scholarly journals How μ-opioid receptor recognizes fentanyl

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Quynh N. Vo ◽  
Paween Mahinthichaichan ◽  
Jana Shen ◽  
Christopher R. Ellis
Keyword(s):  
Opioid Receptor ◽  
Ph Dependence ◽  
Salt Bridge ◽  
Binding Mode ◽  
The United States ◽  
Structural Basis ◽  
General Mechanism ◽  
Binding Modes ◽  
X Ray ◽  
Simulation Techniques

AbstractRoughly half of the drug overdose-related deaths in the United States are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, X-ray crystal structures of mOR in complex with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like opioids remains lacking. Exploiting the X-ray structure of BU72-bound mOR and several molecular simulation techniques, we elucidated the detailed binding mechanism of fentanyl. Surprisingly, in addition to the salt-bridge binding mode common to morphinan opiates, fentanyl can move deeper and form a stable hydrogen bond with the conserved His2976.52, which has been suggested to modulate mOR’s ligand affinity and pH dependence by previous mutagenesis experiments. Intriguingly, this secondary binding mode is only accessible when His2976.52 adopts a neutral HID tautomer. Alternative binding modes may represent a general mechanism in G protein-coupled receptor-ligand recognition.

scholarly journals How µ-Opioid Receptor Recognizes Fentanyl

2020 ◽  
Author(s):  
Quynh N. Vo ◽  
Paween Mahinthichaichan ◽  
Jana Shen ◽  
Christopher R. Ellis
Keyword(s):  
Opioid Receptor ◽  
Ph Dependence ◽  
Salt Bridge ◽  
Binding Mode ◽  
The United States ◽  
Structural Basis ◽  
Ligand Recognition ◽  
Binding Modes ◽  
Synthetic Opioids ◽  
Starting Point

AbstractIn 2019, drug overdose has claimed over 70,000 lives in the United States. More than half of the deaths are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, the crystal structures of mOR in complex with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like synthetic opioids remains lacking. Exploiting the X-ray structure of mOR bound to a morphinan ligand and several state-of-the-art simulation techniques, including weighted ensemble and continuous constant pH molecular dynamics, we elucidated the detailed binding mechanism of fentanyl with mOR. Surprisingly, in addition to forming a salt-bridge with Asp1473.32 in the orthosteric site common to morphinan opiates, fentanyl can move deeper and bind mOR through hydrogen bonding with a conserved histidine His2976.52, which has been shown to modulate mOR’s ligand affinity and pH dependence in mutagenesis experiments, but its precise role remains unclear. Intriguingly, the secondary binding mode is only accessible when His297 adopts a neutral HID tautomer. Alternative binding modes and involvement of tautomer states may represent general mechanisms in G protein-coupled receptor (GPCR)-ligand recognition. Our work provides a starting point for understanding the molecular basis of mOR activation by fentanyl which has many analogs emerging at a rapid pace. The knowledge may also inform the design of safer analgesics to combat the opioid crisis. Current protein simulation studies employ standard protonation and tautomer states; our work demonstrates the need to move beyond the practice to advance our understanding of protein-ligand recognition.

scholarly journals How mu-Opioid Receptor Recognizes Fentanyl

2020 ◽  
Author(s):  
Quynh Vo ◽  
Paween Mahinthichaichan ◽  
Jana Shen ◽  
Christopher Ellis
Keyword(s):  
Opioid Receptor ◽  
Ph Dependence ◽  
Mu Opioid Receptor ◽  
Structural Basis ◽  
Ligand Recognition ◽  
Binding Modes ◽  
Mu Opioid ◽  
Synthetic Opioids ◽  
Opioid Crisis ◽  
Starting Point

Abstract The opioid crisis has escalated during the COVID-19 pandemic. More than half of the overdose-related deaths are related to synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor (mOR). In recent years, crystal structures of mOR complexed with morphine derivatives have been determined; however, structural basis of mOR activation by fentanyl-like synthetic opioids remains lacking. Exploiting the X-ray structure of mOR bound to a morphinan ligand and several state-of-the-art simulation techniques, including weighted ensemble and continuous constant pH molecular dynamics, we elucidated the detailed binding mechanism of fentanyl with mOR. Surprisingly, in addition to the orthosteric site common to morphinan opiates, fentanyl can move deeper and bind mOR through hydrogen bonding with a conserved histidine H297, which has been shown to modulate mOR's ligand affinity and pH dependence in mutagenesis experiments, but its precise role remains unclear. Intriguingly, the secondary binding mode is only accessible when H297 adopts a neutral HID tautomer. Alternative binding modes and involvement of tautomer states may represent general mechanisms in G protein-coupled receptor (GPCR)-ligand recognition. Our work provides a starting point for understanding mOR activation by fentanyl analogs that are emerging at a rapid pace and assisting the design of safer analgesics to combat the opioid crisis. Current protein simulation studies employ standard protonation and tautomer states; our work demonstrates the need to move beyond the practice to advance our understanding of protein-ligand recognition.

Structural basis of the transactivation deficiency of the human PPARγ F360L mutant associated with familial partial lipodystrophy

2014 ◽  
Vol 70 (7) ◽  
pp. 1965-1976 ◽  
Author(s):  
Clorinda Lori ◽  
Alessandra Pasquo ◽  
Roberta Montanari ◽  
Davide Capelli ◽  
Valerio Consalvi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Partial Agonist ◽  
Salt Bridge ◽  
Van Der Waals Interactions ◽  
Structural Basis ◽  
Wild Type ◽  
Partial Lipodystrophy ◽  
X Ray ◽  
Familial Partial Lipodystrophy

The peroxisome proliferator-activated receptors (PPARs) are transcription factors that regulate glucose and lipid metabolism. The role of PPARs in several chronic diseases such as type 2 diabetes, obesity and atherosclerosis is well known and, for this reason, they are the targets of antidiabetic and hypolipidaemic drugs. In the last decade, some rare mutations in human PPARγ that might be associated with partial lipodystrophy, dyslipidaemia, insulin resistance and colon cancer have emerged. In particular, the F360L mutant of PPARγ (PPARγ2 residue 388), which is associated with familial partial lipodystrophy, significantly decreases basal transcriptional activity and impairs stimulation by synthetic ligands. To date, the structural reason for this defective behaviour is unclear. Therefore, the crystal structure of PPARγ F360L together with the partial agonist LT175 has been solved and the mutant has been characterized by circular-dichroism spectroscopy (CD) in order to compare its thermal stability with that of the wild-type receptor. The X-ray analysis showed that the mutation induces dramatic conformational changes in the C-terminal part of the receptor ligand-binding domain (LBD) owing to the loss of van der Waals interactions made by the Phe360 residue in the wild type and an important salt bridge made by Arg357, with consequent rearrangement of loop 11/12 and the activation function helix 12 (H12). The increased mobility of H12 makes the binding of co-activators in the hydrophobic cleft less efficient, thereby markedly lowering the transactivation activity. The spectroscopic analysis in solution and molecular-dynamics (MD) simulations provided results which were in agreement and consistent with the mutant conformational changes observed by X-ray analysis. Moreover, to evaluate the importance of the salt bridge made by Arg357, the crystal structure of the PPARγ R357A mutant in complex with the agonist rosiglitazone has been solved.

scholarly journals Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1

2020 ◽  
Author(s):  
Sophie M. Travis ◽  
Kevin DAmico ◽  
I-Mei Yu ◽  
Safraz Hamid ◽  
Gabriel Ramirez-Arellano ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Relative Orientation ◽  
Snare Complex ◽  
Structural Basis ◽  
Binding Modes ◽  
Range Interaction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Long Range Interaction ◽  
Target Membrane

AbstractMultisubunit tethering complexes (MTCs) are large (250 to >750 kDa), conserved macromolecular machines that are essential for SNARE-mediated membrane fusion in all eukaryotes. MTCs are thought to function as organizers of membrane trafficking, mediating the initial, long-range interaction between a vesicle and its target membrane and promoting the formation of membrane-bridging SNARE complexes. Previously, we reported the structure of the Dsl1 complex, the simplest known MTC, which is essential for COPI-mediated transport from the Golgi to the endoplasmic reticulum (ER). This structure suggested how the Dsl1 complex might function to tether a vesicle to its target membrane by binding at one end to the COPI coat and at the other end to ER SNAREs. Here, we use x-ray crystallography to investigate these Dsl1-SNARE interactions in greater detail. The Dsl1 complex comprises three subunits that together form a two-legged structure with a central hinge. Our results show that distal regions of each leg bind N-terminal Habc domains of the ER SNAREs Sec20 (a Qb-SNARE) and Use1 (a Qc-SNARE). The observed binding modes appear to anchor the Dsl1 complex to the ER target membrane while simultaneously ensuring that both SNAREs are in open conformations with their SNARE motifs available for assembly. The proximity of the two SNARE motifs, and therefore their ability to enter the same SNARE complex, depends on the relative orientation of the two Dsl1 legs.

scholarly journals Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR–RXR

2020 ◽  
Vol 48 (17) ◽  
pp. 9969-9985
Author(s):  
Judit Osz ◽  
Alastair G McEwen ◽  
Maxime Bourguet ◽  
Frédéric Przybilla ◽  
Carole Peluso-Iltis ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Dna Binding ◽  
Structural Dynamics ◽  
Binding Domain ◽  
Retinoic Acid Receptors ◽  
Structural Basis ◽  
Dna Binding Domain ◽  
Binding Modes ◽  
Dna Complexes ◽  
X Ray

Abstract Retinoic acid receptors (RARs) as a functional heterodimer with retinoid X receptors (RXRs), bind a diverse series of RA-response elements (RAREs) in regulated genes. Among them, the non-canonical DR0 elements are bound by RXR–RAR with comparable affinities to DR5 elements but DR0 elements do not act transcriptionally as independent RAREs. In this work, we present structural insights for the recognition of DR5 and DR0 elements by RXR–RAR heterodimer using x-ray crystallography, small angle x-ray scattering, and hydrogen/deuterium exchange coupled to mass spectrometry. We solved the crystal structures of RXR–RAR DNA-binding domain in complex with the Rarb2 DR5 and RXR–RXR DNA-binding domain in complex with Hoxb13 DR0. While cooperative binding was observed on DR5, the two molecules bound non-cooperatively on DR0 on opposite sides of the DNA. In addition, our data unveil the structural organization and dynamics of the multi-domain RXR–RAR DNA complexes providing evidence for DNA-dependent allosteric communication between domains. Differential binding modes between DR0 and DR5 were observed leading to differences in conformation and structural dynamics of the multi-domain RXR–RAR DNA complexes. These results reveal that the topological organization of the RAR binding element confer regulatory information by modulating the overall topology and structural dynamics of the RXR–RAR heterodimers.

scholarly journals Binding Mode Characterization of NBD Series CD4-Mimetic HIV-1 Entry Inhibitors by X-Ray Structure and Resistance Study

2014 ◽  
Vol 58 (9) ◽  
pp. 5478-5491 ◽  
Author(s):  
Francesca Curreli ◽  
Young Do Kwon ◽  
Hongtao Zhang ◽  
Yongping Yang ◽  
Daniel Scacalossi ◽  
...  
Keyword(s):  
Salt Bridge ◽  
Binding Mode ◽  
Piperidine Ring ◽  
X Ray ◽  
Entry Inhibitors ◽  
Biophysical Studies ◽  
Close Proximity ◽  
Gp120 Core ◽  
Hiv 1

ABSTRACTWe previously identified two small-molecule CD4 mimetics—NBD-556 and NBD-557—and synthesized a series of NBD compounds that resulted in improved neutralization activity in a single-cycle HIV-1 infectivity assay. For the current investigation, we selected several of the most active compounds and assessed their antiviral activity on a panel of 53 reference HIV-1 Env pseudoviruses representing diverse clades of clinical isolates. The selected compounds inhibited tested clades with low-micromolar potencies. Mechanism studies indicated that they act as CD4 agonists, a potentially unfavorable therapeutic trait, in that they can bind to the gp120 envelope glycoprotein and initiate a similar physiological response as CD4. However, one of the compounds, NBD-09027, exhibited reduced agonist properties, in both functional and biophysical studies. To understand the binding mode of these inhibitors, we first generated HIV-1-resistant mutants, assessed their behavior with NBD compounds, and determined the X-ray structures of two inhibitors, NBD-09027 and NBD-10007, in complex with the HIV-1 gp120 core at ∼2-Å resolution. Both studies confirmed that the NBD compounds bind similarly to NBD-556 and NBD-557 by inserting their hydrophobic groups into the Phe43 cavity of gp120. The basic nitrogen of the piperidine ring is located in close proximity to D368 of gp120 but it does not form any H-bond or salt bridge, a likely explanation for their nonoptimal antagonist properties. The results reveal the structural and biological character of the NBD series of CD4 mimetics and identify ways to reduce their agonist properties and convert them to antagonists.

scholarly journals Formazanate Complexes of Bis-Cyclometalated Iridium

2019 ◽  
Author(s):  
Evanta Kabir ◽  
Ge Mu ◽  
David A. Momtaz ◽  
Noah A. Bryce ◽  
Thomas Teets
Keyword(s):  
Point Group ◽  
Binding Mode ◽  
Group Symmetry ◽  
Binding Modes ◽  
X Ray Diffraction ◽  
Substitution Pattern ◽  
X Ray ◽  
Redox Active ◽  
Symmetric Geometry ◽  
New Compounds

<div>In this work we describe a series of bis-cyclometalated iridium(III) formazanate complexes, expanding the coordination chemistry of the redox-active formazanate class to iridium. A total of 18 new complexes are described, varying the substituent pattern on the formazanate and the identity of the cyclometalating ligand on iridium. Eight of the new compounds are structurally characterized by single-crystal X-ray diffraction, which along with NMR spectroscopy evinces two binding modes of the formazanate. Two of the compounds are isolated in a C2-symmetric geometry where the formazanate is bound in a six-member chelate “closed” conformation, involving the 1- and 5-positions of the 1,2,4,5-tetraazapentadienyl formazanate core. In most of the examples, the major isomer that forms and is exclusively isolated involves the formazanate bound in a five-member chelate “open” form, coordinating through the 1- and 4-positions of the formazanate core and resulting in C1 point-group symmetry. All complexes are characterized by UV-vis absorption spectroscopy and cyclic voltammetry, with these features depending primarily on the substitution pattern on the formazanate, and to a lesser extent on the identity of the cyclometalating ligand and formazanate binding mode.</div>

scholarly journals Structural basis of human ghrelin receptor signaling by ghrelin and the synthetic agonist ibutamoren

2021 ◽  
Author(s):  
Cheng Zhang ◽  
Heng Liu ◽  
Dapeng Sun ◽  
Alexander Myasnikov ◽  
Marjorie Damian ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Hormone Secretion ◽  
Growth Hormone Secretion ◽  
Salt Bridge ◽  
Binding Pocket ◽  
Binding Mode ◽  
Receptor Activation ◽  
Structural Basis ◽  
Ghrelin Receptor ◽  
Signaling Complex

Abstract The 'hunger hormone' ghrelin activates the ghrelin receptor GHSR to stimulate food intake and growth hormone secretion and regulate reward signaling. Acylation of ghrelin at Ser3 is required for its agonistic action on GHSR. Synthetic agonists of GHSR are under clinical evaluation for disorders related to appetite and growth hormone dysregulation. Here, we report high-resolution cryo-EM structures of the GHSR-Gi signaling complex with ghrelin and the non-peptide agonist ibutamoren as an investigational new drug. Our structures together with mutagenesis data reveal the molecular basis for the binding of ghrelin and ibutamoren. The structural comparison suggests a salt bridge and an aromatic cluster near the agonist-binding pocket as important structural motifs in receptor activation. Notable variations of the Gi binding mode are observed in our cryo-EM analysis, indicating the highly dynamic nature of Gi-coupling to GHSR. Our results provide a framework for understanding GHSR signaling and developing new GHSR agonist drugs.

scholarly journals Dinuclear Complexes of Flexidentate Pyridine-Substituted Formazanate Ligands

2020 ◽  
Author(s):  
Ge Mu ◽  
Thomas Teets
Keyword(s):  
Ligand Binding ◽  
Building Blocks ◽  
Binding Mode ◽  
Redox Properties ◽  
Dinuclear Complexes ◽  
Binding Modes ◽  
X Ray Diffraction ◽  
Frontier Orbitals ◽  
X Ray ◽  
Dinuclear Structure

In this work we show the utility of flexidentate pyridyl‐substituted formazanate ligands in assembling dinuclear coordinationcomplexes with iridium(III) and/or platinum(II) building blocks. The versatile binding modes of these ligands allow the preparation of several different dinuclear structures, highlighting the potential of these formazanates to serve as redoxactive supporting ligands for multimetallic complexes. The dinuclear complexes are typically prepared in a stepwise strategy, adding one metal unit at a time, with the coordination mode of the formazanate with the first metal dictating the binding mode in the final dinuclear structure. Eight of the new complexes, including both mononuclear precursors and dinuclear products, are structurally characterized by single‐crystal X‐ray diffraction, which along with NMR spectroscopy unambiguously establish ligand binding modes and symmetries of the compounds. All complexes are characterized by UVVis absorption spectroscopy and cyclic voltammetry. The frontier orbitals are localized on the formazanate ligand, and a characteristic, intense formazanate‐centered π→π* absorption band is observed in the absorption spectrum. Structureproperty relationships are established, relating the ligand binding mode to the redox properties and spectroscopic features. .<br>

Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase

2017 ◽  
Vol 73 (7) ◽  
pp. 573-580 ◽  
Author(s):  
Kunhua Li ◽  
Elisha N. Fielding ◽  
Heather L. Condurso ◽  
Steven D. Bruner
Keyword(s):  
Catalytic Mechanism ◽  
Binding Pocket ◽  
Binding Mode ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
General Mechanism ◽  
Oxygen Binding ◽  
Migration Pathway ◽  
And Migration ◽  
Key Residues

The enzyme DpgC is included in the small family of cofactor-independent dioxygenases. The chemistry of DpgC is uncommon as the protein binds and utilizes dioxygen without the aid of a metal or organic cofactor. Previous structural and biochemical studies identified the substrate-binding mode and the components of the active site that are important in the catalytic mechanism. In addition, the results delineated a putative binding pocket and migration pathway for the co-substrate dioxygen. Here, structural biology is utilized, along with site-directed mutagenesis, to probe the assigned dioxygen-binding pocket. The key residues implicated in dioxygen trafficking were studied to probe the process of binding, activation and chemistry. The results support the proposed chemistry and provide insight into the general mechanism of dioxygen binding and activation.

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