Binding mode of chitin and TLR2 via molecular docking and dynamics simulation. Issue 11 (23rd July 2016)

• Record Type: Journal Article
• Authors: Shen, Peicheng; Li, Wenwen; Wang, Ying; He, Xiao; He, Liqun
• Is Part Of: Molecular simulation. Volume 42:Issue 11(2016)
• Page Start: 936
• Page End: 941
• Publication Date: 2016-07-23
• Subjects: IgAN -- toll-like receptor -- traditional Chinese Medicine -- molecular docking -- molecular dynamics simulation -- MM/PBSA -- binding free energy; Molecular dynamics -- Computer simulation -- Periodicals; Statistical mechanics -- Computer simulation -- Periodicals; 539.6
• DOI: 10.1080/08927022.2015.1124102
• Languages: English
• ISSNs: 0892-7022

Abstract

Abstract: Innate immunity is an important part of immune system, providing immediate defence for the host against various infections through phagocytes. Toll-like receptors (TLRs) are major proteins expressed on the cell membrane known as pattern recognition receptors (PRR) that recognise non-self molecules (pathogen-associated molecular patterns (PAMPs)). Because TLRs have been implicated in many inflammatory diseases and cancer, TLRs targeted therapeutics have drawn great attention in clinical application in wide range of conditions. Many of them are undergoing evaluation in clinical trials. Chitin is the second most abundant polysaccharide detected in many insects and fungi. Studies have shown that chitin, as major PAMPs in host-infection, can activate TLR2-dependent innate immunity pathway. Therefore, chitin has potential use as an important agonist or antagonist to control key processes in innate immunity. However, no direct evidence has shown that chitin is the direct target of TLR2. This study first demonstrates a binding model of chitin and TLR2 and then confirmed its stability by molecular dynamic simulation and MM/PBSA (molecular mechanics/Poisson−Boltzmann surface area) calculations. The binding between chitin and TLR2 was taken place inside the binding pocket. Two hydrogen bonds were formed between chitin and TLR2, including Ser320 and Lys321. The van der Waals interaction has the major contribution in stabilising the binding of the chitin molecule with the protein. This study also suggests six hot-spots for specific binding of chitin in the binding site of TLR2, namely, Phe296, Phe299, Leu302, Thr309, Ser320 and Val322. Molecular dynamics simulation demonstrates that the complex of chitin and TLR2 is very stable with a total binding affinity of −27.2 kcal/mol from MM/PBSA calculation.