Combination of Molecular Modeling, Site-Directed Mutagenesis, and SAR Studies To Delineate the Binding Site of Pyridopyrimidine Antagonists on the Human CCK1 Receptor

Abstract

A rational combination of site-directed mutagenesis studies, structure-activity relationships, and dynamic-based docking of pyridopyrimidine-derived CCK1R antagonists into a refined three-dimensional model of the CCK1R allowed us to identify the receptor residues and the ligand functional groups implicated in the molecular recognition process. Our results provided unambiguous evidence that the binding site of these antagonists is overlapping that of the C-terminal tetrapeptide of CCK. In particular, Asn333 and Arg336 residues of the CCK1R are essential for high-affinity binding of these ligands. Moreover, the 2-aryl group in the pyridopyrimidine derivatives shares the same binding pocket as the C-terminal Phe side chain of CCK. Our [pyridopyrimidine.CCK1R] complex model is consistent with previous suggestions concerning the molecular basis that governs functional activity and provides useful considerations about the high CCK1 versus CCK2 selectivity of our derivatives and could contribute to fine-tune the rational design of new molecules with optimized properties.

Partial Agonism, Neutral Antagonism, and Inverse Agonism at the Human Wild-Type and Constitutively Active Cholecystokinin-2 Receptors

“…Therefore, conducted refinements show that Asn353 played a donor role in complexes with L365,260, YM022, GV150,013X, and RPR101,048 and an acceptor role in complexes with PD135,158. In accordance with these results, previous study about the identification of the binding site of pyridopyrimidine antagonists on the human CCK1R using a different strategy involved Asn333 (corresponding residues to Asn353 of CCK2R), and this residue was found to play a donor role (Martin-Martinez et al, 2005).…”

“…As we documented previously with the CCK1R, automated docking of small ligands, such as those tested here, is a hazardous task because of their "chemical symmetry", which produced scoring functions similar to those of the binding energy (Martin-Martinez et al, 2005). Indeed, for most of the nonpeptide ligands tested, several plausible positions were generated by in silico docking in the modeled CCK2R binding site.…”

Structural basis of cholecystokinin receptor binding and regulation

“…Indeed, extensive receptor mutagenesis has been performed exploring the basis of binding of these compounds (Kopin et al, 1994). Of note, in both subtypes of CCK receptors, mutagenesis studies point to the importance of a pocket in the upper third of the lipid bilayer within the helical confluence as a potential site of docking these compounds (Martin-Martinez et al, 2005). This location has been further supported with a recent study in which a benzodiazepine ligand for the CCK 1 receptor was directly identified in a photoaffinity labeling experiment (Hadac et al, 2006).…”

Synthesis and Structure Activity Relationship of Some Indole Derivatives as Potential Anti-inflammatory Agents

“…[67][68][69][70] 3D-QSAR and docking studies were carried out on 23 pyrrole derivatives, to model their HIV-1 gp41 inhibitory activities. The 2D, 3D-QSAR studies were performed using CODESSA software package and comparative molecular field analysis (CoMFA It also helps in the interpretation and explanation of the biological results.…”

“…Molecular docking is one of these approaches and is used to predict the binding mode of organic compounds. 68 A molecular docking study had been done using both MOE 2013.08 71 and Leadit 2.1.2 software. 72,73 Possible binding modes of the active compounds inside the active site of COX-2 were estimated.…”