Identification of the binding sites and selectivity of sarpogrelate, a novel 5-HT₂ antagonist, to human 5-HT_2A, 5-HT_2B and 5-HT_2C receptor subtypes by molecular modeling

The aim of the present study was to investigate the binding sites interactions and the selectivity of sarpogrelate to human 5-HT₂ receptor family (5-HT_2A, 5-HT_2B and 5-HT_2C receptor subtypes) using molecular modeling. Rhodopsin (RH) crystal structures were used as template to build structural models of the human serotonin-2A and -2C receptors (5-HT_2AR, 5-HT_2CR), whereas for 5-HT_2BR, we used our previously published three-dimensional (3D) models based on bacteriorhodopsin (BR). Sarpogrelate, a novel 5-HT₂R antagonist, was docked to the receptors. Molecular dynamics (MD) simulations produced the strongest interaction for 5-HT_2AR/sarpogrelate complex. Upon binding, sarpogrelate constraints aromatic residues network (Trp^3.28, Phe^5.47, Trp^6.48, Phe^6.51, Phe^6.52 in 5-HT_2AR; Phe^3.35, Phe^6.51, Trp^7.40 in 5-HT_2BR; Trp^3.28, Phe^3.35, Phe^5.47, Trp^6.48, Phe^6.51, Phe^6.52 in 5-HT_2CR) in a stacked configuration, preventing activation of the receptor. The models suggest that the structural origin of the selectivity of sarpogrelate to 5-HT_2AR vs both 5-HT_2BR and 5-HT_2CR comes from the following results: (1) The tight interaction between the antagonist and the transmembrane domain (TMD) 3. Asp^3.32 neutralizes the cationic head and interacts simultaneously with carboxylic group hydrogen of the antagonist molecule. (2) Due to steric hindrance, Ser^5.46 (vs Ala^5.46 in 5HT_2B and 5HT_2C) prevents sarpogrelate to enter deeply inside the hydrophobic core of the helix bundle and to interact with Pro^5.50. (3) The side chain of Ile^4.56 (vs Ile^4.56 in 5HT_2BR and Val^4.56 in 5HT_2CR) constraints sarpogrelate to adjust its position by translating toward the strongly attractive Asp^3.32. These results are in good agreement with binding affinities (pKi) of sarpogrelate for 5-HT₂ receptor family expressed in transfected cell.