Receptor Activation Process Research Articles

Identification of potential agonist-like molecules for α2-adrenergic receptor by multi-layer virtual screening to combat sinusitis

Sinusitis is one of the most common respiratory inflammatory conditions and a significant health issue that affects millions of people worldwide with a global prevalence of 10–15%. The side effects of available drug regimens of sinus infection demand the urgent development of new drug candidates to combat sinusitis. With the aim of identifying new drug-like candidates to control sinus, we have conducted multifold comprehensive screening of drug-like molecules targeting α2-adrenergic receptor (α2-AR), which serve as the primary drug target in sinusitis. By structure-based virtual screening of in-house compound's database, ten molecules (CP1-CP10) with agonistic effects for α2-AR were selected, and their binding mechanism with critical residues of α2-AR and their physicochemical properties were studied. Moreover, the process of receptor activation by these compounds and the conformational changes in α2-AR caused by these molecules, were further explored by molecular dynamic simulation. The MM-PBSA estimated free energies of compounds are higher than that of reference agonist (ΔGTOTAL = ˗39.0 kcal/mol). Among all, CP2-CP3, CP7-CP8 and CP6 have the highest binding free energies of ˗78.9 kcal/mol, ˗77.3 kcal/mol, ˗75.60 kcal/mol, ˗64.8 kcal/mol, and ˗61.6 kcal/mol, respectively. While CP4 (˗55.0 kcal/mol), CP5 (˗49.2 kcal/mol), CP9 (˗54.8 ± 0.07 kcal/mol), CP10 (˗56.7 ± 0.10 kcal/mol) and CP1 (˗46.0 ± 0.08 kcal/mol) also exhibited significant binding free energies. These energetically favorable binding energies indicate strong binding affinity of our compounds for α2-AR as compared to known partial agonist. Therefore, these molecules can serve as excellent drug-like candidates for sinusitis.

Photoswitchable Probes of Oxytocin and Vasopressin.

Oxytocin (OT) and vasopressin (VP) are related neuropeptides that regulate many biological processes. In humans, OT and VP act via four G protein-coupled receptors, OTR, V1aR, V1bR, and V2R (VPRs), which are associated with several disorders. To investigate the therapeutic potential of these receptors, particularly in the receptor-dense areas of the brain, molecular probes with a high temporal and spatial resolution are required. Such a spatiotemporal resolution can be achieved by incorporating photochromic moieties into OT and VP. Here, we report the design, synthesis, and (photo)pharmacological characterization of 12 OT- and VP-derived photoprobes using different modification strategies. Despite OT's and VP's sensitivity toward structural changes, we identified two photoprobes with good potency and photoswitch window for investigating the OTR and V1bR. These photoprobes should be of high value for producing cutting-edge photocontrollable peptide probes for the study of dynamic and kinetic receptor activation processes in specific regions of the brain.

Autoregulation of GPCR signalling through the third intracellular loop

The third intracellular loop (ICL3) of the G protein-coupled receptor (GPCR) fold is important for the signal transduction process downstream of receptor activation1–3. Despite this, the lack of a defined structure of ICL3, combined with its high sequence divergence among GPCRs, complicates characterization of its involvement in receptor signalling4. Previous studies focusing on the β2 adrenergic receptor (β2AR) suggest that ICL3 is involved in the structural process of receptor activation and signalling5–7. Here we derive mechanistic insights into the role of ICL3 in β2AR signalling, observing that ICL3 autoregulates receptor activity through a dynamic conformational equilibrium between states that block or expose the receptor’s G protein-binding site. We demonstrate the importance of this equilibrium for receptor pharmacology, showing that G protein-mimetic effectors bias the exposed states of ICL3 to allosterically activate the receptor. Our findings additionally reveal that ICL3 tunes signalling specificity by inhibiting receptor coupling to G protein subtypes that weakly couple to the receptor. Despite the sequence diversity of ICL3, we demonstrate that this negative G protein-selection mechanism through ICL3 extends to GPCRs across the superfamily, expanding the range of known mechanisms by which receptors mediate G protein subtype selective signalling. Furthermore, our collective findings suggest ICL3 as an allosteric site for receptor- and signalling pathway-specific ligands.

Regulation of Signaling from the Epidermal Growth Factor Family.

The epidermal growth factor (EGF) system has allowed chemists, biologists, and clinicians to improve our understanding of cell production and cancer therapy. The discovery of EGF led to the recognition of cell surface receptors capable of controlling the proliferation and survival of cells. The detailed structures of the EGF-like ligand and the responses of their receptors (EGFR-family) has revealed the conformational and aggregation changes whereby ligands activate the intracellular kinase domains. Biophysical analysis has revealed the preformed clustering of different EGFR-family members and the processes which occur on ligand binding. Understanding these receptor activation processes and the consequential cytoplasmic signaling has allowed the development of inhibitors which are revolutionizing cancer therapy. This Review describes the recent progress in our understanding of the activation of the EGFR-family, the effects of signaling from the EGFR-family on cell proliferation, and the targeting of the EGFR-family in cancer treatment.

Mechanism Study of Proteins under Membrane Environment.

Membrane proteins play crucial roles in various physiological processes, including molecule transport across membranes, cell communication, and signal transduction. Approximately 60% of known drug targets are membrane proteins. There is a significant need to deeply understand the working mechanism of membrane proteins in detail, which is a challenging work due to the lack of available membrane structures and their large spatial scale. Membrane proteins carry out vital physiological functions through conformational changes. In the current study, we utilized a coarse-grained (CG) model to investigate three representative membrane protein systems: the TMEM16A channel, the family C GPCRs mGlu2 receptor, and the P4-ATPase phospholipid transporter. We constructed the reaction pathway of conformational changes between the two-end structures. Energy profiles and energy barriers were calculated. These data could provide reasonable explanations for TMEM16A activation, the mGlu2 receptor activation process, and P4-ATPase phospholipid transport. Although they all belong to the members of membrane proteins, they behave differently in terms of energy. Our work investigated the working mechanism of membrane proteins and could give novel insights into other membrane protein systems of interest.

Structures of the human cholecystokinin receptors bound to agonists and antagonists.

Cholecystokinin receptors, CCKAR and CCKBR, are important neurointestinal peptide hormone receptors and play a vital role in food intake and appetite regulation. Here, we report three crystal structures of the human CCKAR in complex with different ligands, including one peptide agonist and two small-molecule antagonists, as well as two cryo-electron microscopy structures of CCKBR-gastrin in complex with Gi2 and Gq, respectively. These structures reveal the recognition pattern of different ligand types and the molecular basis of peptide selectivity in the cholecystokinin receptor family. By comparing receptor structures in different conformational states, a stepwise activation process of cholecystokinin receptors is proposed. Combined with pharmacological data, our results provide atomic details for differential ligand recognition and receptor activation mechanisms. These insights will facilitate the discovery of potential therapeutics targeting cholecystokinin receptors.

Probing The Structural Basis of Metabotropic Glutamate Receptor 5 (mGlu 5 ) Activation and Positive Allosteric Modulation

The metabotropic glutamate receptor 5 (mGlu5) is a class C G protein-coupled receptor (GPCR) that has emerged as a promising drug target for multiple central nervous system disorders. Structurally, mGlu5 forms obligate dimers. Each protomer possesses a 7-transmembrane (7TM) domain which is connected through a cysteine-rich domain (CRD) to a large extracellular domain (ECD), encompassing the orthosteric ligand-binding Venus flytrap domain (VFD). Recent spectroscopic studies on mGlu5 signaling demonstrated large-scale conformational changes underlie signal transmission from the ECD to the G protein coupling 7TM domain. Although these studies reported the necessity of extracellular loops (ECL) for activation of mGlu5 by orthosteric agonists, specific residues related to transmission of receptor activation remain unknown. We used a combination of site-directed mutagenesis, Ca2+ mobilization assays and radioligand binding studies to identify residues within the ECLs that aid in the propagation of orthosteric agonist-induced conformational changes in the VFD to the 7TM. Multiple ECL2 residues markedly reduced activation by glutamate but not allosteric agonists. These same mutations had no effect on receptor expression and thus likely contribute to the mGlu­5 activation network. Select mutations that compromised glutamate activation could be rescued with positive allosteric modulators (PAMs). mGlu5 PAMs are promising potential new therapeutic strategies for schizophrenia and cognition, however, structure-activity relationships for mGlu5 PAMs are notoriously difficult to interpret. A deeper understanding of the structural basis of dynamic receptor activation and modulation processes will aid future rational structure-based drug discovery efforts

Insights into the Activation Mechanism of the ALX/FPR2 Receptor.

The formyl peptide receptor 2 (ALX/FPR2), a G-protein-coupled receptor (GPCR), plays an important role in host defense and inflammation. This receptor can be driven as pro- or anti-inflammatory depending on its agonist, such as N-formyl-Met-Leu-Phe-Lys (fMLFK) and resolvin D1 (RvD1) or its aspirin-triggered 17 (R)-epimer, AT-RvD1, respectively. However, the activation mechanism of ALX/FPR2 by pro- and anti-inflammatory agonists remains unclear. In this work, on the basis of molecular dynamics simulations, we evaluated a model of the ALX/FPR2 receptor activation process using two agonists, fMLFK and AT-RvD1, with opposite effects. The simulations by both fMLFK and AT-RvD1 induced the ALX/FPR2 activation through a set of receptor-core residues, in particular, R205, Q258, and W254. In addition, the activation was dependent on the disruption of electrostatic interactions in the cytoplasmic region of the receptor. We also found that in the AT-RvD1 simulations, the position of the H8 helix was similar to that of the same helix in other class-A GPCRs coupled to arrestin. Thus our results shed light on the mechanism of activation of the ALX/FPR2 receptor by pro-inflammatory and pro-resolution agonists.

Design and pharmacological profile of a novel covalent partial agonist for the adenosine A1 receptor

Partial agonists for G protein-coupled receptors (GPCRs) provide opportunities for novel pharmacotherapies with enhanced on-target safety compared to full agonists. For the human adenosine A1 receptor (hA1AR) this has led to the discovery of capadenoson, which has been in phase IIa clinical trials for heart failure. Accordingly, the design and profiling of novel hA1AR partial agonists has become an important research focus. In this study, we report on LUF7746, a capadenoson derivative bearing an electrophilic fluorosulfonyl moiety, as an irreversibly binding hA1AR modulator. Meanwhile, a nonreactive ligand bearing a methylsulfonyl moiety, LUF7747, was designed as a control probe in our study.In a radioligand binding assay, LUF7746’s apparent affinity increased to nanomolar range with longer pre-incubation time, suggesting an increasing level of covalent binding over time. Moreover, compared to the reference full agonist CPA, LUF7746 was a partial agonist in a hA1AR-mediated G protein activation assay and resistant to blockade with an antagonist/inverse agonist. An in silico structure-based docking study combined with site-directed mutagenesis of the hA1AR demonstrated that amino acid Y2717.36 was the primary anchor point for the covalent interaction. Additionally, a label-free whole-cell assay was set up to identify LUF7746’s irreversible activation of an A1 receptor-mediated cell morphological response.These results led us to conclude that LUF7746 is a novel covalent hA1AR partial agonist and a valuable chemical probe for further mapping the receptor activation process. It may also serve as a prototype for a therapeutic approach in which a covalent partial agonist may cause less on-target side effects, conferring enhanced safety compared to a full agonist.

Modeling and Structural Characterization of the Sweet Taste Receptor Heterodimer.

Sweet taste receptor, a heterodimer belonging to the class C G-protein coupled receptor (GPCR) family and composed of the T1R2 and T1R3 subunits, is responsible for the perception of natural sugars, sweet proteins, various d-amino acids, as well as artificial sweeteners. Despite the critical importance of the sweet receptor not only in mediating gustation but also in its role in the food industry, the architecture of the T1R2-T1R3 complex and the mechanism by which extracellular stimuli induce conformational changes that are propagated to the intracellular milieu, i.e., the signal transduction pathway, remain largely unknown. Here, we constructed and characterized a full-length structural model of the T1R2-T1R3 receptor, including both the transmembrane (TM) and extracellular (EC) domains of the heterodimer, using comparative modeling and extensive all-atom molecular dynamics simulations. Several heterodimer interfaces were first examined for the TM domain, and conformational changes occurring at the intracellular side and associated with the receptor's activation were characterized. From the analysis on the simulated data, putative allosteric binding sites for ligands, ions, and cholesterol were proposed. Also, insights into the protein interface of the TM domain upon activation are provided. The EC domain of the heterodimer, including both the Venus flytrap and cysteine-rich domains, was also investigated. Several important intersubunit interactions located at regions responsible for the receptor's proper function were observed, which resemble those recently identified in other class C GPCR members. Integration of the results from the TM and EC domains facilitates the generation of a full-length T1R2-T1R3 receptor. These findings along with the full-length structural model of the T1R2-T1R3 receptor provide a structural framework that may assist in understanding the mechanistic details associated with the receptor activation process for the sweet T1R2-T1R3 receptor as well as other members of the same family.

Novel BQCA- and TBPB-Derived M1 Receptor Hybrid Ligands: Orthosteric Carbachol Differentially Regulates Partial Agonism.

Recently, investigations of the complex mechanisms of allostery have led to a deeper understanding of G protein-coupled receptor (GPCR) activation and signaling processes. In this context, muscarinic acetylcholine receptors (mAChRs) are highly relevant due to their exemplary role in the study of allosteric modulation. In this work, we compare and discuss two sets of putatively dualsteric ligands, which were designed to connect carbachol to different types of allosteric ligands. We chose derivatives of TBPB [1-(1'-(2-tolyl)-1,4'-bipiperidin-4-yl)-1H-benzo[d]imidazol-2(3H)-one] as M1 -selective putative bitopic ligands, and derivatives of benzyl quinolone carboxylic acid (BQCA) as an M1 positive allosteric modulator, varying the distance between the allosteric and orthosteric building blocks. Luciferase protein complementation assays demonstrated that linker length must be carefully chosen to yield either agonist or antagonist behavior. These findings may help to design biased signaling and/or different extents of efficacy.

Simulation of the Dynamics of Primary Immunodeficiencies in B Cells.

Primary immunodeficiencies (PIDs) are a group of over 300 hereditary, heterogeneous, and mainly rare disorders that affect the immune system. Various aspects of immune system and PID proteins and genes have been investigated and facilitate systems biological studies of effects of PIDs on B cell physiology and response. We reconstructed a B cell network model based on data for the core B cell receptor activation and response processes and performed semi-quantitative dynamic simulations for normal and B cell PID failure modes. The results for several knockout simulations correspond to previously reported molecular studies and reveal novel mechanisms for PIDs. The simulations for CD21, CD40, LYN, MS4A1, ORAI1, PLCG2, PTPRC, and STIM1 indicated profound changes to major transcription factor signaling and to the network. Significant effects were observed also in the BCL10, BLNK, BTK, loss-of-function CARD11, IKKB, MALT1, and NEMO, simulations whereas only minor effects were detected for PIDs that are caused by constitutively active proteins (PI3K, gain-of-function CARD11, KRAS, and NFKBIA). This study revealed the underlying dynamics of PID diseases, confirms previous observations, and identifies novel candidates for PID diagnostics and therapy.

Hydration Thermodynamics of a Powdered G-Protein-Coupled Receptor

Membrane proteins such as G protein-coupled receptors (GPCRs) are prominent targets for novel pharmaceutical drugs. Preparation and storage of fully functional GPCRs is crucial to the processes of drug delivery and discovery. Here we describe a novel method of preparing powdered GPCRs using rhodopsin as the prototype. Our new method for generating powdered samples, notable for exceptionally high protein content while retaining photochemical functionality, paves the way for conducting functional and biophysical experiments on the dynamic process of receptor activation. As an illustrative application, powdered rhodopsin is prepared with and without the cofactor 11-cis retinal enabling the partial hydration of the protein with 2H2O in a controlled manner [1]. These samples were used to study the changes in hydrogen-atom dynamics using the quasi-elastic neutron scattering (QENS) technique. Evaluation of QENS data using the interpretations of both spatial motion and energy landscape models offer key insights into the thermodynamics of GPCR activation. The QENS studies reveal a broadly distributed relaxation of the hydrogen atom dynamics of rhodopsin on a picosecond-nanosecond time scale, essential for protein function, previously observed for only globular proteins [2]. Interestingly, the results suggest significant differences in the intrinsic protein dynamics of the dark-state rhodopsin versus the ligand-free apoprotein, opsin. These differences can be attributed to the influence of the covalently bound retinal ligand. Furthermore, preparation of powdered samples from photoilluminated rhodopsin effectively captures the state of the excited protein while undergoing the conformational changes leading to activation. These discoveries create new avenues towards understanding the central role of water in GPCR activation and unlocking the mechanisms of the biologically important signaling process of rhodopsin. [1] S.M.D.C. Perera et al. (2016) J. Phys. Chem. Lett.7, 4239-4235. [2] U.R. Shresta et al. (2016) J. Phys. Chem. Lett. 7, 4130-4136.

The Effect of Nanoparticles on the Cluster Size Distributions of Activated EGFR Measured with Photobleaching Image Correlation Spectroscopy.

The epidermal growth factor receptor (EGFR) is an important cell surface receptor in normal physiology and disease. Recent work has shown that EGF-gold nanoparticle conjugates can influence cell behaviour, but the underlying mechanism at the receptor quaternary structural level remains poorly understood.In the present work, the cluster density and cluster size of activated (phosphorylated) EGFR clusters in HeLa cells were determined with photobleaching image correlation spectroscopy. EGFR activation was probed via immunofluorescence-detected phosphorylation of tyrosines (pY-mAb) located in the kinase domain of EGFR (Y845) and at the EGFR cytoplasmic tail (Y1173). Cell activation was probed via nuclear extracellular-regulated kinase (ERK) phosphorylation. The cluster size of activated EGFR was 1.3-2.4 pY-mAb/cluster in unstimulated HeLa cells. EGF or nanorod treatment led to an increase in EGFR oligomers containing multiple phosphotyrosines (>2 phosphotyrosines per EGFR oligomer, average cluster size range = 3-5 pY-mAb/cluster) which paralleled increases in nuclear p-ERK. In contrast, EGF-nanorods decreased the contribution from higher-order phospho-clusters and decreased nuclear p-ERK relative to the nanorod control. These studies provide direct evidence that targeted nanotechnology can manipulate receptor organization and lead to changes in receptor activation and subsequent signalling processes.

Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling

G protein-coupled receptors (GPCRs) constitute the largest family of cell surface receptors. They can exist and act as dimers, but the requirement of dimers for agonist-induced signal initiation and structural dynamics remains largely unknown. Frizzled 6 (FZD6) is a member of Class F GPCRs, which bind WNT proteins to initiate signaling. Here, we show that FZD6 dimerizes and that the dimer interface of FZD6 is formed by the transmembrane α-helices four and five. Most importantly, we present the agonist-induced dissociation/re-association of a GPCR dimer through the use of live cell imaging techniques. Further analysis of a dimerization-impaired FZD6 mutant indicates that dimer dissociation is an integral part of FZD6 signaling to extracellular signal-regulated kinases1/2. The discovery of agonist-dependent dynamics of dimers as an intrinsic process of receptor activation extends our understanding of Class F and other dimerizing GPCRs, offering novel targets for dimer-interfering small molecules.

A Photoswitchable Dualsteric Ligand Controlling Receptor Efficacy.

The investigation of the mode and time course of the activation of G-protein-coupled receptors (GPCRs), in particular muscarinic acetylcholine (mACh or M) receptors, is still in its infancy despite the tremendous therapeutic relevance of M receptors and GPCRs in general. We herein made use of a dualsteric ligand that can concomitantly interact with the orthosteric, that is, the neurotransmitter, binding site and an allosteric one. We synthetically incorporated a photoswitchable (photochromic) azobenzene moiety. We characterized the photophysical properties of this ligand called BQCAAI and investigated its applicability as a pharmacological tool compound with a set of FRET techniques at the M1 receptor. BQCAAI proved to be an unprecedented molecular tool; it is the first photoswitchable dualsteric ligand, and its activity can be regulated by light. We also applied BQCCAI to investigate the time course of several receptor activation processes.

The Transition from Stochastic to Collective Activation of Nicotinic Acetylcholine Receptors Facilitates Information Transmission Within in vitro Hippocampal Networks

Although modulatory in nature, nicotinic acetylcholine receptors (nAChRs) play a major role in the central nervous system, making them one of the most studied receptor class. While both activation and desensitization are phenomena associated with the functions of individual receptors, their effects will clearly manifest on the network/circuit spatial scale. In this study, nicotine was used to investigate the impact of activation and desensitization of nAChRs on cultured hippocampal networks. We assess network dynamics via the recording of extracellular action potentials using a microelectrode array system (MEA). We bath applied either a single dose or two successive doses of increasing concentration of nicotine. We hypothesize that a high concentration of nicotine will facilitate information transmission but pre‐incubation of the network with a low concentration of nicotine would attenuate facilitation. We show that the low concentration has minimal effects on network activity and we call this a network‐desensitized state. A high concentration significantly impacted both spiking and bursting activity and we call this a network‐activated state. Interestingly, a low concentration pre‐incubation of nicotine blocked or significantly diminished activity when followed by a high concentration. Lastly, network synchronization as well as network efficiency increased with the large nicotine concentration. This suggests that although fleeting, the process of global receptor activation has a longer lasting impact on the network than a stochastic receptor activation.Support or Funding InformationNational Science Foundation grant no. PHY‐1205919

Optical Probing of Metabotropic Glutamate Receptors

G protein-coupled receptors (GPCRs), the largest family of membrane proteins, enable cells to respond to a wide array of extracellular stimuli and control a diverse array of intracellular signaling pathways. The Class C GPCRs, which contain the metabotropic glutamate receptors (mGluRs) and GABAB receptors, are expressed throughout the nervous system where they control excitability and synaptic strength and serve as drug targets for many neurological disorders. Despite the presence of high resolution crystal structures of isolated domains, many questions remain about the dynamic processes of receptor activation and G protein coupling in full length receptors. Furthermore, the limitations of pharmacology and classical assays have made it difficult to control and measure individual receptors with high spatiotemporal precision and subtype specificity. In this study we have developed and refined methods for attaching photoswitchable tethered ligands (PTLs) for the in vivo photocontrol of mGluRs, with a focus on mGluR2. Optical control of mGluR2 via tethering of photoswitches to SNAP-tags allowed for efficient, orthogonal labeling of mGluR2 without the complications of maleimide chemistry. This new approach to PTL tethering allowed for dual optical control of multiple receptors within the same cell. We also used PTLs to selectively ligand one or both memebers of linked mGluR2 homodimers to reveal substantial cooperativity. Strikingly, in mGluR2/3 heterodimers this cooperativity is asymmetric. These experiments were complemented with intersubunit ensemble and single molecule fluorescence resonance energy transfer (FRET) experiments that revealed the role of the dimer interface in the conformational dynamics underling receptor activation. Together this work contributes a number of new tools for optical probing of GPCRs and leads to a model for subunit-dependent activation of mGluRs.

Note: Magnetic targeting for enhancement of the activation efficiency of G protein-coupled receptor with a two-pair coil system.

Insufficient contact of drug with target cells is a primary reason for limited efficiency of G protein-coupled receptor activation. To overcome this limitation, a simple approach based on magnetic targeting for enhancing drug delivery towards the cell surfaces using magnetic nanoparticles and a two-pair coil system consisting of Helmholtz and Maxwell coils was reported. As a proof of the concept, comparative experiments on G protein-coupled receptor activation process were carried out and results show that the efficiency of G protein-coupled receptor activation can be increased about 6 times in the experiments with the aid of the proposed magnetic targeting system.

The Membrane Mimetic Affects the Spatial Structure and Mobility of EGFR Transmembrane and Juxtamembrane Domains.

The epidermal growth factor receptor (EGFR) is one of the most extensively studied receptor tyrosine kinases, as it is involved in a wide range of cellular processes and severe diseases. Recent works reveal that the single-helix transmembrane domains and cytoplasmic juxtamembrane regions play an important role in the receptor activation process. Here we present the results of our investigation of the spatial structure and mobility of the EGFR transmembrane domain and juxtamembrane regions in various membranelike environments, which shed light on the effects of the membrane physical properties and composition on the behavior of the juxtamembrane domain.