Insights from molecular docking and molecular dynamics on the potential of vitexin as an antagonist candidate against lipopolysaccharide (LPS) for microglial activation in neuroinflammation

• Published in: BMC biotechnology 2021-06, Vol.21 (1), p.38-10, Article 38
• Main Authors: Yahaya, M A F, Bakar, A R Abu, Stanslas, J, Nordin, N, Zainol, M, Mehat, M Z
• Format: Article
• Language: English
• Subjects: Alzheimer's disease; Analysis; Antagonist; Anti-inflammatory agents; Anti-Inflammatory Agents - chemistry; Anti-Inflammatory Agents - pharmacology; Apigenin - chemistry; Apigenin - pharmacology; Atomic properties; Binding energy; Binding sites; Cell surface; Cytokines; Donepezil; Energy; Humans; Inflammation; Ligands; Lipopolysaccharides; Lipopolysaccharides - adverse effects; Lipopolysaccharides - antagonists & inhibitors; Lipopolysaccharides - pharmacology; Microenvironments; Microglia; Microglia - drug effects; Microglia - immunology; Microglial cell; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Neurodegenerative diseases; Neuroinflammation; Neuroinflammatory Diseases - immunology; NF-kappa B - chemistry; NF-kappa B - immunology; NF-κB protein; Proteins; Signal transduction; Simulation; Thermodynamics; TLR4 protein; Toll-Like Receptor 4 - chemistry; Toll-Like Receptor 4 - immunology; Toll-like receptors; Tumor necrosis factor-TNF; Vitexin
• ISSN: 1472-6750; 1472-6750
• DOI: 10.1186/s12896-021-00697-4

Neuroinflammation has been identified to be the key player in most neurodegenerative diseases. If neuroinflammation is left to be unresolved, chronic neuroinflammation will be establish. Such situation is due to the overly-activated microglia which have the tendency to secrete an abundance amount of pro-inflammatory cytokines into the neuron microenvironment. The abundance of pro-inflammatory cytokines will later cause toxic and death to neurons. Toll-like receptor 4 (TLR4)/MD-2 complex found on the cell surface of microglia is responsible for the attachment of LPS and activation of nuclear factor-κB (NF-κB) downstream signalling pathway. Albeit vitexin has been shown to possess anti-inflammatory property, however, little is known on its ability to bind at the binding site of TLR4/MD-2 complex of microglia as well as to be an antagonist for LPS. The present study reveals that both vitexin and donepezil are able to bind at the close proximity of LPS binding site located at the TLR4/MD-2 complex with the binding energy of - 4.35 and - 9.14 kcal/mol, respectively. During molecular dynamic simulations, both vitexin and donepezil formed stable complex with TLR4/MD-2 throughout the 100 ns time length with the root mean square deviation (RMSD) values of 2.5 Å and 4.0 Å, respectively. The root mean square fluctuation (RMSF) reveals that both compounds are stable. Interestingly, the radius of gyration (rGyr) for donepezil shows notable fluctuations when compare with vitexin. The MM-GBSA results showed that vitexin has higher binding energy in comparison with donepezil. Taken together, the findings suggest that vitexin is able to bind at the binding site of TLR4/MD-2 complex with more stability than donepezil throughout the course of 100 ns simulation. Hence, vitexin has the potential to be an antagonist candidate for LPS.