Thermostabilization of the Human Endothelin Type B Receptor

Structural insights into endothelin receptor signalling

Endothelins and their receptors, type A (ETA) and type B (ETB), modulate vital cellular processes, including growth, survival, invasion and angiogenesis, through multiple G proteins. This review highlights the structural determinations of these receptors by X-ray crystallography and cryo-electron microscopy, and their activation mechanisms by endothelins. Explorations of the conformational changes upon receptor activation have provided insights into the unique G-protein coupling feature of the endothelin receptors. The review further delves into the binding modes of the clinical antagonist and the inverse agonists. These findings significantly contribute to understanding the mechanism of G-protein activation and have potential implications for drug development, particularly in the context of vasodilatory antagonists and agonists targeting the endothelin receptors.

Cryo-EM structure of the endothelin-1-ETB-Gi complex

The endothelin ET_B receptor is a promiscuous G-protein coupled receptor that is activated by vasoactive peptide endothelins. ET_B signaling induces reactive astrocytes in the brain and vasorelaxation in vascular smooth muscle. Consequently, ET_B agonists are expected to be drugs for neuroprotection and improved anti-tumor drug delivery. Here, we report the cryo-electron microscopy structure of the endothelin-1-ET_B-G_i complex at 2.8 Å resolution, with complex assembly stabilized by a newly established method. Comparisons with the inactive ET_B receptor structures revealed how endothelin-1 activates the ET_B receptor. The NPxxY motif, essential for G-protein activation, is not conserved in ET_B, resulting in a unique structural change upon G-protein activation. Compared with other GPCR-G-protein complexes, ET_B binds G_i in the shallowest position, further expanding the diversity of G-protein binding modes. This structural information will facilitate the elucidation of G-protein activation and the rational design of ET_B agonists.

Transfer mechanism of cell-free synthesized membrane proteins into mammalian cells

Nanodiscs are emerging to serve as transfer vectors for the insertion of recombinant membrane proteins into membranes of living cells. In combination with cell-free expression technologies, this novel process opens new perspectives to analyze the effects of even problematic targets such as toxic, hard-to-express, or artificially modified membrane proteins in complex cellular environments of different cell lines. Furthermore, transferred cells must not be genetically engineered and primary cell lines or cancer cells could be implemented as well. We have systematically analyzed the basic parameters of the nanotransfer approach and compared the transfer efficiencies from nanodiscs with that from Salipro particles. The transfer of five membrane proteins was analyzed: the prokaryotic proton pump proteorhodopsin, the human class A family G-protein coupled receptors for endothelin type B, prostacyclin, free fatty acids type 2, and the orphan GPRC5B receptor as a class C family member. The membrane proteins were cell-free synthesized with a detergent-free strategy by their cotranslational insertion into preformed nanoparticles containing defined lipid environments. The purified membrane protein/nanoparticles were then incubated with mammalian cells. We demonstrate that nanodiscs disassemble and only lipids and membrane proteins, not the scaffold protein, are transferred into cell membranes. The process is detectable within minutes, independent of the nanoparticle lipid composition, and the transfer efficiency directly correlates with the membrane protein concentration in the transfer mixture and with the incubation time. Transferred membrane proteins insert in both orientations, N-terminus in and N-terminus out, in the cell membrane, and the ratio can be modulated by engineering. The viability of cells is not notably affected by the transfer procedure, and transferred membrane proteins stay detectable in the cell membrane for up to 3 days. Transferred G-protein coupled receptors retained their functionality in the cell environment as shown by ligand binding, induction of internalization, and specific protein interactions. In comparison to transfection, the cellular membrane protein concentration is better controllable and more uniformly distributed within the analyzed cell population. A further notable difference to transfection is the accumulation of transferred membrane proteins in clusters, presumably determined by microdomain structures in the cell membranes.

Crystal structure of human endothelin ETB receptor in complex with sarafotoxin S6b

Sarafotoxins (SRTXs) are endothelin-like peptides extracted from snake venom. SRTXs stimulate the endothelin ET_A and ET_B receptors and enhance vasoconstriction, followed by left ventricular dysfunction and bronchoconstriction. SRTXs include four major isopeptides, S6a-d, with different subtype selectivities. Here, we report the crystal structure of the human ET_B receptor in complex with the non-selective sarafotoxin S6b at 3.0 Å resolution. This structure reveals the similarities and differences between the binding modes of the endothelins and S6b. Moreover, molecular dynamics simulations based on the S6b-bound receptor provides structural insight into the subtype selectivity of the sarafotoxins. Our study clarifies the recognition mechanism of the endothelin-like peptide families.

Crystal structure of human endothelin ETB receptor in complex with peptide inverse agonist IRL2500

Endothelin receptors (ETA and ETB) are G-protein-coupled receptors activated by endothelin-1 and are involved in blood pressure regulation. IRL2500 is a peptide-mimetic of the C-terminal tripeptide of endothelin-1, and has been characterized as a potent ETB-selective antagonist, which has preventive effects against brain edema. Here, we report the crystal structure of the human ETB receptor in complex with IRL2500 at 2.7 Å-resolution. The structure revealed the different binding modes between IRL2500 and endothelin-1, and provides structural insights into its ETB-selectivity. Notably, the biphenyl group of IRL2500 penetrates into the transmembrane core proximal to D2.50, thus stabilizing the inactive conformation. Using the newly-established constitutively active mutant, we clearly demonstrate that IRL2500 functions as an inverse agonist for the ETB receptor. The current findings will expand the chemical space of ETR antagonists and facilitate the design of inverse agonists for other class A GPCRs.

Crystal structures of human ETB receptor provide mechanistic insight into receptor activation and partial activation

Endothelin receptors (ET_A and ET_B) are class A GPCRs activated by vasoactive peptide endothelins, and are involved in blood pressure regulation. ET_B-selective signalling induces vasorelaxation, and thus selective ET_B agonists are expected to be utilized for improved anti-tumour drug delivery and neuroprotection. Here, we report the crystal structures of human ET_B receptor in complex with ET_B-selective agonist, endothelin-3 and an ET_B-selective endothelin analogue IRL1620. The structure of the endothelin-3-bound receptor reveals that the disruption of water-mediated interactions between W6.48 and D2.50 is critical for receptor activation, while these hydrogen-bonding interactions are partially preserved in the IRL1620-bound structure. Consistently, functional analysis reveals the partial agonistic effect of IRL1620. The current findings clarify the detailed molecular mechanism for the coupling between the orthosteric pocket and the G-protein binding, and the partial agonistic effect of IRL1620, thus paving the way for the design of improved agonistic drugs targeting ET_B.

Computational design of thermostabilizing point mutations for G protein-coupled receptors

Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational approach to effective prediction of stabilizing mutations in GPCRs, named CompoMug, which employs sequence-based analysis, structural information, and a derived machine learning predictor. Tested experimentally on the serotonin 5-HT_2C receptor target, CompoMug predictions resulted in 10 new stabilizing mutations, with an apparent thermostability gain ~8.8°C for the best single mutation and ~13°C for a triple mutant. Binding of antagonists confers further stabilization for the triple mutant receptor, with total gains of ~21°C as compared to wild type apo 5-HT_2C. The predicted mutations enabled crystallization and structure determination for the 5-HT_2C receptor complexes in inactive and active-like states. While CompoMug already shows high 25% hit rate and utility in GPCR structural studies, further improvements are expected with accumulation of structural and mutation data.

The trillions of cells in the human body rely on receptors that sit in their cell membranes to communicate with each other. Hundreds of different receptors belong to the G protein-coupled receptor superfamily (called GPCRs for short) and play vital roles in the all organs and bodily systems. Indeed, GPCRs are the targets for almost 40% of therapeutic drugs. As such, deciphering the shape and activity of GPCRs is key to understanding the normal workings of the human biology and could help scientists discover new treatments for various diseases, from depression to high blood pressure to cancer. These receptors, however, are notoriously flimsy and unstable, making them difficult to work with in the laboratory.

Different approaches have been developed to make GPCRs more stable, usually by swapping one or a few of the amino acid building blocks in the protein for other amino acids. Currently, this requires a costly and slow trial-and-error approach in which each amino acid out of 300-400 in the protein is mutated and tested experimentally.

To speed up and reduce the cost of the process, Popov et al. asked if a computer could predict which mutations in the protein would stabilize it, meaning that fewer proteins would actually need to be tested. Four computer algorithms based on four different principles were developed and verified. The first one compares the target GPCR to other closely related receptors, trying to detect variations that cause the instability. The second tries to build in specific stabilizing interactions, or “bridges”, between different parts of the receptor. The third algorithm searches the known structures of other GPCRs for useful mutations. Finally, the fourth one uses accumulated data on the stability of hundreds of mutations in different GPCRs to train a machine learning predictor to recognize stabilizing mutations.

All four algorithms produced useful predictions in a real-life project. Indeed, when combined in one computational tool, named CompoMug, the algorithms made it possible to detect optimal mutations in a human GPCR called 5-HT_2C. This made the protein much easier to work with in the laboratory, and ultimately helped to solve its three-dimensional structure (which was reported in a separate study, published earlier in 2018)

The 5-HT_2C receptor is involved in regulating, among other things, mood and appetite. Details of its structure might therefore help researchers to design new antidepressants and obesity treatments. Moreover, CompoMug is already helping structural biologists to solve the structures of other GPCRs, which will further facilitate many aspects of GPCR drug discovery.

X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog

Endothelin receptors (ETRs) have crucial roles in vascular control and are targets for drugs designed to treat circulatory-system diseases and cancer progression. The nonpeptide dual-ETR antagonist bosentan is the first oral drug approved to treat pulmonary arterial hypertension. Here we report crystal structures of human endothelin ET_B receptor bound to bosentan and to the ET_B-selective analog K-8794, at 3.6-Å and 2.2-Å resolution, respectively. The K-8794-bound structure reveals the detailed water-mediated hydrogen-bonding network at the transmembrane core, which could account for the weak negative allosteric modulation of ET_B by Na⁺ ions. The bosentan-bound structure reveals detailed interactions with ET_B, which are probably conserved in the ET_A receptor. A comparison of the two structures shows unexpected similarity between antagonist and agonist binding. Despite this similarity, bosentan sterically prevents the inward movement of transmembrane helix 6 (TM6), and thus exerts its antagonistic activity. These structural insights will facilitate the rational design of new ETR-targeting drugs.

Activation mechanism of endothelin ETB receptor by endothelin-1

Endothelin, a 21-amino-acid peptide, participates in various physiological processes, such as regulation of vascular tone, humoral homeostasis, neural crest cell development and neurotransmission. Endothelin and its G-protein-coupled receptor are involved in the development of various diseases, such as pulmonary arterial hypertension, and thus are important therapeutic targets. Here we report crystal structures of human endothelin type B receptor in the ligand-free form and in complex with the endogenous agonist endothelin-1. The structures and mutation analysis reveal the mechanism for the isopeptide selectivity between endothelin-1 and -3. Transmembrane helices 1, 2, 6 and 7 move and envelop the entire endothelin peptide, in a virtually irreversible manner. The agonist-induced conformational changes are propagated to the receptor core and the cytoplasmic G-protein coupling interface, and probably induce conformational flexibility in TM6. A comparison with the M2 muscarinic receptor suggests a shared mechanism for signal transduction in class A G-protein-coupled receptors.