Resumen de Structure-function studies of bombesin and bradykinin receptors and their ligands for new therapeutic opportunities
G-protein coupled receptors represents the largest family of membrane protein in eukaryotes cells with more than 800 members. The reason of their importance lies in their function, being responsible for the primary mechanism of signal transduction from the extracellular side to the cytosol of cells as well as responsible for controlling vesicle transport, ion channel, and enzyme activity. Defect in the GPCRs signal transduction process cause disorder in body organs such as cancer, color blindness, obesity, pain, depression, hyperthyroid adenoma, diabetes, schizophrenia. Hence, due to the important role they play in the body, they are target for 30% of the drugs in the market. The development of novel drugs targeting GPCRs highly depends on a solid structure-function relationships knowledge.
Despite the variety of the GPCRs encoded in the human genome, they exhibit the same architecture however they represent a large variation in the structure. Also, despite efforts carried out to determine the crystal structures of the G-PCRs, still, there are numerous challenges of for crystallization of them. Despite the publication of a number of crystallographic structures in the last years, there are many GPCrs which structure is not determined. Homology modeling is a method that can help to study both the structure and function of the GPCRs and it can provide more information when the process continues to the virtual screening. Homology modeling with the help of molecular dynamics simulation can discover the dynamic behavior of GPCRs by the means of discovering their conformational change. This method is an economic method for discovering novel drugs as well as explaining their structure-activity relationship and pharmacology in the step before experimental methods.
In the present study, we constructed an 3Dstructure of six GPCRs, including M3 muscarinic receptor, bradykinin B1 receptor, Bradykinin B2 receptor, neuromedin receptor(BB1R), Gastrin-releasing peptide receptor (BB2R), and bombesin receptor subtype 3(BB3R). Models were constructed using the closest the closest structure available in the phylogenetic tree as template. In regard to M3 muscarinic, the aim of the study was the evaluation of structure refinement using molecular dynamics and the effect of the template selection, presence of a ligand in the refinement process on the accuracy of the models constructed. In regards to the bradykinin receptor, the models of bradykinin B1 receptor and bradykinin B2 receptors were constructed in a previous study of the group. Then, pharmacophore definition was done and subsequent virtual screening led to the discovery of some novel small molecules with antagonist activity. In the present study, the pharmacophore of the two receptors was compared to understand specific molecular features of the small molecules bradykinin ligands that make them selective for each one of these receptors. Finally, for discovering the novel chemical scaffolds for the three bombesin receptors the models of each subtype of the bombesin receptor were constructed from neurotensin receptor (NTS1), and the refinement of 500 ns was performed for each one of the models.
The results of the present study show that in the refinement process, the closer the template is to the target receptor and the use of a ligand in the refinement process can lead to model accurate models. Also, the selectivity of the small molecules bradykinin receptors was identified properly by comparison of the pharmacophores of two receptors . Finally, the study of the features of bombesin receptors led to the discovery of novel small molecules with antagonist activity for BB1R and important residues of BB2R and BB3R for further mutagenesis study.
