Exploring the binding mechanism of ferulic acid and ovalbumin: Insights from spectroscopy, molecular docking and dynamics simulation

2021 ◽  
Author(s):  
Lei Chen ◽  
Miao Zhu ◽  
Xing Hu ◽  
Junhui Pan ◽  
Guowen Zhang
Keyword(s):  
Molecular Docking ◽  
Ferulic Acid ◽  
Dynamics Simulation ◽  
Binding Mechanism ◽  
Molecular Docking And Dynamics

Synthesis, Molecular Docking and Dynamics Simulation Studies of New 7-oxycoumarin Derivatives as Potential Antioxidant Agents

2018 ◽  
Vol 18 (18) ◽  
pp. 1572-1587
Author(s):  
Nehad A. Abdel Latif ◽  
Rasha Z. Batran ◽  
Salwa F. Mohamed ◽  
Mohammed A. Khedr ◽  
Mohamed I. Kobeasy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Antioxidant Agents ◽  
Molecular Docking And Dynamics

scholarly journals Study of Caspase 8 Inhibition for the Management of Alzheimer’s Disease: A Molecular Docking and Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2071
Author(s):  
Syed Sayeed Ahmad ◽  
Meetali Sinha ◽  
Khurshid Ahmad ◽  
Mohammad Khalid ◽  
Inho Choi
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Docking ◽  
Md Simulation ◽  
Simulation Analysis ◽  
Dynamics Simulation ◽  
Caspase 8 ◽  
Amino Acid Residues ◽  
The Stability ◽  
Molecular Docking And Dynamics

Alzheimer’s disease (AD) is the most common type of dementia and usually manifests as diminished episodic memory and cognitive functions. Caspases are crucial mediators of neuronal death in a number of neurodegenerative diseases, and caspase 8 is considered a major therapeutic target in the context of AD. In the present study, we performed a virtual screening of 200 natural compounds by molecular docking with respect to their abilities to bind with caspase 8. Among them, rutaecarpine was found to have the highest (negative) binding energy (−6.5 kcal/mol) and was further subjected to molecular dynamics (MD) simulation analysis. Caspase 8 was determined to interact with rutaecarpine through five amino acid residues, specifically Thr337, Lys353, Val354, Phe355, and Phe356, and two hydrogen bonds (ligand: H35-A: LYS353:O and A:PHE355: N-ligand: N5). Furthermore, a 50 ns MD simulation was conducted to optimize the interaction, to predict complex flexibility, and to investigate the stability of the caspase 8–rutaecarpine complex, which appeared to be quite stable. The obtained results propose that rutaecarpine could be a lead compound that bears remarkable anti-Alzheimer’s potential against caspase 8.

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