases and includes potential antibacterial agents. Herein, we performed molecular docking-based virtual screening to discover novel TonB-dependent siderophore receptor inhibitors from traditional Chinese medicine and provide information for developing novel antibacterial agents. Firstly, we efficiently obtained 11 potential inhibitors with desirable drug-like characteristics from thousands of compounds in the TCM library based on virtual screening and property prediction. The antibacterial activity of Enoxolone, along with its interaction characteristics, were determined via an MIC assay and molecular dynamic simulation. Transcriptional profiling, along with validation experiments, subsequently revealed that an insufficient uptake of iron ions by bacteria upon binding to the TonB-dependent siderophore receptors is the antibacterial mechanism of Enoxolone. Finally, Enoxolone's acceptable toxicity was illustrated through immersion experiments. In summary, we have used virtual screening techniques for the first time in the development of antimicrobial agents in aquaculture. Through this process, we have identified Enoxolone as a promising compound targeting the TonB-dependent siderophore receptor of F. columnare. In addition, our findings will provide new ideas for the advancement of innovative antimicrobial medications in aquaculture.

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Section: Methodsmentioning

confidence: 99%

Identification of TonB-dependent siderophore receptor inhibitors against Flavobacterium columnare using a structure-based high-throughput virtual screening method

Li,

Chen,

et al. 2024

Front. Microbiol.

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“…After the analysis, the most reasonable site for the binding of isoflucypram and HSA was selected. We selected Pymol to visualize the complex [48].…”

Section: Molecular Dockingmentioning

confidence: 99%

Probing the Interaction between Isoflucypram Fungicides and Human Serum Albumin: Multiple Spectroscopic and Molecular Modeling Investigations

Li,

Yan,

Yang

et al. 2023

IJMS

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To better understand the potential toxicity risks of isoflucypram in humans, The interaction between isoflucypram and HSA (human serum albumin) was studied through molecular docking, molecular dynamics simulations, ultraviolet–visible absorption, fluorescence, synchronous fluorescence, three-dimensional fluorescence, Fourier transform infrared spectroscopies, and circular dichroism spectroscopies. The interaction details were studied using the molecular docking method and molecular dynamics simulation method. The results revealed that the effect of isoflucypram on human serum albumin was mixed (static and dynamic) quenching. Additionally, we were able to obtain important information on the number of binding sites, binding constants, and binding distance. The interaction between isoflucypram and human serum albumin occurred mainly through hydrogen bonds and van der Waals forces. Spectroscopic results showed that isoflucypram caused conformational changes in HSA (human serum albumin), in which the α-helix was transformed into a β-turn, β-sheet, and random coil, causing the HSA structure to loosen. By providing new insights into the mechanism of binding between isoflucypram and human serum albumin, our study has important implications for assessing the potential toxicity risks associated with isoflucypram exposure.

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Directed evolution of tripartite ATP-independent periplasmic transporter for 3-Hydroxypropionate biosynthesis

Liang

Meng

Wang

et al. 2022

Appl Microbiol Biotechnol

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PyFepRestr: Plugin to PyMOL Molecular Graphics System for Calculating the Free Energy of Ligand‒Receptor Binding

Cited by 7 publications

References 19 publications

Identification of TonB-dependent siderophore receptor inhibitors against Flavobacterium columnare using a structure-based high-throughput virtual screening method

Identification of TonB-dependent siderophore receptor inhibitors against Flavobacterium columnare using a structure-based high-throughput virtual screening method

Probing the Interaction between Isoflucypram Fungicides and Human Serum Albumin: Multiple Spectroscopic and Molecular Modeling Investigations

Directed evolution of tripartite ATP-independent periplasmic transporter for 3-Hydroxypropionate biosynthesis

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