The impact of GPCR structures on pharmacology and structure-based drug design (original) (raw)
Related papers
Journal of Medicinal Chemistry, 2009
Homology modeling of the human A 2A adenosine receptor (AR) based on bovine rhodopsin predicted a protein structure that was very similar to the recently determined crystallographic structure. The inaccuracy of previous antagonist docking is related to the loop structure of rhodopsin being carried over to the model of the A 2A AR and was rectified when the β 2-adrenergic receptor was used as a template is used for homology modeling. Docking of the triazolotriazine antagonist ligand ZM241385 1 was greatly improved by including water molecules of the X-ray structure or by using a constraint from mutagenesis. Automatic agonists docking to both a new homology modeled receptor and the A 2A AR crystallographic structure produced similar results. Heterocyclic nitrogen atoms closely corresponded when the docked adenine moiety of agonists and 1 were overlayed. The cumulative mutagenesis data, which support the proposed mode of agonist docking, can be reexamined in light of the crystallographic structure. Thus, homology modeling of GPCRs remains a useful technique in probing the structure of the protein and predicting modes of ligand docking.
Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures
Protein Science
G protein-coupled receptors (GPCRs) are important drug targets characterized by a canonical seven transmembrane (TM) helix architecture. Recent advances in X-ray crystallography and cryo-EM have resulted in a wealth of GPCR structures that have been used in drug design and formed the basis for mechanistic activation hypotheses. Here, ensemble refinement (ER) of crystallographic structures is applied to explore the impact of binding of agonists and antagonist/inverse agonists to selected structures of cannabinoid receptor 1 (CB1R), β 2 adrenergic receptor (β 2 AR), and A 2A adenosine receptor (A 2A AR). To assess the conformational flexibility and its role in GPCR activation, hydrogen bond (H-bond) networks are analyzed by calculating and comparing H-bond propensities. Mapping pairwise propensity differences between agonist-and inverse agonist/antagonist-bound structures for CB1R and β 2 AR shows that agonist binding destabilizes H-bonds in the intracellular parts of TM 5-7, forming the G protein binding cavity, while H-bonds of the extracellular segment of TMs surrounding the orthosteric site are conversely stabilized. Certain class A GPCRs, for example, A 2A AR, bind an allosteric sodium ion that negatively modulates agonist binding. The impact of sodium-excluding mutants (D52 2.50 N, S91 3.39 A) of A 2A AR on agonist binding is examined by applying ER analysis to structures of wildtype and the two mutants in complex with a full agonist. While S91 3.39 A exhibits normal activity, D52 2.50 N quenches the downstream signaling. The mainchain H-bond pattern of the latter is stabilized in the intracellular part of TM 7 containing the NPxxY motif, indicating that an induced rigidity of the mutation prevents conformational selection of G proteins resulting in receptor inactivation.
A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors
2014
drug design 25 G protein-coupled receptor 26 Drug discovery 27 2 8 a b s t r a c t 29 We have developed a new method for the building of pharmacophores for G protein-coupled receptors, a 30 major drug target family. The method is a combination of the ligand-and target-based pharmacophore 31 methods and founded on the extraction of structural fragments, interacting ligand moiety and receptor 32 residue pairs, from crystal structure complexes. We describe the procedure to collect a library with more 33 than 250 fragments covering 29 residue positions within the generic transmembrane binding pocket. We 34 describe how the library fragments are recombined and inferred to build pharmacophores for new 35 targets. A validating retrospective virtual screening of histamine H 1 and H 3 receptor pharmacophores 36 yielded area-under-the-curves of 0.88 and 0.82, respectively. The fragment-based method has the unique 37 advantage that it can be applied to targets for which no (homologous) crystal structures or ligands are 38 known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element phar-39 macophores. The fragment libraries can also be used to grow known ligands or for rotamer refinement of 40 homology models. Researchers can download the complete fragment library or a subset matching their 41 receptor of interest using our new tool in GPCRDB.
Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation
Nature, 2011
The adenosine receptors and β-adrenoceptors (βARs) are G protein-coupled receptors (GPCRs) that activate intracellular G proteins upon binding agonist such as adenosine 1 or noradrenaline 2 , respectively. GPCRs have similar structures consisting of 7 transmembrane helices that contain well-conserved sequence motifs, suggesting that they are probably activated by a common mechanism 3,4 . Recent structures of βARs highlight residues in transmembrane region 5 that initially bind specifically to agonists rather than to antagonists, suggesting an important role in agonist-induced activation of receptors 5-7 . Here we present two crystal structures of the thermostabilised human adenosine A 2A receptor (A 2A R-GL31) bound to its endogenous agonist adenosine and the synthetic agonist NECA. The structures represent an intermediate conformation between the inactive and active states, because they share all the features of GPCRs that are thought to be in a fully activated state, except that the cytoplasmic end of transmembrane helix 6 partially occludes the G protein binding site. The adenine substituent of the agonists bind in a similar fashion to the chemically-related region of the inverse agonist ZM241385 8 . Both agonists contain a ribose group, not found in ZM241385, which extends deep into the ligand binding pocket where it makes polar interactions with conserved residues in H7 (Ser277 7.42 and His278 7.43 ; superscripts refer to Ballesteros-Weinstein numbering 9 ) and non-polar interactions with residues in H3. In contrast, the inverse agonist ZM241385 does not interact with any of these residues and comparison with the agonist-bound structures suggests that ZM241385 sterically prevents the conformational change in H5 and therefore it acts as an inverse agonist. Comparison of the agonist-bound structures of A 2A R with the agonist-bound structures of β-adrenoceptors suggests that the contraction of the ligand binding pocket caused by the inward motion of helices 3, 5 and 7 may be a common feature in the activation of all GPCRs.
2009
G protein-coupled receptors (GPCRs) constitute a very large family of heptahelical, integral membrane proteins that mediate a wide variety of physiological processes, ranging from the transmission of the light and odorant signals to the mediation of neurotransmission and hormonal actions. GPCRs are dysfunctional or deregulated in several human diseases and are estimated to be the target of more than 40% of drugs used in clinical medicine today. The crystal structures of rhodopsin and the recent published crystal structures of beta-adrenergic receptors and human A2A Adrenergic Receptor provide the information of the three-dimensional structure of GPCRs, which supports homology modeling studies and structure-based drug-design approaches. Rhodopsin-based homology modeling has represented for many years a widely used approach to built GPCR three-dimensional models. Structural models can be used to describe the interatomic interactions between ligand and receptor and how the binding info...
Plos One, 2014
We studied patterns of off-target receptor interactions, mostly at G protein-coupled receptors (GPCRs) in the mM range, of nucleoside derivatives that are highly engineered for nM interaction with adenosine receptors (ARs). Because of the considerable interest of using AR ligands for treating diseases of the CNS, we used the Psychoactive Drug Screening Program (PDSP) for probing promiscuity of these adenosine/adenine congeners at 41 diverse receptors, channels and a transporter. The step-wise truncation of rigidified, trisubstituted (at N 6 , C2, and 59 positions) nucleosides revealed unanticipated interactions mainly with biogenic amine receptors, such as adrenergic receptors and serotonergic receptors, with affinities as high as 61 nM. The unmasking of consistent sets of structure activity relationship (SAR) at novel sites suggested similarities between receptor families in molecular recognition. Extensive molecular modeling of the GPCRs affected suggested binding modes of the ligands that supported the patterns of SAR at individual receptors. In some cases, the ligand docking mode closely resembled AR binding and in other cases the ligand assumed different orientations. The recognition patterns for different GPCRs were clustered according to which substituent groups were tolerated and explained in light of the complementarity with the receptor binding site. Thus, some likely off-target interactions, a concern for secondary drug effects, can be predicted for analogues of this set of substructures, aiding the design of additional structural analogues that either eliminate or accentuate certain off-target activities. Moreover, similar analyses could be performed for unrelated structural families for other GPCRs.
Structure and dynamics of G-protein coupled receptors
Advances in experimental medicine and biology, 2014
G-protein coupled receptors (GPCRs) are seven helical transmembrane proteins that mediate cell-to-cell communication. They also form the largest superfamily of drug targets. Hence detailed studies of the three dimensional structure and dynamics are critical to understanding the functional role of GPCRs in signal transduction pathways, and for drug design. In this chapter we compare the features of the crystal structures of various biogenic amine receptors, such as β1 and β2 adrenergic receptors, dopamine D3 receptor, M2 and M3 muscarinic acetylcholine receptors. This analysis revealed that conserved residues are located facing the inside of the transmembrane domain in these GPCRs improving the efficiency of packing of these structures. The NMR structure of the chemokine receptor CXCR1 without any ligand bound, shows significant dynamics of the transmembrane domain, especially the helical kink angle on the transmembrane helix6. The activation mechanism of the β2-adrenergic receptor h...
Journal of Structural Biology, 2010
a b s t r a c t G protein-coupled receptors (GPCRs) are therapeutic targets for many diseases, but progress in developing active and selective therapeutics has been severely hampered by the difficulty in obtaining accurate structures. We have been developing methods for predicting the structures for GPCR ligand complexes, but validation has been hampered by a lack of experimental structures with which to compare our predictions. We report here the predicted structures of the human adenosine GPCR subtypes (A 1 , A 2A , A 2B , and A 3 ) and the binding sites for adenosine agonist and eight antagonists to this predicted structure, making no use of structural data, and compare with recent experimental crystal structure for ZM241385 bound human A 2A receptor. The predicted structure correctly identifies 9 of the 12 crystal binding site residues. Moreover, the predicted binding energies of eight antagonists to the predicted structure of A 2A correlate quite well with experiment. These excellent predictions resulted when we used Monte Carlo techniques to optimize the loop structures, particularly the cysteine linkages. Ignoring these linkages led to a much worse predicted binding site (identifying only 3 of the 12 important residues).