3-Dimensional Structures of G Protein-Coupled Receptors and Binding Sites of Agonists and Antagonists

Goddard, William A.; Abrol, Ravinder

doi:10.1093/jn/137.6.1528s

Cited by 40 publications

(39 citation statements)

References 32 publications

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“…The results reported here are comparable to those from other similar works [19][20][21][22] which showed that GPCR modeling [23][24][25][26][27][28][29][30][31] in the absence of a crystal structure can be a valid replacement [32][33][34][35][36][37][38][39] for structural and functional exploration of GPCR receptors, and for the discovery [21,[40][41][42][43], VS [44][45][46][47][48][49][50][51][52] and optimisation [23,53] of their ligands.…”

Section: Introductionsupporting

confidence: 90%

From Receptors to Ligands: Fragment-assisted Drug Design for GPCRs Applied to the Discovery of H3 and H4 Receptor Antagonists

Àlex¹,

Heifetz²,

Mazanetz³

et al. 2013

Med chem

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G-Protein Coupled Receptors (GPCRs) have enormous physiological and biomedical importance, being the primary target of a large number of modern drugs. The availability of structural information of the binding site of the targeted GPCR plays a key role in rationalization, efficiency and cost-effectiveness of the drug discovery process. However, obtaining structural information on GPCRs using X-ray crystallography or NMR requires a large investment of time and is technically very challenging. This situation significantly limits the ability of these methods to have an impact in drug discovery for GPCR targets in the short term and hence there is an urgent need for other effective and cost-efficient alternatives. We present here a practical approach that integrates GPCR modelling with fragment based screening to provide structural insights on the H3 and H4 histamine receptor binding sites. This approach creates a cost-efficient new avenue for structure-based drug design (SBDD) against GPCR targets. We report here a success of using this protocol for the discovery of selective and dual H3 and H4 antagonists. Our fragment screen yielded 44 H3, 21 H4 selective and 20 dual fragment hits. These fragments were used to construct high-quality H3 and H4 models followed by binding site exploration and structure based virtual screening (VS). Overall, 172 compounds were purchased for testing based on the virtual screening results. Of the 74 compounds predicted to have dual activity, 33 had activity against one or other of the two receptors (44%), of which 17 had activity against both. Of the 19 compounds predicted to be H3 selective, 13 were active against H3 (68%) and 10 of these also had selectivity over H4. Of the 79 compounds predicted to be H4 selective, 36 were active against H4 (45%) and 2 of these also had selectivity over H3.

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Section: Introductionsupporting

confidence: 90%

From Receptors to Ligands: Fragment-assisted Drug Design for GPCRs Applied to the Discovery of H3 and H4 Receptor Antagonists

Àlex¹,

Heifetz²,

Mazanetz³

et al. 2013

Med chem

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“…Unlike most nonolfactory GPCRs, which use ionic or hydrogen bond interactions to ensure selectivity and sensitivity in binding their agonists or antagonists (22), ORs bind to their ligands via much weaker van der Waals interactions (14,16,23). It is conceivable that at least some ORs have a permissive binding The total response is the sum of the responses to all five odorants at 300 μM, normalized to that of WT MOR256-3 tested on the same plate and corrected for surface expression.…”

Section: Discussionmentioning

confidence: 99%

Responsiveness of G protein-coupled odorant receptors is partially attributed to the activation mechanism

March²,

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Mammals detect and discriminate numerous odors via a large family of G protein-coupled odorant receptors (ORs). However, little is known about the molecular and structural basis underlying OR response properties. Using site-directed mutagenesis and computational modeling, we studied ORs sharing high sequence homology but with different response properties. When tested in heterologous cells by diverse odorants, MOR256-3 responded broadly to many odorants, whereas MOR256-8 responded weakly to a few odorants. Out of 36 mutant MOR256-3 ORs, the majority altered the responses to different odorants in a similar manner and the overall response of an OR was positively correlated with its basal activity, an indication of ligand-independent receptor activation. Strikingly, a single mutation in MOR256-8 was sufficient to confer both high basal activity and broad responsiveness to this receptor. These results suggest that broad responsiveness of an OR is at least partially attributed to its activation likelihood.

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“…Chitobiose units were then docked into the two binding sites, determined by unbiased scanning of the OmpA receptor (see supplemental Methods) using our GenDock procedure (32). GenDock has been validated to predict accurate binding sites in previous studies (33)(34)(35)(36)(37)(38). Here, we generated Ͼ2,000,000 ligand poses and selected the best pose based on the ligand interaction energy with the binding pocket.…”

Section: Methodsmentioning

confidence: 99%

Experimental Validation of the Predicted Binding Site of Escherichia coli K1 Outer Membrane Protein A to Human Brain Microvascular Endothelial Cells

Pascal

Abrol

Mittal

et al. 2010

Journal of Biological Chemistry

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Escherichia coli K1, the most common cause of meningitis in neonates, has been shown to interact with GlcNAc1-4GlcNAc epitopes of Ecgp96 on human brain microvascular endothelial cells (HBMECs) via OmpA (outer membrane protein A). However, the precise domains of extracellular loops of OmpA interacting with the chitobiose epitopes have not been elucidated. We report the loop-barrel model of these OmpA interactions with the carbohydrate moieties of Ecgp96 predicted from molecular modeling. To test this model experimentally, we generated E. coli K1 strains expressing OmpA with mutations of residues predicted to be critical for interaction with the HBMEC and tested E. coli invasion efficiency. For these same mutations, we predicted the interaction free energies (including explicit calculation of the entropy) from molecular dynamics (MD), finding excellent correlation (R 2 ‫؍‬ 90%) with experimental invasion efficiency. Particularly important is that mutating specific residues in loops 1, 2, and 4 to alanines resulted in significant inhibition of E. coli K1 invasion in HBMECs, which is consistent with the complete lack of binding found in the MD simulations for these two cases. These studies suggest that inhibition of the interactions of these residues of Loop 1, 2, and 4 with Ecgp96 could provide a therapeutic strategy to prevent neonatal meningitis due to E. coli K1.Neonatal bacterial meningitis is one of the most serious infections of the central nervous system, resulting in significant neurological sequelae (such as hearing loss, convulsive disorders, abnormal speech patterns, cortical blindness, and mental retardation) in half of the survivors (1-4). The incidence of bacterial meningitis in infants is about five cases per 100,000 live births per year in developed countries but can be 10 times higher in underdeveloped countries (5).Escherichia coli K1 is the predominant pathogen causing neonatal meningitis and septicemia (6). The mortality and morbidity due to E. coli K1 has remained significant in the last few decades, despite the use of effective antimicrobial therapy. This poor outcome is due to increased antibiotic resistance of E. coli, possibly due to their use in food stock (7) and the high adaptive mutation ability of E. coli (shown to be on the order of 10 Ϫ5 per genome per generation) (8).Our previous experimental studies in the newborn rat model of hematogenous meningitis demonstrated that a high degree of bacteremia is required for the onset of meningitis (9). We showed that the entry of E. coli K1 into human brain microvascular endothelial cells (HBMEC), 3 which comprise the lining of the blood-brain barrier, requires the expression of a 35-kDa OmpA (outer membrane protein A) in E. coli K1 (10).In addition, we and others (9 -12) showed that OmpA expression is important for entry of monocytes, macrophages, and dendritic cells, indicating the important role of this protein in the pathogenesis of neonatal meningitis by E. coli K1. We also showed that the interaction of OmpA with Ecgp96 (a homologue of Hs...

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3-Dimensional Structures of G Protein-Coupled Receptors and Binding Sites of Agonists and Antagonists

Cited by 40 publications

References 32 publications

From Receptors to Ligands: Fragment-assisted Drug Design for GPCRs Applied to the Discovery of H3 and H4 Receptor Antagonists

From Receptors to Ligands: Fragment-assisted Drug Design for GPCRs Applied to the Discovery of H3 and H4 Receptor Antagonists

Responsiveness of G protein-coupled odorant receptors is partially attributed to the activation mechanism

Experimental Validation of the Predicted Binding Site of Escherichia coli K1 Outer Membrane Protein A to Human Brain Microvascular Endothelial Cells

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