In silico selections for design of anti-inflammatory therapeutic molecules

• Main Authors: Wen-Yi Chen, 陳文藝
• Other Authors: Je-Wen Liou
• Format: Others
• Language: en_US
• Published: 2012
• Online Access: http://ndltd.ncl.edu.tw/handle/54215293572649529406

碩士 === 慈濟大學 === 微生物學免疫學暨生物化學碩士班 === 100 === Background: Human CXCL8 plays important roles in inflammation by activation of neutrophils through hCXCR1 and hCXCR2 receptors. The role of hCXCR1 and hCXCR2 in the pathogenesis of inflammatory responses has encouraged the development of antagonists of these receptors. Due to the fact that hCXCR1 and hCXCR2 are membrane proteins, they are difficult to be purified for X-ray crystallography. Therefore, hCXCR1 and hCXCR2 structures have not yet existed in ProteinDataBank. In this study, we simulated the three-dimensional structure of CXCR1 using homology modeling. And this structure is used for molecular docking in order to design anti-inflammatory drugs. Methodology/Principal Findings: Using the Phyre2 which applies a profile-profile alignment algorithm for searching the ideal template, 1U19, a new high-resolution (2.2 A) structure, was found. We performed homology modeling to construct 100 structures of hCXCR1 using Discovery Studio v. 3.1 by superimposed and analyzed top 10 structures with minimized energy. The Root Mean Squarer Deviation (RMSD) of these 10 structures was less than 0.4 A. The CXCR1 model was obtained by averaging the top10 structures. Subsequently, the CXCL8 and CXCR1 were docked to simulate the specific binding sites. The results showed that there were three fragments which might be important for the ligand-receptor binding. All the forces between the receptor and the ligand were calculated with the ZRank. The selected peptides were then synthesized and tested for their functions on the THP-1cell using flow cytometry. Summary/Significance: Our simulation results demonstrated that there are a large number of attractions between the selected peptides and CXCR1, such us hydrogen bonds and van der Waals forces. As observed in flow cytometry study, selected peptides did indeed associate with the cells. However, it is still not certain if the selected peptides have the ability to compete with CXCL8 so far.