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1.
Cell ; 147(5): 1011-23, 2011 Nov 23.
Article in English | MEDLINE | ID: mdl-22118459

ABSTRACT

Atypical antipsychotic drugs, such as clozapine and risperidone, have a high affinity for the serotonin 5-HT(2A) G protein-coupled receptor (GPCR), the 2AR, which signals via a G(q) heterotrimeric G protein. The closely related non-antipsychotic drugs, such as ritanserin and methysergide, also block 2AR function, but they lack comparable neuropsychological effects. Why some but not all 2AR inhibitors exhibit antipsychotic properties remains unresolved. We now show that a heteromeric complex between the 2AR and the G(i)-linked GPCR, metabotropic glutamate 2 receptor (mGluR2), integrates ligand input, modulating signaling output and behavioral changes. Serotonergic and glutamatergic drugs bind the mGluR2/2AR heterocomplex, which then balances Gi- and Gq-dependent signaling. We find that the mGluR2/2AR-mediated changes in Gi and Gq activity predict the psychoactive behavioral effects of a variety of pharmocological compounds. These observations provide mechanistic insight into antipsychotic action that may advance therapeutic strategies for disorders including schizophrenia and dementia.


Subject(s)
Antipsychotic Agents/pharmacology , Receptors, Adrenergic, beta-2/metabolism , Receptors, Metabotropic Glutamate/metabolism , Signal Transduction , Amphetamines/pharmacology , Animals , Clozapine/pharmacology , Dimerization , Dose-Response Relationship, Drug , Frontal Lobe/drug effects , Frontal Lobe/metabolism , Methysergide/pharmacology , Mice , Oocytes , Potassium Channels, Inwardly Rectifying/metabolism , Xenopus
2.
Nat Methods ; 17(8): 777-787, 2020 08.
Article in English | MEDLINE | ID: mdl-32661425

ABSTRACT

G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.


Subject(s)
Molecular Dynamics Simulation , Receptors, G-Protein-Coupled/chemistry , Software , Metabolome , Models, Molecular , Protein Conformation
4.
J Chem Inf Model ; 63(16): 5056-5065, 2023 08 28.
Article in English | MEDLINE | ID: mdl-37555591

ABSTRACT

Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown to abolish brain reward deficits in rodents during withdrawal, as well as to reduce the escalation of opioid use in rats with extended access to opioids. Although KOR antagonists represent promising candidates for the treatment of opioid addiction, very few potent selective KOR antagonists are known to date and most of them exhibit significant safety concerns. Here, we used a generative deep-learning framework for the de novo design of chemotypes with putative KOR antagonistic activity. Molecules generated by models trained with this framework were prioritized for chemical synthesis based on their predicted optimal interactions with the receptor. Our models and proposed training protocol were experimentally validated by binding and functional assays.


Subject(s)
Deep Learning , Opioid-Related Disorders , Rats , Animals , Receptors, Opioid, kappa/metabolism , Narcotic Antagonists/pharmacology , Analgesics, Opioid/pharmacology
5.
J Chem Inf Model ; 62(22): 5607-5621, 2022 11 28.
Article in English | MEDLINE | ID: mdl-36279366

ABSTRACT

Inhibitors of integrin αVß3 have therapeutic promise for a variety of diseases. Most αVß3-targeting small molecules patterned after the RGD motif are partial agonists because they induce a high-affinity, ligand-binding conformation and prime the receptor to bind the ligand without an activating stimulus, in part via a charge-charge interaction between their aspartic acid carboxyl group and the metal ion in the metal-ion-dependent adhesion site (MIDAS). Building upon our previous studies on the related integrin αIIbß3, we searched for pure αVß3 antagonists that lack this typical aspartic acid carboxyl group and instead engage through direct binding to one of the coordinating residues of the MIDAS metal ion, specifically ß3 E220. By in silico screening of two large chemical libraries for compounds interacting with ß3 E220, we indeed discovered a novel molecule that does not contain an acidic carboxyl group and does not induce the high-affinity, ligand-binding state of the receptor. Functional and structural characterization of a chemically optimized version of this compound led to the discovery of a novel small-molecule pure αVß3 antagonist that (i) does not prime the receptor to bind the ligand and does not induce hybrid domain swing-out or receptor extension as judged by antibody binding and negative-stain electron microscopy, (ii) binds at the RGD-binding site as predicted by metadynamics rescoring of induced-fit docking poses and confirmed by a cryo-electron microscopy structure of the compound-bound integrin, and (iii) coordinates the MIDAS metal ion via a quinoline moiety instead of an acidic carboxyl group.


Subject(s)
Aspartic Acid , Integrin alphaVbeta3 , Integrin alphaVbeta3/chemistry , Ligands , Aspartic Acid/metabolism , Cryoelectron Microscopy , Metals/metabolism , Oligopeptides/pharmacology
6.
Biochemistry ; 60(18): 1420-1429, 2021 05 11.
Article in English | MEDLINE | ID: mdl-33274929

ABSTRACT

Pain management devoid of serious opioid adverse effects is still far from reach despite vigorous research and development efforts. Alternatives to classical opioids have been sought for years, and mounting reports of individuals finding pain relief with kratom have recently intensified research on this natural product. Although the composition of kratom is complex, the pharmacological characterization of its most abundant alkaloids has drawn attention to three molecules in particular, owing to their demonstrated antinociceptive activity and limited side effects in vivo. These three molecules are mitragynine (MG), its oxidized active metabolite, 7-hydroxymitragynine (7OH), and the indole-to-spiropseudoindoxy rearrangement product of MG known as mitragynine pseudoindoxyl (MP). Although these three alkaloids have been shown to preferentially activate the G protein signaling pathway by binding and allosterically modulating the µ-opioid receptor (MOP), a molecular level understanding of this process is lacking and yet important for the design of improved therapeutics. The molecular dynamics study and experimental validation reported here provide an atomic level description of how MG, 7OH, and MP bind and allosterically modulate the MOP, which can eventually guide structure-based drug design of improved therapeutics.


Subject(s)
Analgesics, Opioid/pharmacology , Mitragyna/chemistry , Receptors, Opioid, mu/agonists , Secologanin Tryptamine Alkaloids/pharmacology , Allosteric Regulation , Analgesics, Opioid/chemistry , Humans , Models, Molecular , Molecular Docking Simulation , Molecular Structure , Phytotherapy , Protein Binding , Protein Conformation , Secologanin Tryptamine Alkaloids/chemistry , Structure-Activity Relationship
7.
Arterioscler Thromb Vasc Biol ; 40(3): 624-637, 2020 03.
Article in English | MEDLINE | ID: mdl-31969014

ABSTRACT

OBJECTIVE: The αIIbß3 antagonist antiplatelet drug abciximab is the chimeric antigen-binding fragment comprising the variable regions of murine monoclonal antibody 7E3 and the constant domains of human IgG1 and light chain κ. Previous mutagenesis studies suggested that abciximab binds to the ß3 C177-C184 specificity-determining loop (SDL) and Trp129 on the adjacent ß1-α1 helix. These studies could not, however, assess whether 7E3 or abciximab prevents fibrinogen binding by steric interference, disruption of either the αIIbß3-binding pocket for fibrinogen or the ß3 SDL (which is not part of the binding pocket but affects fibrinogen binding), or some combination of these effects. To address this gap, we used cryo-electron microscopy to determine the structure of the αIIbß3-abciximab complex at 2.8 Å resolution. Approach and Results: The interacting surface of abciximab is comprised of residues from all 3 complementarity-determining regions of both the light and heavy chains, with high representation of aromatic residues. Binding is primarily to the ß3 SDL and neighboring residues, the ß1-α1 helix, and ß3 residues Ser211, Val212 and Met335. Unexpectedly, the structure also indicated several interactions with αIIb. As judged by the cryo-electron microscopy model, molecular-dynamics simulations, and mutagenesis, the binding of abciximab does not appear to rely on the interaction with the αIIb residues and does not result in disruption of the fibrinogen-binding pocket; it does, however, compress and reduce the flexibility of the SDL. CONCLUSIONS: We deduce that abciximab prevents ligand binding by steric interference, with a potential contribution via displacement of the SDL and limitation of the flexibility of the SDL residues.


Subject(s)
Abciximab/ultrastructure , Cryoelectron Microscopy , Integrin alpha2/ultrastructure , Integrin beta3/ultrastructure , Platelet Aggregation Inhibitors , Abciximab/metabolism , Binding Sites , Binding, Competitive , HEK293 Cells , Humans , Integrin alpha2/genetics , Integrin alpha2/metabolism , Integrin beta3/genetics , Integrin beta3/metabolism , Ligands , Molecular Dynamics Simulation , Mutagenesis, Site-Directed , Mutation , Platelet Aggregation Inhibitors/metabolism , Protein Binding , Protein Interaction Domains and Motifs , Recombinant Proteins/ultrastructure , Structure-Activity Relationship
8.
Biophys J ; 118(4): 909-921, 2020 02 25.
Article in English | MEDLINE | ID: mdl-31676132

ABSTRACT

In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the µ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, are monovalent and divalent cations. Specifically, the monovalent sodium cation (Na+) has been known for decades to affect MOP receptor signaling by reducing agonist binding, whereas the divalent magnesium cation (Mg2+) has been shown to have the opposite effect, notwithstanding the presence of sodium chloride. Although ultra-high-resolution opioid receptor crystal structures have revealed a specific Na+ binding site and molecular dynamics (MD) simulation studies have supported the idea that this monovalent ion reduces agonist binding by stabilizing the receptor inactive state, the putative binding site of Mg2+ on the MOP receptor, as well as the molecular determinants responsible for its positive allosteric modulation of the receptor, are unknown. In this work, we carried out tens of microseconds of all-atom MD simulations to investigate the simultaneous binding of Mg2+ and Na+ cations to inactive and active crystal structures of the MOP receptor embedded in an explicit lipid-water environment and confirmed adequate sampling of Mg2+ ion binding with a grand canonical Monte Carlo MD method. Analyses of these simulations shed light on 1) the preferred binding sites of Mg2+ on the MOP receptor, 2) details of the competition between Mg2+ and Na+ cations for specific sites, 3) estimates of binding affinities, and 4) testable hypotheses of the molecular mechanism underlying the positive allosteric modulation of the MOP receptor by the Mg2+ cation.


Subject(s)
Magnesium , Pharmaceutical Preparations , Binding Sites , Molecular Dynamics Simulation , Receptors, Opioid
9.
Mol Pharmacol ; 98(4): 475-486, 2020 10.
Article in English | MEDLINE | ID: mdl-32680919

ABSTRACT

Methadone is a synthetic opioid agonist with notoriously unique properties, such as lower abuse liability and induced relief of withdrawal symptoms and drug cravings, despite acting on the same opioid receptors triggered by classic opioids-in particular the µ-opioid receptor (MOR). Its distinct pharmacologic properties, which have recently been attributed to the preferential activation of ß-arrestin over G proteins, make methadone a standard-of-care maintenance medication for opioid addiction. Although a recent biophysical study suggests that methadone stabilizes different MOR active conformations from those stabilized by classic opioid drugs or G protein-biased agonists, how this drug modulates the conformational equilibrium of MOR and what specific active conformation of the receptor it stabilizes are unknown. Here, we report the results of submillisecond adaptive sampling molecular dynamics simulations of a predicted methadone-bound MOR complex and compare them with analogous data obtained for the classic opioid morphine and the G protein-biased ligand TRV130. The model, which is supported by existing experimental data, is analyzed using Markov state models and transfer entropy analysis to provide testable hypotheses of methadone-specific conformational dynamics and activation kinetics of MOR. SIGNIFICANCE STATEMENT: Opioid addiction has reached epidemic proportions in both industrialized and developing countries. Although methadone maintenance treatment represents an effective therapeutic approach for opioid addiction, it is not as widely used as needed. In this study, we contribute an atomic-level understanding of how methadone exerts its unique function in pursuit of more accessible treatments for opioid addiction. In particular, we present details of a methadone-specific active conformation of the µ-opioid receptor that has thus far eluded experimental structural characterization.


Subject(s)
Analgesics, Opioid/pharmacology , Methadone/pharmacology , Receptors, Opioid, mu/chemistry , Receptors, Opioid, mu/metabolism , Spiro Compounds/pharmacology , Thiophenes/pharmacology , Analgesics, Opioid/chemistry , Animals , Binding Sites , Entropy , Humans , Markov Chains , Methadone/chemistry , Mice , Models, Molecular , Molecular Dynamics Simulation , Protein Binding , Protein Conformation/drug effects , Spiro Compounds/chemistry , Thiophenes/chemistry
10.
PLoS Comput Biol ; 15(1): e1006689, 2019 01.
Article in English | MEDLINE | ID: mdl-30677023

ABSTRACT

The differential modulation of agonist and antagonist binding to opioid receptors (ORs) by sodium (Na+) has been known for decades. To shed light on the molecular determinants, thermodynamics, and kinetics of Na+ translocation through the µ-OR (MOR), we used a multi-ensemble Markov model framework combining equilibrium and non-equilibrium atomistic molecular dynamics simulations of Na+ binding to MOR active or inactive crystal structures embedded in an explicit lipid bilayer. We identify an energetically favorable, continuous ion pathway through the MOR active conformation only, and provide, for the first time: i) estimates of the energy differences and required timescales of Na+ translocation in inactive and active MORs, ii) estimates of Na+-induced changes to agonist binding validated by radioligand measurements, and iii) testable hypotheses of molecular determinants and correlated motions involved in this translocation, which are likely to play a key role in MOR signaling.


Subject(s)
Receptors, Opioid, mu/chemistry , Receptors, Opioid, mu/metabolism , Sodium/chemistry , Sodium/metabolism , Animals , Kinetics , Machine Learning , Markov Chains , Mice , Molecular Dynamics Simulation , Protein Binding , Thermodynamics
11.
J Chem Phys ; 153(12): 124105, 2020 Sep 28.
Article in English | MEDLINE | ID: mdl-33003748

ABSTRACT

Determining the drug-target residence time (RT) is of major interest in drug discovery given that this kinetic parameter often represents a better indicator of in vivo drug efficacy than binding affinity. However, obtaining drug-target unbinding rates poses significant challenges, both computationally and experimentally. This is particularly palpable for complex systems like G Protein-Coupled Receptors (GPCRs) whose ligand unbinding typically requires very long timescales oftentimes inaccessible by standard molecular dynamics simulations. Enhanced sampling methods offer a useful alternative, and their efficiency can be further improved by using machine learning tools to identify optimal reaction coordinates. Here, we test the combination of two machine learning techniques, automatic mutual information noise omission and reweighted autoencoded variational Bayes for enhanced sampling, with infrequent metadynamics to efficiently study the unbinding kinetics of two classical drugs with different RTs in a prototypic GPCR, the µ-opioid receptor. Dissociation rates derived from these computations are within one order of magnitude from experimental values. We also use the simulation data to uncover the dissociation mechanisms of these drugs, shedding light on the structures of rate-limiting transition states, which, alongside metastable poses, are difficult to obtain experimentally but important to visualize when designing drugs with a desired kinetic profile.


Subject(s)
Machine Learning , Molecular Dynamics Simulation , Pharmaceutical Preparations/chemistry , Receptors, G-Protein-Coupled/chemistry , Kinetics
12.
Biophys J ; 115(2): 300-312, 2018 07 17.
Article in English | MEDLINE | ID: mdl-30021106

ABSTRACT

G-protein-coupled receptors (GPCRs) control vital cellular signaling pathways. GPCR oligomerization is proposed to increase signaling diversity. However, many reports have arrived at disparate conclusions regarding the existence, stability, and stoichiometry of GPCR oligomers, partly because of cellular complexity and ensemble averaging of intrareconstitution heterogeneities that complicate the interpretation of oligomerization data. To overcome these limitations, we exploited fluorescence-microscopy-based high-content analysis of single proteoliposomes. This allowed multidimensional quantification of intrinsic monomer-monomer interactions of three class A GPCRs (ß2-adrenergic receptor, cannabinoid receptor type 1, and opsin). Using a billion-fold less protein than conventional assays, we quantified oligomer stoichiometries, association constants, and the influence of two ligands and membrane curvature on oligomerization, revealing key similarities and differences for three GPCRs with decidedly different physiological functions. The assays introduced here will assist with the quantitative experimental observation of oligomerization for transmembrane proteins in general.


Subject(s)
Protein Multimerization , Proteolipids/metabolism , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/metabolism , Ligands , Protein Structure, Quaternary , Signal Transduction , Solubility
13.
J Biol Chem ; 292(49): 19989-19998, 2017 12 08.
Article in English | MEDLINE | ID: mdl-29042444

ABSTRACT

Gαs (Gs) and Gαolf (Golf) are highly homologous G-protein α subunits that activate adenylate cyclase, thereby serving as crucial mediators of intracellular signaling. Because of their dramatically different brain expression patterns, we studied similarities and differences between their activation processes with the aim of comparing their receptor coupling mechanisms. We engineered novel luciferase- and Venus-fused Gα constructs that can be used in bioluminescence resonance energy transfer assays. In conjunction with molecular simulations, these novel biosensors were used to determine receptor activation-induced changes in conformation. Relative movements in Gs were consistent with the crystal structure of ß2 adrenergic receptor in complex with Gs Conformational changes in Golf activation are shown to be similar to those in Gs Overall the current study reveals general similarities between Gs and Golf activation at the molecular level and provides a novel set of tools to search for Gs- and Golf-specific receptor pharmacology. In view of the wide functional and pharmacological roles of Gs- and Golf-coupled dopamine D1 receptor and adenosine A2A receptor in the brain and other organs, elucidating their differential structure-function relationships with Gs and Golf might provide new approaches for the treatment of a variety of neuropsychiatric disorders. In particular, these novel biosensors can be used to reveal potentially therapeutic dopamine D1 receptor and adenosine A2A receptor ligands with functionally selective properties between Gs and Golf signaling.


Subject(s)
Biosensing Techniques/methods , GTP-Binding Protein alpha Subunits, Gs/metabolism , GTP-Binding Protein alpha Subunits/metabolism , Adenylyl Cyclases/metabolism , Animals , Bioluminescence Resonance Energy Transfer Techniques , Biosensing Techniques/instrumentation , Humans , Ligands , Protein Conformation , Receptor, Adenosine A2A/metabolism , Receptors, Dopamine D1/metabolism , Signal Transduction
14.
J Chem Phys ; 149(22): 224101, 2018 Dec 14.
Article in English | MEDLINE | ID: mdl-30553249

ABSTRACT

Computational strategies aimed at unveiling the thermodynamic and kinetic properties of G Protein-Coupled Receptor (GPCR) activation require extensive molecular dynamics simulations of the receptor embedded in an explicit lipid-water environment. A possible method for efficiently sampling the conformational space of such a complex system is metadynamics (MetaD) with path collective variables (CVs). Here, we applied well-tempered MetaD with path CVs to one of the few GPCRs for which both inactive and fully active experimental structures are available, the µ-opioid receptor (MOR), and assessed the ability of this enhanced sampling method to estimate the thermodynamic properties of receptor activation in line with those obtained by more computationally expensive adaptive sampling protocols. While n-body information theory analysis of these simulations confirmed that MetaD can efficiently characterize ligand-induced allosteric communication across the receptor, standard MetaD cannot be used directly to derive kinetic rates because transitions are accelerated by a bias potential. Applying the principle of Maximum Caliber (MaxCal) to the free-energy landscape of morphine-bound MOR reconstructed from MetaD, we obtained Markov state models that yield kinetic rates of MOR activation in agreement with those obtained by adaptive sampling. Taken together, these results suggest that the MetaD-MaxCal combination creates an efficient strategy for estimating the thermodynamic and kinetic properties of GPCR activation at an affordable computational cost.


Subject(s)
Receptors, Opioid, mu/chemistry , Thermodynamics , Kinetics , Molecular Dynamics Simulation , Morphine/chemistry
15.
Proc Natl Acad Sci U S A ; 112(15): E1898-907, 2015 Apr 14.
Article in English | MEDLINE | ID: mdl-25827233

ABSTRACT

Next-generation sequencing is transforming our understanding of human genetic variation but assessing the functional impact of novel variants presents challenges. We analyzed missense variants in the integrin αIIbß3 receptor subunit genes ITGA2B and ITGB3 identified by whole-exome or -genome sequencing in the ThromboGenomics project, comprising ∼32,000 alleles from 16,108 individuals. We analyzed the results in comparison with 111 missense variants in these genes previously reported as being associated with Glanzmann thrombasthenia (GT), 20 associated with alloimmune thrombocytopenia, and 5 associated with aniso/macrothrombocytopenia. We identified 114 novel missense variants in ITGA2B (affecting ∼11% of the amino acids) and 68 novel missense variants in ITGB3 (affecting ∼9% of the amino acids). Of the variants, 96% had minor allele frequencies (MAF) < 0.1%, indicating their rarity. Based on sequence conservation, MAF, and location on a complete model of αIIbß3, we selected three novel variants that affect amino acids previously associated with GT for expression in HEK293 cells. αIIb P176H and ß3 C547G severely reduced αIIbß3 expression, whereas αIIb P943A partially reduced αIIbß3 expression and had no effect on fibrinogen binding. We used receiver operating characteristic curves of combined annotation-dependent depletion, Polyphen 2-HDIV, and sorting intolerant from tolerant to estimate the percentage of novel variants likely to be deleterious. At optimal cut-off values, which had 69-98% sensitivity in detecting GT mutations, between 27% and 71% of the novel αIIb or ß3 missense variants were predicted to be deleterious. Our data have implications for understanding the evolutionary pressure on αIIbß3 and highlight the challenges in predicting the clinical significance of novel missense variants.


Subject(s)
High-Throughput Nucleotide Sequencing/methods , Mutation, Missense , Platelet Glycoprotein GPIIb-IIIa Complex/genetics , Thrombasthenia/genetics , Alleles , Databases, Nucleic Acid , Exome/genetics , Fibrinogen/chemistry , Fibrinogen/metabolism , Gene Frequency , HEK293 Cells , Humans , Immunoblotting , Models, Molecular , Platelet Glycoprotein GPIIb-IIIa Complex/chemistry , Platelet Glycoprotein GPIIb-IIIa Complex/metabolism , Protein Binding , Protein Conformation , Protein Structure, Tertiary , Thrombasthenia/metabolism
16.
PLoS Comput Biol ; 12(12): e1005240, 2016 12.
Article in English | MEDLINE | ID: mdl-27959924

ABSTRACT

The lipid composition of cell membranes has increasingly been recognized as playing an important role in the function of various membrane proteins, including G Protein-Coupled Receptors (GPCRs). For instance, experimental and computational evidence has pointed to lipids influencing receptor oligomerization directly, by physically interacting with the receptor, and/or indirectly, by altering the bulk properties of the membrane. While the exact role of oligomerization in the function of class A GPCRs such as the µ-opioid receptor (MOR) is still unclear, insight as to how these receptors oligomerize and the relevance of the lipid environment to this phenomenon is crucial to our understanding of receptor function. To examine the effect of lipids and different MOR conformations on receptor oligomerization we carried out extensive coarse-grained molecular dynamics simulations of crystal structures of inactive and/or activated MOR embedded in an idealized mammalian plasma membrane composed of 63 lipid types asymmetrically distributed across the two leaflets. The results of these simulations point, for the first time, to specific direct and indirect effects of the lipids, as well as the receptor conformation, on the spatio-temporal organization of MOR in the plasma membrane. While sphingomyelin-rich, high-order lipid regions near certain transmembrane (TM) helices of MOR induce an effective long-range attractive force on individual protomers, both long-range lipid order and interface formation are found to be conformation dependent, with a larger number of different interfaces formed by inactive MOR compared to active MOR.


Subject(s)
Cell Membrane , Lipids , Models, Molecular , Receptors, Opioid, mu , Animals , Cell Membrane/chemistry , Cell Membrane/metabolism , Lipid Metabolism/physiology , Lipids/analysis , Lipids/chemistry , Mice , Receptors, Opioid, mu/chemistry , Receptors, Opioid, mu/metabolism
17.
Pharmacol Rev ; 66(2): 413-34, 2014.
Article in English | MEDLINE | ID: mdl-24515647

ABSTRACT

Most evidence indicates that, as for family C G protein-coupled receptors (GPCRs), family A GPCRs form homo- and heteromers. Homodimers seem to be a predominant species, with potential dynamic formation of higher-order oligomers, particularly tetramers. Although monomeric GPCRs can activate G proteins, the pentameric structure constituted by one GPCR homodimer and one heterotrimeric G protein may provide a main functional unit, and oligomeric entities can be viewed as multiples of dimers. It still needs to be resolved if GPCR heteromers are preferentially heterodimers or if they are mostly constituted by heteromers of homodimers. Allosteric mechanisms determine a multiplicity of possible unique pharmacological properties of GPCR homomers and heteromers. Some general mechanisms seem to apply, particularly at the level of ligand-binding properties. In the frame of the dimer-cooperativity model, the two-state dimer model provides the most practical method to analyze ligand-GPCR interactions when considering receptor homomers. In addition to ligand-binding properties, unique properties for each GPCR oligomer emerge in relation to different intrinsic efficacy of ligands for different signaling pathways (functional selectivity). This gives a rationale for the use of GPCR oligomers, and particularly heteromers, as novel targets for drug development. Herein, we review the functional and pharmacological properties of GPCR oligomers and provide some guidelines for the application of discrete direct screening and high-throughput screening approaches to the discovery of receptor-heteromer selective compounds.


Subject(s)
Drug Design , Protein Multimerization , Receptors, G-Protein-Coupled/chemistry , Receptors, G-Protein-Coupled/metabolism , Allosteric Regulation , Animals , Humans , Ligands , Protein Binding , Protein Conformation
18.
Biochemistry ; 55(46): 6456-6466, 2016 Nov 22.
Article in English | MEDLINE | ID: mdl-27778501

ABSTRACT

Substantial attention has recently been devoted to G protein-biased agonism of the µ-opioid receptor (MOR) as an ideal new mechanism for the design of analgesics devoid of serious side effects. However, designing opioids with appropriate efficacy and bias is challenging because it requires an understanding of the ligand binding process and of the allosteric modulation of the receptor. Here, we investigated these phenomena for TRV-130, a G protein-biased MOR small-molecule agonist that has been shown to exert analgesia with less respiratory depression and constipation than morphine and that is currently being evaluated in human clinical trials for acute pain management. Specifically, we carried out multimicrosecond, all-atom molecular dynamics (MD) simulations of the binding of this ligand to the activated MOR crystal structure. Analysis of >50 µs of these MD simulations provides insights into the energetically preferred binding pathway of TRV-130 and its stable pose at the orthosteric binding site of MOR. Information transfer from the TRV-130 binding pocket to the intracellular region of the receptor was also analyzed, and was compared to a similar analysis carried out on the receptor bound to the classical unbiased agonist morphine. Taken together, these studies lead to a series of testable hypotheses of ligand-receptor interactions that are expected to inform the structure-based design of improved opioid analgesics.


Subject(s)
Protein Conformation , Receptors, Opioid, mu/chemistry , Signal Transduction , Spiro Compounds/chemistry , Thiophenes/chemistry , Amino Acids/genetics , Binding Sites/genetics , Binding, Competitive , Crystallization , Humans , Kinetics , Ligands , Models, Molecular , Molecular Dynamics Simulation , Molecular Structure , Protein Domains , Protein Stability , Receptors, Opioid, mu/genetics , Receptors, Opioid, mu/metabolism , Spiro Compounds/metabolism , Thiophenes/metabolism
19.
J Am Chem Soc ; 138(21): 6754-64, 2016 06 01.
Article in English | MEDLINE | ID: mdl-27192616

ABSTRACT

Mu-opioid receptor agonists represent mainstays of pain management. However, the therapeutic use of these agents is associated with serious side effects, including potentially lethal respiratory depression. Accordingly, there is a longstanding interest in the development of new opioid analgesics with improved therapeutic profiles. The alkaloids of the Southeast Asian plant Mitragyna speciosa, represented by the prototypical member mitragynine, are an unusual class of opioid receptor modulators with distinct pharmacological properties. Here we describe the first receptor-level functional characterization of mitragynine and related natural alkaloids at the human mu-, kappa-, and delta-opioid receptors. These results show that mitragynine and the oxidized analogue 7-hydroxymitragynine, are partial agonists of the human mu-opioid receptor and competitive antagonists at the kappa- and delta-opioid receptors. We also show that mitragynine and 7-hydroxymitragynine are G-protein-biased agonists of the mu-opioid receptor, which do not recruit ß-arrestin following receptor activation. Therefore, the Mitragyna alkaloid scaffold represents a novel framework for the development of functionally biased opioid modulators, which may exhibit improved therapeutic profiles. Also presented is an enantioselective total synthesis of both (-)-mitragynine and its unnatural enantiomer, (+)-mitragynine, employing a proline-catalyzed Mannich-Michael reaction sequence as the key transformation. Pharmacological evaluation of (+)-mitragynine revealed its much weaker opioid activity. Likewise, the intermediates and chemical transformations developed in the total synthesis allowed the elucidation of previously unexplored structure-activity relationships (SAR) within the Mitragyna scaffold. Molecular docking studies, in combination with the observed chemical SAR, suggest that Mitragyna alkaloids adopt a binding pose at the mu-opioid receptor that is distinct from that of classical opioids.


Subject(s)
Mitragyna/chemistry , Narcotic Antagonists/chemical synthesis , Receptors, Opioid, mu/agonists , Secologanin Tryptamine Alkaloids/chemistry , Drug Partial Agonism , Humans , Molecular Docking Simulation , Narcotic Antagonists/chemistry , Narcotic Antagonists/pharmacology , Protein Binding , Receptors, Opioid, delta/antagonists & inhibitors , Receptors, Opioid, kappa/antagonists & inhibitors , Secologanin Tryptamine Alkaloids/isolation & purification , Secologanin Tryptamine Alkaloids/pharmacology , Structure-Activity Relationship
20.
PLoS Comput Biol ; 11(3): e1004148, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25822938

ABSTRACT

Substantial evidence in support of the formation of opioid receptor (OR) di-/oligomers suggests previously unknown mechanisms used by these proteins to exert their biological functions. In an attempt to guide experimental assessment of the identity of the minimal signaling unit for ORs, we conducted extensive coarse-grained (CG) molecular dynamics (MD) simulations of different combinations of the three major OR subtypes, i.e., µ-OR, δ-OR, and κ-OR, in an explicit lipid bilayer. Specifically, we ran multiple, independent MD simulations of each homomeric µ-OR/µ-OR, δ-OR/δ-OR, and κ-OR/κ-OR complex, as well as two of the most studied heteromeric complexes, i.e., δ-OR/µ-OR and δ-OR/κ-OR, to derive the preferred supramolecular organization and dimer interfaces of ORs in a cell membrane model. These simulations yielded over 250 microseconds of accumulated data, which correspond to approximately 1 millisecond of effective simulated dynamics according to established scaling factors of the CG model we employed. Analysis of these data indicates similar preferred supramolecular organization and dimer interfaces of ORs across the different receptor subtypes, but also important differences in the kinetics of receptor association at specific dimer interfaces. We also investigated the kinetic properties of interfacial lipids, and explored their possible role in modulating the rate of receptor association and in promoting the formation of filiform aggregates, thus supporting a distinctive role of the membrane in OR oligomerization and, possibly, signaling.


Subject(s)
Protein Multimerization/physiology , Receptors, Opioid/metabolism , Receptors, Opioid/ultrastructure , Computational Biology , Humans , Lipids/chemistry , Models, Molecular , Molecular Dynamics Simulation , Protein Subunits/chemistry , Protein Subunits/metabolism , Receptors, Opioid/chemistry
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