3D Structure Homology Modeling Of Somatostatin Receptors And The Study Of The Interaction To Its Ligands

Somatostatin Receptor (SSTR) is 7 trans membrane helices structure. SST is its endogenetic ligand. SSTR with five subtypes belongs to G-protein coupled receptor (GPCR) family, which structures are trans membrane helices. Because membrane protein is hard to be separated and purified so far, there are not so many crystal structures of GPCR protein in PDB. GPCRs have conservative and inerratic trans membrane helices region that could build their models by comparative molecular modeling, or called homology modeling. Homology modeling has most successful examples in GPCR family.To build a high quality 3D structure of SSTR, which could be a target for drug design, Bioinformatics and Molecular Dynamics Methods are used. 10 crystal structures of G-Protein coupled receptor (GPCR) in PDB were used as homological models to construct the 3D structures of Homo sapiens somatostatin receptor. Blast 2 software was used to align the sequence homology and similarity between the targets and the models. The conformation of the 3D structures refined with free energy minimized by GROMOS force field. To study the interaction between the receptor and the ligand, GRAMM program for protein-protein molecular docking was used to dock the modeled receptor's 3D structure and one of the ligands—octreotide. This article has built 5 subtype 3D structures of SSTR by homology modeling, and molecular docking between the hSSTR2 model and one of its ligand, octreotide was processed for analyzing the interaction between them. The active site in the receptor probably composed by phe 116 in 2nd extracell loop, cys 182,Ile184, phe 197, thr201 in 3rd extracell loop, and val288 in 4th extracell loop, which formed a hydrophobic pocket, embedding octreotide molecule. Also, Asn114 in 2nd loop, thr201 in 3rd loop contribute electrostatic interaction to the ligand. Benzene ring of phe197 is parallel to the benzazole ring of the ligand in Trp4 approximately, which produces aπ-πbond.To synthesize SST-14 and a new SST analogue (sequence is ala-[cys-lys-trp-lys-phe-thr-ser-cys]), solid phase method is used. Wang resin was used as loader; coupler was HBTU and cleaver was TFA. 2 SH- were oxidized to form a S-S bind. Mass spectrum and amino acid analysis methods were used to verify the structures, and the results show the synthesized peptides are correct.