Binding site analysis of full-length alpha1a adrenergic receptor using homology modeling and molecular docking (original) (raw)
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Biochemical and Biophysical Research Communications, 2004
The recent availability of crystal structure of bovine rhodopsin offers new opportunities in order to approach the construction of G protein coupled receptors. This study focuses the attention on the modeling of full-length a 1a adrenergic receptor (a 1a-AR) due to its biological role and significant implications in pharmacological treatment of benign prostate hyperplasia. This work could be considered made up by two main steps: (a) the construction of full structure of a 1a-AR, through homology modeling methods; (b) the automated docking of an endogenous agonist, norepinephrine, and of an antagonist, WB-4101, using BioDock program. The obtained results highlight the key residues involved in binding sites of both agonists and antagonists, confirming the mutagenesis data and giving new suggestions for the rational design of selective ligands.
Proceedings of the International Conference on Bio-inspired Systems and Signal Processing, 2009
Availability of realistic models for human G-Protein Coupled Receptors (hGPCRs) will aid structure-based drug design (SBDD), thus shortening the time period needed for drug development and minimizing crossreactivity of drugs with other hGPCRs. Many researchers have constructed models for hGPCRs with homology modeling techniques based on the X-ray structure of bovine rhodopsin and recently to β2adrenergic receptor which are the only two GPCRs that have high resolution crystal structures. In this study, we evaluate the usefulness of the bovine rhodopsin crystal structures for modeling hGPCRs by analysis of large database of human G-protein coupled receptors that are members of family A (rhodopsin family). The recently released structure of β2-adrenergic receptor was used as a test case for validation purposes of our findings. From pair-wise sequence alignment of each of the receptors in the database to bovine rhodopsin, we come to the conclusion that only for few hGPCRs, X-ray structure of rhodopsin could be used as a template for modeling the trans-membrane domains (TMDs).The detailed analysis of the whole database shows that in general, similarity to bovine rhodopsin is found more in the middle/endoplasmic part than in the exoplasmic part. The shift in the cytoplasmic end of TMD-6 that has been seen in the recently released crystal structure of β2-adrenergic receptor could be understood well from our bioinformatics study. On the basis of our results from this research, we propose to regard specific parts from the endoplasmic domain of the rhodopsin helices as appropriate template for constructing models of other GPCRs, while most of the exoplasmic parts of GPCRs in this family require other techniques for their modeling, due to the low sequence similarity between the receptors and rhodopsin in that region.
Journal of Computer-Aided Molecular Design, 2009
A three-dimensional model of the human adenosine A 2B receptor was generated by means of homology modelling, using the crystal structures of bovine rhodopsin, the b 2-adrenergic receptor, and the human adenosine A 2A receptor as templates. In order to compare the three resulting models, the binding modes of the adenosine A 2B receptor antagonists theophylline, ZM241385, MRS1706, and PSB601 were investigated. The A 2A-based model was much better able to stabilize the ligands in the binding site than the other models reflecting the high degree of similarity between A 2A and A 2B receptors: while the A 2B receptor shares about 21% of the residues with rhodopsin, and 31% with the b 2-adrenergic receptor, it is 56% identical to the adenosine A 2A receptor. The A 2A-based model was used for further studies. The model included the transmembrane domains, the extracellular and the intracellular hydrophilic loops as well as the terminal domains. In order to validate the usefulness of this model, a docking analysis of several selective and nonselective agonists and antagonists was carried out including a study of binding affinities and selectivities of these ligands with respect to the adenosine A 2A and A 2B receptors. A common binding site is proposed for antagonists and agonists based on homology modelling combined with site-directed mutagenesis and a comparison between experimental and calculated affinity data. The new, validated A 2B receptor model may serve as a basis for developing more potent and selective drugs.
Homology Modelling and Docking Studies of Human α2-Adrenergic Receptor Subtypes
Journal of Computer Science & Systems Biology, 2015
α2-adrenergic receptors play a key role in the regulation of sympathetic system, neurotransmitter release, blood pressure and intraocular pressure. Although α2-adrenergic receptors mediate a number of physiological functions in vivo and have great therapeutic potential, the absence of crystal structure of α2-adrenergic receptor subtypes is a major hindrance in the drug design efforts. The therapeutic efficacy of the available drugs is not selective for subtype specificity (α2a, α2b and α2c) leading to unwanted side effects. We used Homology modelling and docking studies to understand and analyze the residues important for agonist and antagonist binding. We have also analyzed binding site volume, and the residue variations which may play important role in ligand binding. We have identified residues through our modelling and docking studies, which would be critical in giving subtype specificity and may help in the development of future subtype-selective drugs.
2009
Availability of realistic models for human G-Protein Coupled Receptors (hGPCRs) will aid structure-based drug design (SBDD), thus shortening the time period needed for drug development and minimizing crossreactivity of drugs with other hGPCRs. Many researchers have constructed models for hGPCRs with homology modeling techniques based on the X-ray structure of bovine rhodopsin and recently to β2adrenergic receptor which are the only two GPCRs that have high resolution crystal structures. In this study, we evaluate the usefulness of the bovine rhodopsin crystal structures for modeling hGPCRs by analysis of large database of human G-protein coupled receptors that are members of family A (rhodopsin family). The recently released structure of β2-adrenergic receptor was used as a test case for validation purposes of our findings. From pair-wise sequence alignment of each of the receptors in the database to bovine rhodopsin, we come to the conclusion that only for few hGPCRs, X-ray structure of rhodopsin could be used as a template for modeling the trans-membrane domains (TMDs).The detailed analysis of the whole database shows that in general, similarity to bovine rhodopsin is found more in the middle/endoplasmic part than in the exoplasmic part. The shift in the cytoplasmic end of TMD-6 that has been seen in the recently released crystal structure of β2-adrenergic receptor could be understood well from our bioinformatics study. On the basis of our results from this research, we propose to regard specific parts from the endoplasmic domain of the rhodopsin helices as appropriate template for constructing models of other GPCRs, while most of the exoplasmic parts of GPCRs in this family require other techniques for their modeling, due to the low sequence similarity between the receptors and rhodopsin in that region.
Journal of Structural Biology, 2005
Antagonist binding to-2 adrenoceptors (2-ARs) is not well understood. Structural models were constructed for the three human 2-AR subtypes based on the bovine rhodopsin X-ray structure. Twelve antagonist ligands (including covalently binding phenoxybenzamine) were automatically docked to the models. A hallmark of agonist binding is the electrostatic interaction between a positive charge on the agonist and the negatively charged side chain of D3.32. For antagonist binding, ion-pair formation would require deviations of the models from the rhodopsin structural template, e.g., a rotation of TM3 to relocate D3.32 more centrally within the binding cavity, and/or creation of new space near TM2/TM7 such that antagonists would be shifted away from TM5. Thus, except for the quinazolines, antagonist ligands automatically docked to the model structures did not form ion-pairs with D3.32. This binding mode represents a valid alternative, whereby the positive charge on the antagonists is stabilized by cation-interactions with aromatic residues (e.g., F6.51) and antagonists interact with D3.32 via carboxylate-aromatic interactions. This binding mode is in good agreement with maps derived from a molecular interaction library that predicts favorable atomic contacts; similar interaction environments are seen for unrelated proteins in complex with ligands sharing similarities with the 2-AR antagonists.
Journal of Computer-Aided Molecular Design, 2006
It is well known that G protein-coupled receptors are prime targets for drug discovery. At the present time there is only one protein from this class that has an X-ray crystal structure, bovine rhodopsin. Crystal structures of rhodopsin have become invaluable templates for the modeling of class-A G proteincoupled receptors as they likely represent the overall topology of this family of proteins. However, because of low sequence homology within the class and the inherent mobility of integral membrane proteins, it is unlikely that this single structural template reflects the ensemble of conformations accessible for any given receptor. We have devised a procedure based upon comparative modeling that uses induced fit modeling coupled with binding site expansion. The modeling protocol enables an ensemble approach to binding mode prediction. The utility of models for b-2 adrenergic receptor will be discussed.
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...
Journal of Medicinal Chemistry
In the present study, more than 75 compounds structurally related to BMY 7378 have been designed and synthesized. Structural variations of each part of the reference molecule have been introduced, obtaining highly selective ligands for the R 1d adrenergic receptor. The molecular determinants for selectivity at this receptor are essentially held by the phenyl substituent in the phenylpiperazine moiety. The integration of an extensive SAR analysis with docking simulations using the rhodopsin-based models of the three R 1-AR subtypes and of the 5-HT 1A receptor provides significant insights into the characterization of the receptor binding sites as well as into the molecular determinants of ligand selectivity at the R 1d-AR and the 5-HT 1A receptors. The results of multiple copies simultaneous search (MCSS) on the substituted phenylpiperazines together with those of manual docking of compounds BMY 7378 and 69 into the putative binding sites of the R 1a-AR, R 1b-AR, R 1d-AR, and the 5-HT 1A receptors suggest that the phenylpiperazine moiety would dock into a site formed by amino acids in helices 3, 4, 5, 6 and extracellular loop 2 (E2), whereas the spirocyclic ring of the ligand docks into a site formed by amino acids of helices 1, 2, 3, and 7. This docking mode is consistent with the SAR data produced in this work. Furthermore, the binding site of the imide moiety does not allow for the simultaneous involvement of the two carbonyl oxygen atoms in H-bonding interactions, consistent with the SAR data, in particular with the results obtained with the lactam derivative 128. The results of docking simulations also suggest that the second and third extracellular loops may act as selectivity filters for the substituted phenylpiperazines. The most potent and selective compounds for R 1d adrenergic receptor, i.e., 69 (Rec 26D/038) and 128 (Rec 26D/073), are characterized by the presence of the 2,5-dichlorophenylpiperazine moiety.