GPCRHomology Model Development and Application

Abstract

G‐protein‐coupled receptors (GPCRs) are a very important class of proteins for drug discovery. Exciting progress has been made recently in the determination of X‐ray crystal structures. However, despite this, structural coverage of the receptor family is still thin. We lack direct structural knowledge of many important subfamilies, we have only modest detail of the conformational changes associated with receptor activation and we lack robust crystallographic systems for the rapid determination of ligand binding modes. As a consequence, the ability to build and apply homology models for drug discovery at these targets is very valuable. The accuracy of the models has improved in parallel with the increase in available structural data and the models have been successfully applied to a wide range of lead generation and optimization problems.

Biophysical Mapping of the Adenosine A2A Receptor

“…Differences, not surprisingly, were also seen in residues emanating from the loops which are notoriously difficult to model, notably in the exact position of Phe168 on ECL2, which forms stacking interactions with the ligand in the site. 11 , 32 However, the most important difference affecting the binding pose of the ligand ZM241385 between our model and the crystal structure (PDB: 3EML ) was the chi1 angle of Tyr271. In the 3EML crystal structure, chi1 of Tyr271 is in a gauche negative rotameric state, compared to the trans conformation in our model, which causes the flexible phenolic portion of ZM241385 to sit in quite different positions comparing the two binding poses.…”

“…This technique is extremely powerful in identifying which residues are involved in ligand recognition and binding or catalysis. 11 Typically, mutations that cause significant changes in binding affinity are consistent with the participation of their side chains in direct ligand interactions, although confounding factors such as “second shell” effects, changes in solvent structure, and conformational rearrangements or perturbations may complicate interpretation. Critically, the requirement for binding measurements using labeled compounds typically limits studies to one or a few exemplary ligands, and literature data is consequently often incomplete or conflicting, comprising a sparse matrix of data.…”

“…SDM is a technique commonly used in molecular pharmacology whereby residues of a protein with a known sequence are mutated to differing residues so that the effect on binding of the radioligand being used in the assay can be determined. This technique is extremely powerful in identifying which residues are involved in ligand recognition and binding or catalysis . Typically, mutations that cause significant changes in binding affinity are consistent with the participation of their side chains in direct ligand interactions, although confounding factors such as “second shell” effects, changes in solvent structure, and conformational rearrangements or perturbations may complicate interpretation.…”

Progress in Structure Based Drug Design for G Protein-Coupled Receptors

“…This and additional structures of the inactive dark-state rhodopsin then provided the basis for GPCR modeling during the following 8 years . A great deal of work has been done using bovine rhodopsin as the template for homology modeling of other GPCRs, and there are a number of reviews dealing with these developments. − However, there are several problems associated with rhodopsin as a starting point for GPCR modeling. , First, although rhodopsin shares overall structural features with other family A GPCRs, the actual homology is less than 25% and for other GPCR families such as the secretin, adhesion, and metabotropic receptors, there is no detectable sequence homology at all with rhodopsin. Second, since retinal is covalently bound to the receptor, rhodopsin is likely to have a very different mechanism of activation to other receptors with noncovalent ligands.…”

Are GPCRs Still a Source of New Targets?

“…166 There is also a substantial amount of expertise in the use of homology models for drug design. 167 This is still highly relevant given the relatively small number of receptors for which there is currently structural information. There remain major gaps in our structural knowledge as compared with the GPCR classification scheme outlined above, although the availability of crystal structures for an increasing range of aminergic receptors, certain peptide receptors, and a lipid receptor is a major step forward.…”