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Feng BM, Zhang YY, Zhou XC, Wang JL, Feng YF. MolLoG: A Molecular Level Interpretability Model Bridging Local to Global for Predicting Drug Target Interactions. J Chem Inf Model 2024; 64:4348-4358. [PMID: 38709146 DOI: 10.1021/acs.jcim.4c00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Developing new pharmaceuticals is a costly and time-consuming endeavor fraught with significant safety risks. A critical aspect of drug research and disease therapy is discerning the existence of interactions between drugs and proteins. The evolution of deep learning (DL) in computer science has been remarkably aided in this regard in recent years. Yet, two challenges remain: (i) balancing the extraction of profound, local cohesive characteristics while warding off gradient disappearance and (ii) globally representing and understanding the interactions between the drug and target local attributes, which is vital for delivering molecular level insights indispensable to drug development. In response to these challenges, we propose a DL network structure, MolLoG, primarily comprising two modules: local feature encoders (LFE) and global interactive learning (GIL). Within the LFE module, graph convolution networks and leap blocks capture the local features of drug and protein molecules, respectively. The GIL module enables the efficient amalgamation of feature information, facilitating the global learning of feature structural semantics and procuring multihead attention weights for abstract features stemming from two modalities, providing biologically pertinent explanations for black-box results. Finally, predictive outcomes are achieved by decoding the unified representation via a multilayer perceptron. Our experimental analysis reveals that MolLoG outperforms several cutting-edge baselines across four data sets, delivering superior overall performance and providing satisfactory results when elucidating various facets of drug-target interaction predictions.
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Affiliation(s)
- Bao-Ming Feng
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, 266520 Shandong, China
| | - Yuan-Yuan Zhang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, 266520 Shandong, China
| | - Xiao-Chen Zhou
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, 266520 Shandong, China
| | - Jin-Long Wang
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, 266520 Shandong, China
| | - Yin-Fei Feng
- School of Information and Control Engineering, Qingdao University of Technology, Qingdao, 266520 Shandong, China
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2
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Dubey T, Bhanukiran K, Hemalatha S. Development of phytosterol-loaded silver nanoparticles for ameliorating haemorrhoidal complications via the AMPK pathway-a mechanistic approach. Biomed Mater 2024; 19:035030. [PMID: 38518371 DOI: 10.1088/1748-605x/ad3703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/22/2024] [Indexed: 03/24/2024]
Abstract
The aim of the current study was to synthesize silver nanoparticles (PLSNPs) using green technology by means of phytosterol-enriched fractions fromBlumea laceraextracts (EAF) and evaluate their toxicological and anti-haemorrhoidal potential. The average size of the synthesized particles was found to be 85.64 nm by scanning electron microscopy and transmission electron microscopy. Energy dispersive spectroscopy showed the elemental composition of PLSNPs to be 12.59% carbon and 87.41% silver, indicating the capping of phytochemicals on the PLSNPs. The PLSNPs were also standardized for total phytosterol content using chemical methods and high-perfromance liquid chromatography. The PLSNPs were found to be safe up to 1000 mg kg-1as no toxicity was observed in the acute and sub-acute toxicity studies performed as per OECD guidelines. After the induction of haemorrhoids, experimental animals were treated with different doses of EAF, PLSNPs and a standard drug (Pilex) for 7 d, and on the eighth day the ameliorative potential was assessed by evaluating the haemorrhoidal (inflammatory severity index, recto-anal coefficient) and biochemical (tumour necrosis factor-alpha and interleukin-6) parameters and histology of the recto-anal tissue. The results showed that treatment with PLSNPs and Pilex significantly (p< 0.05) reduced haemorrhoidal and biochemical parameters. This was further supported by restoration of altered antioxidant status. Further, a marked reduction in the inflammatory zones along with minimal dilated blood vessels was observed in the histopathological study. The results of molecular docking studies also confirmed the amelioration of haemorrhoids via AMP-activated protein kinase (AMPK)-mediated reduction of inflammation and endothelin B receptor modification by PLSNPs. In conclusion, PLSNPs could be a good alternative for the management of haemorrhoids.
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Affiliation(s)
- Tarkeshwar Dubey
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi 221005, India
| | - Kancharla Bhanukiran
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi 221005, India
| | - Siva Hemalatha
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi 221005, India
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Oshima HS, Sano FK, Akasaka H, Iwama A, Shihoya W, Nureki O. Optimizing cryo-EM structural analysis of G i-coupling receptors via engineered G t and Nb35 application. Biochem Biophys Res Commun 2024; 693:149361. [PMID: 38128244 DOI: 10.1016/j.bbrc.2023.149361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Cryo-EM single particle analysis has recently facilitated the high-resolution structural determination of numerous GPCR-G complexes. Diverse methodologies have been devised with this trend, and in the case of GPCR-Gi complexes, scFv16, an antibody that recognizes the intricate interface of the complex, has been mainly implemented to stabilize the complex. However, owing to their flexibility and heterogeneity, structural determinations of GPCR-Gi complexes remain both challenging and resource-intensive. By employing eGαt, which exhibits binding affinity to modified nanobody Nb35, the cryo-EM structure of Rhodopsin-eGαt complex was previously reported. Using this modified G protein, we determined the structure of the ETB-eGt complex bound to the modified Nb35. The determined structure of ETB receptor was the same as the previously reported ETB-Gi complex, and the resulting dataset demonstrated significantly improved anisotropy. This modified G protein will be utilized for the structural determination of other GPCR-Gi complexes.
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Affiliation(s)
- Hidetaka S Oshima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroaki Akasaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Aika Iwama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Yin Q, Zhang H, Huang T, Liu B, Negm S, El-Kott AF. Anti-collagenase, Anti-elastase, Anti-urease, and Anti-cancer Potentials of Isokaempferide as Natural Compound: In vitro and in silico Study. J Oleo Sci 2024; 73:187-199. [PMID: 38311409 DOI: 10.5650/jos.ess23176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
One of the main goals of medicinal chemistry in recent years has been the development of new enzyme inhibitors and anti-cancer medicines. The isokaempferide' ability to inhibit the enzymes urease, elastase, and collagenase were also studied. The results showed that isokaempferide was the most effective compound against the assigned enzymes, with IC 50 values of 23.05 µM for elastase, 12.83 µM for urease, and 33.62 µM for collagenase respectively. It should be emphasized that natural compound was more effective at inhibiting some enzymes. Additionally, the compound was tested for their anti-cancer properties using colon, lung, breast cancer cell lines. The chemical activities of isokaempferide against urease, collagenase, and elastase were investigated utilizing the molecular docking study. The anti-cancer activities of the compound were evaluated against lung cancer cells such as SPC-A-1, SK-LU-1, 95D, breast cancer cells like MCF7, Hs 578Bst, Hs 319.T, and UACC-3133 cell lines, and colon cancer cell lines like CL40, SW1417, LS1034, and SW480. The chemical activities of isokaempferide against some of the expressed surface receptor proteins (EGFR, estrogen receptor, CD47, progesterone receptor, folate receptor, CD44, HER2, CD155, CXCR4, CD97, and endothelin receptor) in the mentioned cell lines were assessed using the molecular docking calculations. The results showed the probable interactions and their characteristics at an atomic level. The docking scores revealed that isokaempferide has a strong binding affinity to the enzymes and proteins. In addition, the compound formed powerful contact with the enzymes and receptors. Thus, isokaempferide could be potential inhibitor for enzymes and cancer cells.
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Affiliation(s)
- Qian Yin
- Department of Pathology, The Third Clinical Medical College of China Three Gorges University·Gezhouba Central Hospital of Sinopharm
| | - Hao Zhang
- Department of Endocrinology, The Third Clinical Medical College of China Three Gorges University·Gezhouba Central Hospital of Sinopharm
| | - Ting Huang
- Department of Oncology, No. 215 Hospital of Shaanxi Nuclear Industry
| | - Bin Liu
- Department of General Surgery, Dalian University Affiliated Xinhua Hospital
| | - Sally Negm
- Department of Life Sciences, College of Science and Art Mahyel Aseer, King Khalid University
| | - Attalla F El-Kott
- Department of Biology, College of Science, King Khalid University
- Department of Zoology, Faculty of Science, Damanhour University
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Li L, Zhu Y, Huang YG, Hou DZ, Ahmed Zaki MS, Sideeg AM, Mohammed H, El-Kott AF, Al-Saeed FA, Ling P. Therapeutic properties, biological effects, antiliver cancer, and anticolon cancer effects of some natural compounds: A biochemical approach. J Biochem Mol Toxicol 2024; 38:e23573. [PMID: 37934567 DOI: 10.1002/jbt.23573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/19/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Natural compounds, such as carotenoids, flavonoids, anthocyanins, or terpenoids, are physiologically active components found in plants (pigments), often known as phytochemicals or phytonutrients. The in vitro cytotoxic and anticolon cancer effects of biologically bavachin, bavachinin, artepillin C, and aromadendrin compounds against SW48, SNU-C1, COLO 205, RKO, LS411N, and SW1417 cancer cell lines were assessed. Results of enzymes and antibacterial, antifungal were in level of micromolar that is good impacts. These natural compounds may be antidiabetic, anticancer, and antibacterial candidates for drug design. IC50 results were obtained between 14-19 and 5-119 µM for α-amylase and α-glucosidase, respectively. Good inhibitor Bavachinin was detected for both enzymes (IC50 for α-amylase: 14.37 µM and IC50 for α-glucosidase: 5.27 µM). The chemical activities of aromadendrin, artepillin C, bavachin, and bavachinin against pancreatic α-amylase and α-glucosidase were assessed by conducting the molecular docking study. The chemical activities of aromadendrin, artepillin C, bavachin, and bavachinin against some of the expressed surface receptor proteins (CD44, CD47, CXCR4, EGFR, folate receptor, HER2, and endothelin receptor) in the mentioned cell lines were investigated using the molecular docking calculations. The results illustrated the atomic-level properties and potential interactions. These chemicals have high binding affinities to the enzymes and proteins, according to the docking scores. In addition, the compounds formed strong contacts with the enzymes and receptors. Thus, these compounds could be potential inhibitors for enzymes and cancer cells.
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Affiliation(s)
- Long Li
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yu Zhu
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Ying-Guang Huang
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - De-Zhi Hou
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | | | - Abulqasim M Sideeg
- Department of Anatomy, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Heitham Mohammed
- Department of Anatomy, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Attalla F El-Kott
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Department of Zoology, College of Science, Damanhour University, Damanhour, Egypt
| | - Fatimah A Al-Saeed
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
| | - Ping Ling
- Department of General Surgery I, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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Vila-Julià G, Rubio-Martinez J, Perez JJ. Assessment of the bound conformation of bombesin to the BB1 and BB2 receptors. Int J Biol Macromol 2024; 255:127843. [PMID: 37956803 DOI: 10.1016/j.ijbiomac.2023.127843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Bombesin is an endogenous peptide involved in a wide spectrum of physiological activities ranging from satiety, control of circadian rhythm and thermoregulation in the central nervous system, to stimulation of gastrointestinal hormone release, activation of macrophages and effects on development in peripheral tissues. Actions of the peptide are mediated through the two high affinity G-protein coupled receptors BB1R and BB2R. Under pathophysiological conditions, these receptors are overexpressed in many different types of tumors, such as prostate cancer, breast cancer, small and non-small cell lung cancer and pancreatic cancer. This observation has been used for designing cell markers, but it has not been yet exploited for therapeutical purposes. Despite the enormous biological interest of the peptide, little is known about the stereochemical features that contribute to their activity. On the one hand, mutagenesis studies identified a few receptor residues important for high bombesin affinity and on the other, a few studies focused on the relevance of diverse residues of the peptide for receptor activation. Models of the peptide bound to BB1R and BB2R can be helpful to improve our understanding of the stereochemical features granting bombesin activity. Accordingly, the present study describes the computational process followed to construct such models by means of Steered Molecular Dynamics, using models of the peptide and its receptors. Present results provide new insights into the structure-activity relationships of bombesin and its receptors, as well as render an explanation for the differential binding affinity observed towards BB1R and BB2R. Finally, these models can be further exploited to help for designing novel small molecule peptidomimetics with improved pharmacokinetics profile.
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Affiliation(s)
- Guillem Vila-Julià
- Department of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Barcelona, Spain; Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech., Av. Diagonal, 647, 08028 Barcelona, Spain
| | - Jaime Rubio-Martinez
- Department of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), Barcelona, Spain
| | - Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya- Barcelona Tech., Av. Diagonal, 647, 08028 Barcelona, Spain.
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Panchal J, Jaiswal S, Jain S, Kumawat J, Sharma A, Jain P, Jain S, Verma K, Dwivedi J, Sharma S. Development of novel bosentan analogues as endothelin receptor antagonists for pulmonary arterial hypertension. Eur J Med Chem 2023; 259:115681. [PMID: 37515921 DOI: 10.1016/j.ejmech.2023.115681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 07/31/2023]
Abstract
Since decades, bosentan has been in use for the treatment of pulmonary arterial hypertension (PAH). However, chronic exposure to bosentan leads to the development of resistance, tolerance, and serious adverse effects that have restricted its usage in clinical practices. To surmount these limitations, some new bosentan derivatives have been synthesized and evaluated for their therapeutic efficacy in PAH. Molecular docking analyses of all the synthesized derivatives were carried out using the endothelin (ET) receptor. In addition, the inhibitory ability of synthesized derivatives was determined in in vitro assay employing an ET-1 human ELISA kit. Among the synthesized derivatives, three derivatives namely 17d, 16j, and 16h with higher docking scores and lower IC50 values were selected for determination of the magnitude of the binding force between the derivative and ET receptor using molecular dynamics (MD) simulations study. Further, these derivatives were subjected to in vivo studies using monocrotaline (MCT) induced PAH in rat model. Results of in vivo studies inferred that the derivatives exhibit impressive ability to reduce PAH. Besides, its protective role was also evidenced in hemodynamic and right ventricular hypertrophy analyses, histological analysis, cardiac biomarkers, hypoxia-inducible factor 1 alpha (HIF1α) levels, and biochemical studies. Furthermore, gene quantification by quantitative RT-PCR and Western blot analysis was also performed to examine its effect on the expression of key proteins in PAH. Notably, amongst three, derivative 16h exhibited the most encouraging results in molecular docking analysis, in vitro, in vivo, histopathological, biochemical, protein expression, and MD studies. Besides, derivative 16h also showed impressive pharmacokinetic features in ADMET analysis. In conclusion, derivative 16 h could act as a reliable ET receptor antagonist and requires further exploration to attain its therapeutic utility in PAH management.
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Affiliation(s)
- Jigar Panchal
- Department of Chemistry, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Shivangi Jaiswal
- Department of Chemistry, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Sonika Jain
- Department of Chemistry, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India.
| | - Jyoti Kumawat
- Department of Chemistry, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Ashima Sharma
- Department of Pharmacy, Panjab University, Chandigarh, 160014, Punjab, India
| | - Pankaj Jain
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Smita Jain
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Kanika Verma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Jaya Dwivedi
- Department of Chemistry, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India.
| | - Swapnil Sharma
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India.
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Shihoya W, Sano FK, Nureki O. Structural insights into endothelin receptor signalling. J Biochem 2023; 174:317-325. [PMID: 37491722 PMCID: PMC10533325 DOI: 10.1093/jb/mvad055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 07/01/2023] [Indexed: 07/27/2023] Open
Abstract
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.
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Affiliation(s)
- Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
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9
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Delahaye J, Stölting M, Geyer C, Vogl T, Eisenblätter M, Helfen A, Höltke C. Development, synthesis and evaluation of novel fluorescent Endothelin-B receptor probes. Eur J Med Chem 2023; 258:115568. [PMID: 37379676 DOI: 10.1016/j.ejmech.2023.115568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
The endothelin (ET) signaling system is comprised of three endothelin peptides (ET-1, -2 and -3) and two corresponding endothelin-A and -B receptors (ETAR and ETBR), which belong to the G-protein coupled receptor (GPCR) superfamily. The endothelin axis, as this system is also referred to, contributes to the maintenance of vascular tone, functions as regulator of inflammation and proliferation and helps in balancing water homeostasis. In pathological settings, the ET axis is known to contribute to endothelial activation in cardiovascular diseases, to cell proliferation, chemoresistance and metastasis in cancer and to inflammation and fibrosis in renal disease. Antagonists of ETAR and ETBR, either subtype-specific compounds or substances with high affinity to both receptors, have been developed for more than 30 years. In the preclinical context, in vivo imaging of endothelin receptor expression has been utilized to assess ET-axis contribution to e.g. cancer or myocardial infarction. In this work, we present the development and synthesis of two novel ETBR-specific fluorescent probes, based on the available antagonists BQ788 and IRL2500 and their preliminary evaluation in a breast cancer context.
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Affiliation(s)
| | - Miriam Stölting
- Clinic for Radiology, University Hospital Münster, Münster, Germany
| | - Christiane Geyer
- Clinic for Radiology, University Hospital Münster, Münster, Germany
| | - Thomas Vogl
- Institute of Immunology, University of Münster, Münster, Germany
| | - Michel Eisenblätter
- Clinic for Radiology, University Hospital Münster, Münster, Germany; Department of Diagnostic and Interventional Radiology, Medical Faculty OWL, Bielefeld University, Bielefeld, Germany
| | - Anne Helfen
- Clinic for Radiology, University Hospital Münster, Münster, Germany
| | - Carsten Höltke
- Clinic for Radiology, University Hospital Münster, Münster, Germany.
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Sano FK, Akasaka H, Shihoya W, Nureki O. Cryo-EM structure of the endothelin-1-ET B-G i complex. eLife 2023; 12:85821. [PMID: 37096326 PMCID: PMC10129325 DOI: 10.7554/elife.85821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/23/2023] [Indexed: 04/26/2023] Open
Abstract
The endothelin ETB receptor is a promiscuous G-protein coupled receptor that is activated by vasoactive peptide endothelins. ETB signaling induces reactive astrocytes in the brain and vasorelaxation in vascular smooth muscle. Consequently, ETB 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-ETB-Gi complex at 2.8 Å resolution, with complex assembly stabilized by a newly established method. Comparisons with the inactive ETB receptor structures revealed how endothelin-1 activates the ETB receptor. The NPxxY motif, essential for G-protein activation, is not conserved in ETB, resulting in a unique structural change upon G-protein activation. Compared with other GPCR-G-protein complexes, ETB binds Gi 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 ETB agonists.
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Affiliation(s)
- Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Akasaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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11
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Liessmann F, Künze G, Meiler J. Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection. Int J Mol Sci 2023; 24:7788. [PMID: 37175495 PMCID: PMC10178219 DOI: 10.3390/ijms24097788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of drug targets and undergo substantial conformational changes in response to ligand binding. Despite recent progress in GPCR structure determination, static snapshots fail to reflect the conformational space of putative binding pocket geometries to which small molecule ligands can bind. In comparative modeling of GPCRs in the absence of a ligand, often a shrinking of the orthosteric binding pocket is observed. However, the exact prediction of the flexible orthosteric binding site is crucial for adequate structure-based drug discovery. In order to improve ligand docking and guide virtual screening experiments in computer-aided drug discovery, we developed RosettaGPCRPocketSize. The algorithm creates a conformational ensemble of biophysically realistic conformations of the GPCR binding pocket between the TM bundle, which is consistent with a knowledge base of expected pocket geometries. Specifically, tetrahedral volume restraints are defined based on information about critical residues in the orthosteric binding site and their experimentally observed range of Cα-Cα-distances. The output of RosettaGPCRPocketSize is an ensemble of binding pocket geometries that are filtered by energy to ensure biophysically probable arrangements, which can be used for docking simulations. In a benchmark set, pocket shrinkage observed in the default RosettaGPCR was reduced by up to 80% and the binding pocket volume range and geometric diversity were increased. Compared to models from four different GPCR homology model databases (RosettaGPCR, GPCR-Tasser, GPCR-SSFE, and GPCRdb), the here-created models showed more accurate volumes of the orthosteric pocket when evaluated with respect to the crystallographic reference structure. Furthermore, RosettaGPCRPocketSize was able to generate an improved realistic pocket distribution. However, while being superior to other homology models, the accuracy of generated model pockets was comparable to AlphaFold2 models. Furthermore, in a docking benchmark using small-molecule ligands with a higher molecular weight between 400 and 700 Da, a higher success rate in creating native-like binding poses was observed. In summary, RosettaGPCRPocketSize can generate GPCR models with realistic orthosteric pocket volumes, which are useful for structure-based drug discovery applications.
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Affiliation(s)
- Fabian Liessmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Jens Meiler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105 Leipzig, Germany
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12
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Structural basis of peptide recognition and activation of endothelin receptors. Nat Commun 2023; 14:1268. [PMID: 36882417 PMCID: PMC9992518 DOI: 10.1038/s41467-023-36998-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Abstract
Endothelin system comprises three endogenous 21-amino-acid peptide ligands endothelin-1, -2, and -3 (ET-1/2/3), and two G protein-coupled receptor (GPCR) subtypes-endothelin receptor A (ETAR) and B (ETBR). Since ET-1, the first endothelin, was identified in 1988 as one of the most potent endothelial cell-derived vasoconstrictor peptides with long-lasting actions, the endothelin system has attracted extensive attention due to its critical role in vasoregulation and close relevance in cardiovascular-related diseases. Here we present three cryo-electron microscopy structures of ETAR and ETBR bound to ET-1 and ETBR bound to the selective peptide IRL1620. These structures reveal a highly conserved recognition mode of ET-1 and characterize the ligand selectivity by ETRs. They also present several conformation features of the active ETRs, thus revealing a specific activation mechanism. Together, these findings deepen our understanding of endothelin system regulation and offer an opportunity to design selective drugs targeting specific ETR subtypes.
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13
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Kurihara Y, Ekimoto T, Gordon CT, Uchijima Y, Sugiyama R, Kitazawa T, Iwase A, Kotani R, Asai R, Pingault V, Ikeguchi M, Amiel J, Kurihara H. Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding. J Clin Invest 2023; 133:151536. [PMID: 36637912 PMCID: PMC9927936 DOI: 10.1172/jci151536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/16/2022] [Indexed: 01/14/2023] Open
Abstract
Mutations of G protein-coupled receptors (GPCRs) cause various human diseases, but the mechanistic details are limited. Here, we establish p.E303K in the gene encoding the endothelin receptor type A (ETAR/EDNRA) as a recurrent mutation causing mandibulofacial dysostosis with alopecia (MFDA), with craniofacial changes similar to those caused by p.Y129F. Mouse models carrying either of these missense mutations exhibited a partial maxillary-to-mandibular transformation, which was rescued by deleting the ligand endothelin 3 (ET3/EDN3). Pharmacological experiments confirmed the causative ETAR mutations as gain of function, dependent on ET3. To elucidate how an amino acid substitution far from the ligand binding site can increase ligand affinity, we used molecular dynamics (MD) simulations. E303 is located at the intracellular end of transmembrane domain 6, and its replacement by a lysine increased flexibility of this portion of the helix, thus favoring G protein binding and leading to G protein-mediated enhancement of agonist affinity. The Y129F mutation located under the ligand binding pocket reduced the sodium-water network, thereby affecting the extracellular portion of helices in favor of ET3 binding. These findings provide insight into the pathogenesis of MFDA and into allosteric mechanisms regulating GPCR function, which may provide the basis for drug design targeting GPCRs.
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Affiliation(s)
- Yukiko Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | | | - Yasunobu Uchijima
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Sugiyama
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taro Kitazawa
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akiyasu Iwase
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Risa Kotani
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Medical Science, Graduate School of Medicine, University of Hiroshima, Hiroshima, Japan
| | - Rieko Asai
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Véronique Pingault
- Department of Genomic Medicine for Rare Diseases, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.,Center for Computational Science, RIKEN, Yokohama, Japan
| | - Jeanne Amiel
- INSERM UMR 1163, Institut Imagine and Université Paris-Cité, Paris, France.,Department of Genomic Medicine for Rare Diseases, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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14
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Yao H, Cai H, Li D. Fluorescence-Detection Size-Exclusion Chromatography-Based Thermostability Assay for Membrane Proteins. Methods Mol Biol 2023; 2564:299-315. [PMID: 36107350 DOI: 10.1007/978-1-0716-2667-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Green fluorescent proteins (GFPs) have lightened up almost every aspect of biological research including protein sciences. In the field of membrane protein structural biology, GFPs have been used widely to monitor membrane protein localization, expression level, the purification process and yield, and the stability inside the cells and in the test tube. Of particular interest is the fluorescence-detector size-exclusion chromatography-based thermostability assay (FSEC-TS). By simple heating and FSEC, the generally applicable method allows rapid assessment of the thermostability of GFP-fused membrane proteins without purification. Here we describe the experimental details and some typical results for the FSEC-TS method.
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Affiliation(s)
| | | | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
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15
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Tang YQ, Lim J, Gew L. Biocomputational-mediated screening and molecular docking platforms for discovery of coumarin-derived antimelanogenesis agents. DERMATOL SIN 2023. [DOI: 10.4103/ds.ds-d-22-00087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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16
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Fukunishi Y, Higo J, Kasahara K. Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles. Biophys Rev 2022; 14:1423-1447. [PMID: 36465086 PMCID: PMC9703445 DOI: 10.1007/s12551-022-01015-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/06/2022] [Indexed: 11/29/2022] Open
Abstract
Prediction of ligand-receptor complex structure is important in both the basic science and the industry such as drug discovery. We report various computation molecular docking methods: fundamental in silico (virtual) screening, ensemble docking, enhanced sampling (generalized ensemble) methods, and other methods to improve the accuracy of the complex structure. We explain not only the merits of these methods but also their limits of application and discuss some interaction terms which are not considered in the in silico methods. In silico screening and ensemble docking are useful when one focuses on obtaining the native complex structure (the most thermodynamically stable complex). Generalized ensemble method provides a free-energy landscape, which shows the distribution of the most stable complex structure and semi-stable ones in a conformational space. Also, barriers separating those stable structures are identified. A researcher should select one of the methods according to the research aim and depending on complexity of the molecular system to be studied.
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Affiliation(s)
- Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo 650-0047 Japan ,Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu, Shiga 525-8577 Japan
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17
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Caniceiro AB, Bueschbell B, Schiedel AC, Moreira IS. Class A and C GPCR Dimers in Neurodegenerative Diseases. Curr Neuropharmacol 2022; 20:2081-2141. [PMID: 35339177 PMCID: PMC9886835 DOI: 10.2174/1570159x20666220327221830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 11/22/2022] Open
Abstract
Neurodegenerative diseases affect over 30 million people worldwide with an ascending trend. Most individuals suffering from these irreversible brain damages belong to the elderly population, with onset between 50 and 60 years. Although the pathophysiology of such diseases is partially known, it remains unclear upon which point a disease turns degenerative. Moreover, current therapeutics can treat some of the symptoms but often have severe side effects and become less effective in long-term treatment. For many neurodegenerative diseases, the involvement of G proteincoupled receptors (GPCRs), which are key players of neuronal transmission and plasticity, has become clearer and holds great promise in elucidating their biological mechanism. With this review, we introduce and summarize class A and class C GPCRs, known to form heterodimers or oligomers to increase their signalling repertoire. Additionally, the examples discussed here were shown to display relevant alterations in brain signalling and had already been associated with the pathophysiology of certain neurodegenerative diseases. Lastly, we classified the heterodimers into two categories of crosstalk, positive or negative, for which there is known evidence.
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Affiliation(s)
- Ana B. Caniceiro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Beatriz Bueschbell
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Anke C. Schiedel
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany;
| | - Irina S. Moreira
- University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; ,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal,Address correspondence to this author at the Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal; E-mail:
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18
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Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule. Sci Rep 2022; 12:13792. [PMID: 35963875 PMCID: PMC9376114 DOI: 10.1038/s41598-022-17920-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/02/2022] [Indexed: 11/08/2022] Open
Abstract
A GA-guided multidimensional virtual-system coupled molecular dynamics (GA-mD-VcMD) simulation was conducted to elucidate binding mechanisms of a middle-sized flexible molecule, bosentan, to a GPCR protein, human endothelin receptor type B (hETB). GA-mD-VcMD is a generalized ensemble method that produces a free-energy landscape of the ligand-receptor binding by searching large-scale motions accompanied with stable maintenance of the fragile cell-membrane structure. All molecular components (bosentan, hETB, membrane, and solvent) were represented with an all-atom model. Then sampling was conducted from conformations where bosentan was distant from the binding site in the hETB binding pocket. The deepest basin in the resultant free-energy landscape was assigned to native-like complex conformation. The following binding mechanism was inferred. First, bosentan fluctuating randomly in solution is captured using a tip region of the flexible N-terminal tail of hETB via nonspecific attractive interactions (fly casting). Bosentan then slides occasionally from the tip to the root of the N-terminal tail (ligand–sliding). During this sliding, bosentan passes the gate of the binding pocket from outside to inside of the pocket with an accompanying rapid reduction of the molecular orientational variety of bosentan (orientational selection). Last, in the pocket, ligand–receptor attractive native contacts are formed. Eventually, the native-like complex is completed. The bosentan-captured conformations by the tip-region and root-region of the N-terminal tail correspond to two basins in the free-energy landscape. The ligand-sliding corresponds to overcoming of a free-energy barrier between the basins.
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19
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Wang L, Wang L, Yan F. Understanding the molecular mechanism of endothelin ETA receptor selecting isopeptides endothelin-1 and -3. Biophys J 2022; 121:2490-2502. [DOI: 10.1016/j.bpj.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/02/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022] Open
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20
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Endothelin and the Cardiovascular System: The Long Journey and Where We Are Going. BIOLOGY 2022; 11:biology11050759. [PMID: 35625487 PMCID: PMC9138590 DOI: 10.3390/biology11050759] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022]
Abstract
Simple Summary In this review, we describe the basic functions of endothelin and related molecules, including their receptors and enzymes. Furthermore, we discuss the important role of endothelin in several cardiovascular diseases, the relevant clinical evidence for targeting the endothelin pathway, and the scope of endothelin-targeting treatments in the future. We highlight the present uses of endothelin receptor antagonists and the advancements in the development of future treatment options, thereby providing an overview of endothelin research over the years and its future scope. Abstract Endothelin was first discovered more than 30 years ago as a potent vasoconstrictor. In subsequent years, three isoforms, two canonical receptors, and two converting enzymes were identified, and their basic functions were elucidated by numerous preclinical and clinical studies. Over the years, the endothelin system has been found to be critical in the pathogenesis of several cardiovascular diseases, including hypertension, pulmonary arterial hypertension, heart failure, and coronary artery disease. In this review, we summarize the current knowledge on endothelin and its role in cardiovascular diseases. Furthermore, we discuss how endothelin-targeting therapies, such as endothelin receptor antagonists, have been employed to treat cardiovascular diseases with varying degrees of success. Lastly, we provide a glimpse of what could be in store for endothelin-targeting treatment options for cardiovascular diseases in the future.
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21
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Speck D, Kleinau G, Szczepek M, Kwiatkowski D, Catar R, Philippe A, Scheerer P. Angiotensin and Endothelin Receptor Structures With Implications for Signaling Regulation and Pharmacological Targeting. Front Endocrinol (Lausanne) 2022; 13:880002. [PMID: 35518926 PMCID: PMC9063481 DOI: 10.3389/fendo.2022.880002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/18/2022] [Indexed: 12/28/2022] Open
Abstract
In conjunction with the endothelin (ET) type A (ETAR) and type B (ETBR) receptors, angiotensin (AT) type 1 (AT1R) and type 2 (AT2R) receptors, are peptide-binding class A G-protein-coupled receptors (GPCRs) acting in a physiologically overlapping context. Angiotensin receptors (ATRs) are involved in regulating cell proliferation, as well as cardiovascular, renal, neurological, and endothelial functions. They are important therapeutic targets for several diseases or pathological conditions, such as hypertrophy, vascular inflammation, atherosclerosis, angiogenesis, and cancer. Endothelin receptors (ETRs) are expressed primarily in blood vessels, but also in the central nervous system or epithelial cells. They regulate blood pressure and cardiovascular homeostasis. Pathogenic conditions associated with ETR dysfunctions include cancer and pulmonary hypertension. While both receptor groups are activated by their respective peptide agonists, pathogenic autoantibodies (auto-Abs) can also activate the AT1R and ETAR accompanied by respective clinical conditions. To date, the exact mechanisms and differences in binding and receptor-activation mediated by auto-Abs as opposed to endogenous ligands are not well understood. Further, several questions regarding signaling regulation in these receptors remain open. In the last decade, several receptor structures in the apo- and ligand-bound states were determined with protein X-ray crystallography using conventional synchrotrons or X-ray Free-Electron Lasers (XFEL). These inactive and active complexes provide detailed information on ligand binding, signal induction or inhibition, as well as signal transduction, which is fundamental for understanding properties of different activity states. They are also supportive in the development of pharmacological strategies against dysfunctions at the receptors or in the associated signaling axis. Here, we summarize current structural information for the AT1R, AT2R, and ETBR to provide an improved molecular understanding.
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Affiliation(s)
- David Speck
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Gunnar Kleinau
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Michal Szczepek
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Dennis Kwiatkowski
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Rusan Catar
- Department of Nephrology and Critical Care Medicine, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Aurélie Philippe
- Department of Nephrology and Medical Intensive Care, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Center for Cardiovascular Research, Berlin, Germany
| | - Patrick Scheerer
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
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22
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Nakai H, Isshiki K, Hattori M, Maehira H, Yamaguchi T, Masuda K, Shimizu Y, Watanabe T, Hohsaka T, Shihoya W, Nureki O, Kato Y, Watanabe H, Matsuura T. Cell-Free Synthesis of Human Endothelin Receptors and Its Application to Ribosome Display. Anal Chem 2022; 94:3831-3839. [PMID: 35188389 DOI: 10.1021/acs.analchem.1c04714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Engineering G-protein-coupled receptors (GPCRs) for improved stability or altered function is of great interest, as GPCRs consist of the largest protein family, are involved in many important signaling pathways, and thus, are one of the major drug targets. Here, we report the development of a high-throughput screening method for GPCRs using a reconstituted in vitro transcription-translation (IVTT) system. Human endothelin receptor type-B (ETBR), a class A GPCR that binds endothelin-1 (ET-1), a 21-residue peptide hormone, was synthesized in the presence of nanodisc (ND) composed of a phospholipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG). The ET-1 binding of ETBR was significantly reduced or was undetectable when other phospholipids were used for ND preparation. However, when functional ETBR purified from Sf9 cells was reconstituted into NDs, ET-1 binding was observed with two different phospholipids tested, including POPG. These results suggest that POPG likely supports the folding of ETBR into its functional form in the IVTT system. Using the same conditions as ETBR, whose three-dimensional structure has been solved, human endothelin receptor type-A (ETAR), whose three-dimensional structure remains unsolved, was also synthesized in its functional form. By adding POPG-ND to the IVTT system, both ETAR and ETBR were successfully subjected to ribosome display, a method of in vitro directed evolution that facilitates the screening of up to 1012 mutants. Finally, using a mock library, we showed that ribosome display can be applied for gene screening of ETBR, suggesting that high-throughput screening and directed evolution of GPCRs is possible in vitro.
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Affiliation(s)
- Hiroki Nakai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kinuka Isshiki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masato Hattori
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiromasa Maehira
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsumi Yamaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
| | - Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystem Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystem Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yasuhiko Kato
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
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23
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van Aalst E, Koneri J, Wylie BJ. In Silico Identification of Cholesterol Binding Motifs in the Chemokine Receptor CCR3. MEMBRANES 2021; 11:570. [PMID: 34436333 PMCID: PMC8401243 DOI: 10.3390/membranes11080570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 01/14/2023]
Abstract
CC motif chemokine receptor 3 (CCR3) is a Class A G protein-coupled receptor (GPCR) mainly responsible for the cellular trafficking of eosinophils. As such, it plays key roles in inflammatory conditions, such as asthma and arthritis, and the metastasis of many deadly forms of cancer. However, little is known about how CCR3 functionally interacts with its bilayer environment. Here, we investigate cholesterol binding sites in silico through Coarse-Grained Molecular Dynamics (MD) and Pylipid analysis using an extensively validated homology model based on the crystal structure of CCR5. These simulations identified several cholesterol binding sites containing Cholesterol Recognition/Interaction Amino Acid Consensus motif (CRAC) and its inversion CARC motifs in CCR3. One such site, a CARC site in TM1, in conjunction with aliphatic residues in TM7, emerged as a candidate for future investigation based on the cholesterol residency time within the binding pocket. This site forms the core of a cholesterol binding site previously observed in computational studies of CCR2 and CCR5. Most importantly, these cholesterol binding sites are conserved in other chemokine receptors and may provide clues to cholesterol regulation mechanisms in this subfamily of Class A GPCRs.
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Affiliation(s)
| | | | - Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79423, USA; (E.v.A.); (J.K.)
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24
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Albanese V, Ruzza C, Marzola E, Bernardi T, Fabbri M, Fantinati A, Trapella C, Reinscheid RK, Ferrari F, Sturaro C, Calò G, Amendola G, Cosconati S, Pacifico S, Guerrini R, Preti D. Structure-Activity Relationship Studies on Oxazolo[3,4- a]pyrazine Derivatives Leading to the Discovery of a Novel Neuropeptide S Receptor Antagonist with Potent In Vivo Activity. J Med Chem 2021; 64:4089-4108. [PMID: 33733768 PMCID: PMC8041306 DOI: 10.1021/acs.jmedchem.0c02223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Neuropeptide S modulates important neurobiological functions including locomotion, anxiety, and drug abuse through interaction with its G protein-coupled receptor known as neuropeptide S receptor (NPSR). NPSR antagonists are potentially useful for the treatment of substance abuse disorders against which there is an urgent need for new effective therapeutic approaches. Potent NPSR antagonists in vitro have been discovered which, however, require further optimization of their in vivo pharmacological profile. This work describes a new series of NPSR antagonists of the oxazolo[3,4-a]pyrazine class. The guanidine derivative 16 exhibited nanomolar activity in vitro and 5-fold improved potency in vivo compared to SHA-68, a reference pharmacological tool in this field. Compound 16 can be considered a new tool for research studies on the translational potential of the NPSergic system. An in-depth molecular modeling investigation was also performed to gain new insights into the observed structure-activity relationships and provide an updated model of ligand/NPSR interactions.
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Affiliation(s)
- Valentina Albanese
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Chiara Ruzza
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Erika Marzola
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Tatiana Bernardi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Martina Fabbri
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Anna Fantinati
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Claudio Trapella
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Rainer K Reinscheid
- Institute of Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
- Institute of Physiology I, University Hospital Münster, University of Münster, 48149 Münster, Germany
| | - Federica Ferrari
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
| | - Chiara Sturaro
- Department of Neuroscience and Rehabilitation, Section of Pharmacology, University of Ferrara, Via Fossato di Mortara 17/19, 44121 Ferrara, Italy
| | - Girolamo Calò
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Largo Meneghetti, 2, 35131 Padova, Italy
| | - Giorgio Amendola
- "DiSTABiF", Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Sandro Cosconati
- "DiSTABiF", Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Salvatore Pacifico
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Remo Guerrini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
- LTTA Laboratory for Advanced Therapies, Technopole of Ferrara, 44121 Ferrara, Italy
| | - Delia Preti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
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25
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Marlow B, Kuenze G, Li B, Sanders CR, Meiler J. Structural determinants of cholesterol recognition in helical integral membrane proteins. Biophys J 2021; 120:1592-1604. [PMID: 33640379 DOI: 10.1016/j.bpj.2021.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/12/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Cholesterol is an integral component of mammalian membranes. It has been shown to modulate membrane fluidity and dynamics and alter integral membrane protein function. However, understanding the molecular mechanisms of how cholesterol impacts protein function is complicated by limited and conflicting structural data. Because of the nature of the crystallization and cryo-EM structure determination, it is difficult to distinguish between specific and biologically relevant interactions and a nonspecific association. The only widely recognized search algorithm for cholesterol-integral-membrane-protein interaction sites is sequence based, i.e., searching for the so-called "Cholesterol Recognition/interaction Amino acid Consensus" motif. Although these motifs are present in numerous integral membrane proteins, there is inconclusive evidence to support their necessity or sufficiency for cholesterol binding. Here, we leverage the increasing number of experimental cholesterol-integral-membrane-protein structures to systematically analyze putative interaction sites based on their spatial arrangement and evolutionary conservation. This analysis creates three-dimensional representations of general cholesterol interaction sites that form clusters across multiple integral membrane protein classes. We also classify cholesterol-integral-membrane-protein interaction sites as either likely-specific or nonspecific. Information gleaned from our characterization will eventually enable a structure-based approach to predict and design cholesterol-integral-membrane-protein interaction sites.
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Affiliation(s)
- Brennica Marlow
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Bian Li
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany.
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26
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Lemel L, Nieścierowicz K, García-Fernández MD, Darré L, Durroux T, Busnelli M, Pezet M, Rébeillé F, Jouhet J, Mouillac B, Domene C, Chini B, Cherezov V, Moreau CJ. The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules. J Lipid Res 2021; 62:100059. [PMID: 33647276 PMCID: PMC8050779 DOI: 10.1016/j.jlr.2021.100059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/11/2021] [Indexed: 12/30/2022] Open
Abstract
Cholesterol is a major component of mammalian plasma membranes that not only affects the physical properties of the lipid bilayer but also is the function of many membrane proteins including G protein-coupled receptors. The oxytocin receptor (OXTR) is involved in parturition and lactation of mammals and in their emotional and social behaviors. Cholesterol acts on OXTR as an allosteric modulator inducing a high-affinity state for orthosteric ligands through a molecular mechanism that has yet to be determined. Using the ion channel-coupled receptor technology, we developed a functional assay of cholesterol modulation of G protein-coupled receptors that is independent of intracellular signaling pathways and operational in living cells. Using this assay, we discovered a stable binding of cholesterol molecules to the receptor when it adopts an orthosteric ligand-bound state. This stable interaction preserves the cholesterol-dependent activity of the receptor in cholesterol-depleted membranes. This mechanism was confirmed using time-resolved FRET experiments on WT OXTR expressed in CHO cells. Consequently, a positive cross-regulation sequentially occurs in OXTR between cholesterol and orthosteric ligands.
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Affiliation(s)
- Laura Lemel
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | | | - Leonardo Darré
- Functional Genomics Laboratory and Biomolecular Simulations Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Thierry Durroux
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Marta Busnelli
- CNR, Institute of Neuroscience, U28 and NeuroMI Center for Neuroscience, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Mylène Pezet
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Grenoble Alpes University, Grenoble, France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Carmen Domene
- Department of Chemistry, University of Bath, Bath, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Bice Chini
- CNR, Institute of Neuroscience, U28 and NeuroMI Center for Neuroscience, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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27
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Jakubík J, El-Fakahany EE. Allosteric Modulation of GPCRs of Class A by Cholesterol. Int J Mol Sci 2021; 22:1953. [PMID: 33669406 PMCID: PMC7920425 DOI: 10.3390/ijms22041953] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/16/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are membrane proteins that convey extracellular signals to the cellular milieu. They represent a target for more than 30% of currently marketed drugs. Here we review the effects of membrane cholesterol on the function of GPCRs of Class A. We review both the specific effects of cholesterol mediated via its direct high-affinity binding to the receptor and non-specific effects mediated by cholesterol-induced changes in the properties of the membrane. Cholesterol binds to many GPCRs at both canonical and non-canonical binding sites. It allosterically affects ligand binding to and activation of GPCRs. Additionally, it changes the oligomerization state of GPCRs. In this review, we consider a perspective of the potential for the development of new therapies that are targeted at manipulating the level of membrane cholesterol or modulating cholesterol binding sites on to GPCRs.
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Affiliation(s)
- Jan Jakubík
- Department of Neurochemistry, Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Esam E. El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN 55455, USA
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28
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Bertalan É, Lešnik S, Bren U, Bondar AN. Protein-water hydrogen-bond networks of G protein-coupled receptors: Graph-based analyses of static structures and molecular dynamics. J Struct Biol 2020; 212:107634. [DOI: 10.1016/j.jsb.2020.107634] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/06/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022]
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29
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Crystal structure of human endothelin ET B receptor in complex with sarafotoxin S6b. Biochem Biophys Res Commun 2020; 528:383-388. [PMID: 32001000 DOI: 10.1016/j.bbrc.2019.12.091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/27/2019] [Indexed: 12/28/2022]
Abstract
Sarafotoxins (SRTXs) are endothelin-like peptides extracted from snake venom. SRTXs stimulate the endothelin ETA and ETB 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 ETB 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.
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30
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Sutkeviciute I, Vilardaga JP. Structural insights into emergent signaling modes of G protein-coupled receptors. J Biol Chem 2020; 295:11626-11642. [PMID: 32571882 DOI: 10.1074/jbc.rev120.009348] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/21/2020] [Indexed: 12/21/2022] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of cell membrane proteins, with >800 GPCRs in humans alone, and recognize highly diverse ligands, ranging from photons to large protein molecules. Very important to human medicine, GPCRs are targeted by about 35% of prescription drugs. GPCRs are characterized by a seven-transmembrane α-helical structure, transmitting extracellular signals into cells to regulate major physiological processes via heterotrimeric G proteins and β-arrestins. Initially viewed as receptors whose signaling via G proteins is delimited to the plasma membrane, it is now recognized that GPCRs signal also at various intracellular locations, and the mechanisms and (patho)physiological relevance of such signaling modes are actively investigated. The propensity of GPCRs to adopt different signaling modes is largely encoded in the structural plasticity of the receptors themselves and of their signaling complexes. Here, we review emerging modes of GPCR signaling via endosomal membranes and the physiological implications of such signaling modes. We further summarize recent structural insights into mechanisms of GPCR activation and signaling. We particularly emphasize the structural mechanisms governing the continued GPCR signaling from endosomes and the structural aspects of the GPCR resensitization mechanism and discuss the recently uncovered and important roles of lipids in these processes.
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Affiliation(s)
- Ieva Sutkeviciute
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jean-Pierre Vilardaga
- Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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31
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Gu X, Wang Y, Wang H, Wu H, Li W, Wang J, Li N. Homology modeling, molecular dynamics and virtual screening of endothelin-A receptor for the treatment of pulmonary arterial hypertension. J Biomol Struct Dyn 2020; 39:3912-3923. [PMID: 32431219 DOI: 10.1080/07391102.2020.1772106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a progressive disease of pulmonary arteries, causing serious shortness of breath and right ventricular failure with high mortality. Numerous studies have verified that the symptoms of PAH could be attenuated effectively with endothelin-A receptor (ETAR) antagonists. Unfortunately, the 3D structure of ETAR has not been released, making it difficult to understand the interactions between ETAR and its antagonists. In this study, computational methods including homology modeling, molecular docking and molecular dynamics simulations were performed to build the structure of ETAR and predict the binding patterns of ETAR with its two antagonists. Based on these results, virtual screening study was implemented against Traditional Chinese Medicine (TCM) database to identify novel natural ETAR antagonists. Six compounds with best binding energies were screened out and two of them were found to bind steadily with ETAR validated through molecular dynamics simulations and MM-GBSA calculation, indicating that they were potential antagonists of ETAR. In a word, our research provided a deep exploration into the interaction between ETAR and its antagonists, which could promote the development of novel therapy against PAH.[Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xi Gu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Ying Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Hairui Wu
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Life Sciences and Biopharmaceutical Science, Shenyang Pharmaceutical University, Shenyang, P.R. China
| | - Wei Li
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Ning Li
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
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32
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Doi T, Kikuta K, Tani K. Characterization of Critical Residues in the Extracellular and Transmembrane Domains of the Endothelin Type B Receptor for Propagation of the Endothelin-1 Signal. Biochemistry 2020; 59:1718-1727. [PMID: 32343134 DOI: 10.1021/acs.biochem.0c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have previously reported the crystal structures of endothelin-1 (ET-1)-bound, ligand-free, and antagonist bosentan-bound forms of the thermostabilized ET type B receptor (ETB). Although other agonist-bound structures of ETB have been determined, the interactions for high-affinity binding and ETB receptor activation, as well as the roles of rearrangement of the hydrogen-bond network surrounding the ligand in G protein activation, remain elusive. ET-1, a 21-amino acid residue peptide, plays fundamental roles in basal vascular tone, sodium balance, cell proliferation, and stress-responsive regulation. We studied the interactions between the ET-1(8-21) peptide and ETB in the ligand binding and activation of ETB using a series of Ala-substituted ET-1(8-21) analogues and the mutated ETB. We found that while D8, L17, D18, I20, and W21 were responsible for high-affinity binding and potent G protein activation, Y13 and F14 in the helical region of ET-1 are prerequisites for the full activation of ETB via interactions near the extracellular side. Furthermore, we introduced the mutation into the residues around the ET-1 binding pocket of ETB. The results showed that while S1843.35, W3366.48, N3787.45, and S3797.46 in a conserved polar network are required for full activation, N1191.50, D1472.50, and N3827.49 are essential for G protein activation via direct interactions after rearrangement upon ET-1 binding. These results demonstrate that both interactions near the extracellular side and within the transmembrane helices with ET-1 play crucial roles in the full activation of the ETB receptor.
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Affiliation(s)
- Tomoko Doi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kohei Kikuta
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Tani
- Graduate School of Medicine, Mie University, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
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33
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Intagliata S, Helal MA, Materia L, Pittalà V, Salerno L, Marrazzo A, Cagnotto A, Salmona M, Modica MN, Romeo G. Synthesis and Molecular Modelling Studies of New 1,3-Diaryl-5-Oxo-Proline Derivatives as Endothelin Receptor Ligands. Molecules 2020; 25:molecules25081851. [PMID: 32316541 PMCID: PMC7221592 DOI: 10.3390/molecules25081851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 11/17/2022] Open
Abstract
The synthesis of seventeen new 1,3-diaryl-5-oxo-proline derivatives as endothelin receptor (ETR) ligands is described. The structural configuration of the new molecules was determined by analyzing selected signals in proton NMR spectra. In vitro binding assays of the human ETA and ETB receptors allowed us to identify compound 31h as a selective ETAR ligand. The molecular docking of the selected compounds and the ETA antagonist atrasentan in the ETAR homology model provided insight into the structural elements required for the affinity and the selectivity of the ETAR subtype.
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Affiliation(s)
- Sebastiano Intagliata
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (S.I.); (V.P.); (L.S.); (A.M.); (G.R.)
| | - Mohamed A. Helal
- University of Science and Technology, Biomedical Sciences Program, Zewail City of Science and Technology, October Gardens, 6th of October, Giza 12578, Egypt;
- Medicinal Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Luisa Materia
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (S.I.); (V.P.); (L.S.); (A.M.); (G.R.)
| | - Valeria Pittalà
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (S.I.); (V.P.); (L.S.); (A.M.); (G.R.)
| | - Loredana Salerno
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (S.I.); (V.P.); (L.S.); (A.M.); (G.R.)
| | - Agostino Marrazzo
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (S.I.); (V.P.); (L.S.); (A.M.); (G.R.)
| | - Alfredo Cagnotto
- Istituto di Ricerche Farmacologiche “Mario Negri”, IRCCS. Via Mario Negri, 2, 20156 Milano, Italy; (A.C.); (M.S.)
| | - Mario Salmona
- Istituto di Ricerche Farmacologiche “Mario Negri”, IRCCS. Via Mario Negri, 2, 20156 Milano, Italy; (A.C.); (M.S.)
| | - Maria N. Modica
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (S.I.); (V.P.); (L.S.); (A.M.); (G.R.)
- Correspondence: ; Tel.: +39-095-738-6061
| | - Giuseppe Romeo
- Department of Drug Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy; (S.I.); (V.P.); (L.S.); (A.M.); (G.R.)
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34
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Sejdiu BI, Tieleman DP. Lipid-Protein Interactions Are a Unique Property and Defining Feature of G Protein-Coupled Receptors. Biophys J 2020; 118:1887-1900. [PMID: 32272057 DOI: 10.1016/j.bpj.2020.03.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are membrane-bound proteins that depend on their lipid environment to carry out their physiological function. Combined efforts from many theoretical and experimental studies on the lipid-protein interaction profile of several GPCRs hint at an intricate relationship of these receptors with their surrounding membrane environment, with several lipids emerging as particularly important. Using coarse-grained molecular dynamics simulations, we explore the lipid-protein interaction profiles of 28 different GPCRs, spanning different levels of classification and conformational states and totaling to 1 ms of simulation time. We find a close relationship with lipids for all GPCRs simulated, in particular, cholesterol and phosphatidylinositol phosphate (PIP) lipids, but the number, location, and estimated strength of these interactions is dependent on the specific GPCR as well as its conformational state. Although both cholesterol and PIP lipids bind specifically to GPCRs, they utilize distinct mechanisms. Interactions with PIP lipids are mediated by charge-charge interactions with intracellular loop residues and stabilized by one or both of the transmembrane helices linked by the loop. Interactions with cholesterol, on the other hand, are mediated by a hydrophobic environment, usually made up of residues from more than one helix, capable of accommodating its ring structure and stabilized by interactions with aromatic and charged/polar residues. Cholesterol binding to GPCRs occurs in a small number of sites, some of which (like the binding site on the extracellular side of transmembrane 6/7) are shared among many class A GPCRs. Combined with a thorough investigation of the local membrane structure, our results provide a detailed picture of GPCR-lipid interactions. Additionally, we provide an accompanying website to interactively explore the lipid-protein interaction profile of all GPCRs simulated to facilitate analysis and comparison of our data.
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Affiliation(s)
- Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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35
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Cryo-EM structure of the human PAC1 receptor coupled to an engineered heterotrimeric G protein. Nat Struct Mol Biol 2020; 27:274-280. [PMID: 32157248 DOI: 10.1038/s41594-020-0386-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/23/2020] [Indexed: 01/17/2023]
Abstract
Pituitary adenylate cyclase-activating polypeptide (PACAP) is a pleiotropic neuropeptide hormone. The PACAP receptor PAC1R, which belongs to the class B G-protein-coupled receptors (GPCRs), is a drug target for mental disorders and dry eye syndrome. Here, we present a cryo-EM structure of human PAC1R bound to PACAP and an engineered Gs heterotrimer. The structure revealed that transmembrane helix TM1 plays an essential role in PACAP recognition. The extracellular domain (ECD) of PAC1R tilts by ~40° compared with that of the glucagon-like peptide-1 receptor (GLP-1R) and thus does not cover the peptide ligand. A functional analysis demonstrated that the PAC1R ECD functions as an affinity trap and is not required for receptor activation, whereas the GLP-1R ECD plays an indispensable role in receptor activation, illuminating the functional diversity of the ECDs in class B GPCRs. Our structural information will facilitate the design and improvement of better PAC1R agonists for clinical applications.
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36
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Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
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Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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37
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Abstract
Discovered in 1987 as a potent endothelial cell-derived vasoconstrictor peptide, endothelin-1 (ET-1), the predominant member of the endothelin peptide family, is now recognized as a multifunctional peptide with cytokine-like activity contributing to almost all aspects of physiology and cell function. More than 30 000 scientific articles on endothelin were published over the past 3 decades, leading to the development and subsequent regulatory approval of a new class of therapeutics-the endothelin receptor antagonists (ERAs). This article reviews the history of the discovery of endothelin and its role in genetics, physiology, and disease. Here, we summarize the main clinical trials using ERAs and discuss the role of endothelin in cardiovascular diseases such as arterial hypertension, preecclampsia, coronary atherosclerosis, myocardial infarction in the absence of obstructive coronary artery disease (MINOCA) caused by spontaneous coronary artery dissection (SCAD), Takotsubo syndrome, and heart failure. We also discuss how endothelins contributes to diabetic kidney disease and focal segmental glomerulosclerosis, pulmonary arterial hypertension, as well as cancer, immune disorders, and allograft rejection (which all involve ETA autoantibodies), and neurological diseases. The application of ERAs, dual endothelin receptor/angiotensin receptor antagonists (DARAs), selective ETB agonists, novel biologics such as receptor-targeting antibodies, or immunization against ETA receptors holds the potential to slow the progression or even reverse chronic noncommunicable diseases. Future clinical studies will show whether targeting endothelin receptors can prevent or reduce disability from disease and improve clinical outcome, quality of life, and survival in patients.
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Affiliation(s)
- Matthias Barton
- From Molecular Internal Medicine, University of Zürich, Switzerland (M.B.)
- Andreas Grüntzig Foundation, Zürich, Switzerland (M.B.)
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS) and Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Japan (M.Y.)
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX (M.Y.)
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38
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Abstract
GPCRs (G-protein [guanine nucleotide-binding protein]-coupled receptors) play a central physiological role in the regulation of cardiac function in both health and disease and thus represent one of the largest class of surface receptors targeted by drugs. Several antagonists of GPCRs, such as βARs (β-adrenergic receptors) and Ang II (angiotensin II) receptors, are now considered standard of therapy for a wide range of cardiovascular disease, such as hypertension, coronary artery disease, and heart failure. Although the mechanism of action for GPCRs was thought to be largely worked out in the 80s and 90s, recent discoveries have brought to the fore new and previously unappreciated mechanisms for GPCR activation and subsequent downstream signaling. In this review, we focus on GPCRs most relevant to the cardiovascular system and discuss traditional components of GPCR signaling and highlight evolving concepts in the field, such as ligand bias, β-arrestin-mediated signaling, and conformational heterogeneity.
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Affiliation(s)
- Jialu Wang
- From the Department of Medicine (J.W., C.G., H.A.R.)
| | | | - Howard A Rockman
- From the Department of Medicine (J.W., C.G., H.A.R.).,Department of Cell Biology (H.A.R.).,Department of Molecular Genetics and Microbiology (H.A.R.), Duke University Medical Center, Durham, NC
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39
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Zarzycka B, Zaidi SA, Roth BL, Katritch V. Harnessing Ion-Binding Sites for GPCR Pharmacology. Pharmacol Rev 2019; 71:571-595. [PMID: 31551350 PMCID: PMC6782022 DOI: 10.1124/pr.119.017863] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Endogenous ions play important roles in the function and pharmacology of G-protein coupled receptors (GPCRs). Historically the evidence for ionic modulation of GPCR function dates to 1973 with studies of opioid receptors, where it was demonstrated that physiologic concentrations of sodium allosterically attenuated agonist binding. This Na+-selective effect was distinct from effects of other monovalent and divalent cations, with the latter usually counteracting sodium's negative allosteric modulation of binding. Since then, numerous studies documenting the effects of mono- and divalent ions on GPCR function have been published. While ions can act selectively and nonselectively at many sites in different receptors, the discovery of the conserved sodium ion site in class A GPCR structures in 2012 revealed the unique nature of Na+ site, which has emerged as a near-universal site for allosteric modulation of class A GPCR structure and function. In this review, we synthesize and highlight recent advances in the functional, biophysical, and structural characterization of ions bound to GPCRs. Taken together, these findings provide a molecular understanding of the unique roles of Na+ and other ions as GPCR allosteric modulators. We will also discuss how this knowledge can be applied to the redesign of receptors and ligand probes for desired functional and pharmacological profiles. SIGNIFICANCE STATEMENT: The function and pharmacology of GPCRs strongly depend on the presence of mono and divalent ions in experimental assays and in living organisms. Recent insights into the molecular mechanism of this ion-dependent allosterism from structural, biophysical, biochemical, and computational studies provide quantitative understandings of the pharmacological effects of drugs in vitro and in vivo and open new avenues for the rational design of chemical probes and drug candidates with improved properties.
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Affiliation(s)
- Barbara Zarzycka
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Saheem A Zaidi
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bryan L Roth
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Vsevolod Katritch
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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40
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Shihoya W, Inoue K, Singh M, Konno M, Hososhima S, Yamashita K, Ikeda K, Higuchi A, Izume T, Okazaki S, Hashimoto M, Mizutori R, Tomida S, Yamauchi Y, Abe-Yoshizumi R, Katayama K, Tsunoda SP, Shibata M, Furutani Y, Pushkarev A, Béjà O, Uchihashi T, Kandori H, Nureki O. Crystal structure of heliorhodopsin. Nature 2019; 574:132-136. [DOI: 10.1038/s41586-019-1604-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 08/20/2019] [Indexed: 11/10/2022]
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41
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Molecular Determinants of Cholesterol Binding to Soluble and Transmembrane Protein Domains. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1135:47-66. [PMID: 31098810 DOI: 10.1007/978-3-030-14265-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Cholesterol-protein interactions play a critical role in lipid metabolism and maintenance of cell integrity. To elucidate the molecular mechanisms underlying these interactions, a growing number of studies have focused on determining the crystal structures of a variety of proteins complexed with cholesterol. These include structures in which cholesterol binds to transmembrane domains, and structures in which cholesterol interacts with soluble ones. However, it remains unknown whether there are differences in the prerequisites for cholesterol binding to these two types of domains. Thus, to define the molecular determinants that characterize the binding of cholesterol to these two distinct protein domains, we employed the database of crystal structures of proteins complexed with cholesterol. Our analysis suggests that cholesterol may bind more strongly to soluble domains than to transmembrane domains. The interactions between cholesterol and the protein in both cases critically depends on hydrophobic and aromatic residues. In addition, cholesterol binding sites in both types of domains involve polar and/or charged residues. However, the percentage of appearance of the different types of polar/charged residues in cholesterol binding sites differs between soluble and transmembrane domains. No differences were observed in the conformational characteristics of the cholesterol molecules bound to soluble versus transmembrane protein domains suggesting that cholesterol is insensitive to the environment provided by the different protein domains.
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42
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Nagiri C, Shihoya W, Inoue A, Kadji FMN, Aoki J, Nureki O. Crystal structure of human endothelin ET B receptor in complex with peptide inverse agonist IRL2500. Commun Biol 2019; 2:236. [PMID: 31263780 PMCID: PMC6588608 DOI: 10.1038/s42003-019-0482-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/21/2019] [Indexed: 01/01/2023] Open
Abstract
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.
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Affiliation(s)
- Chisae Nagiri
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578 Miyagi Japan
| | - Francois Marie Ngako Kadji
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578 Miyagi Japan
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578 Miyagi Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan
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43
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Wink LH, Baker DL, Cole JA, Parrill AL. A benchmark study of loop modeling methods applied to G protein-coupled receptors. J Comput Aided Mol Des 2019; 33:573-595. [PMID: 31123958 DOI: 10.1007/s10822-019-00196-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCR) are important drug discovery targets. Despite progress, many GPCR structures have not yet been solved. For these targets, comparative modeling is used in virtual ligand screening to prioritize experimental efforts. However, the structure of extracellular loop 2 (ECL2) is often poorly predicted. This is significant due to involvement of ECL2 in ligand binding for many Class A GPCR. Here we examine the performance of loop modeling protocols available in the Rosetta (cyclic coordinate descent [CCD], KIC with fragments [KICF] and next generation KIC [NGK]) and Molecular Operating Environment (MOE) software suites (de novo search). ECL2 from GPCR crystal structures served as the structure prediction targets and were divided into four sets depending on loop length. Results suggest that KICF and NGK sampled and scored more loop models with sub-angstrom and near-atomic accuracy than CCD or de novo search for loops of 24 or fewer residues. None of the methods were able to sample loop conformations with near-atomic accuracy for the longest targets ranging from 25 to 32 residues based on 1000 models generated. For these long loop targets, increased conformational sampling is necessary. The strongly conserved disulfide bond between Cys3.25 and Cys45.50 in ECL2 proved an effective filter. Setting an upper limit of 5.1 Å on the S-S distance improved the lowest RMSD model included in the top 10 scored structures in Groups 1-4 on average between 0.33 and 1.27 Å. Disulfide bond formation and geometry optimization of ECL2 provided an additional incremental benefit in structure quality.
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Affiliation(s)
- Lee H Wink
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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44
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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45
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Hirata K, Yamashita K, Ueno G, Kawano Y, Hasegawa K, Kumasaka T, Yamamoto M. ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography. Acta Crystallogr D Struct Biol 2019; 75:138-150. [PMID: 30821703 PMCID: PMC6400253 DOI: 10.1107/s2059798318017795] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
Owing to the development of brilliant microfocus beamlines, rapid-readout detectors and sample changers, protein microcrystallography is rapidly becoming a popular technique for accessing structural information from complex biological samples. However, the method is time-consuming and labor-intensive and requires technical expertise to obtain high-resolution protein crystal structures. At SPring-8, an automated data-collection system named ZOO has been developed. This system enables faster data collection, facilitates advanced data-collection and data-processing techniques, and permits the collection of higher quality data. In this paper, the key features of the functionality put in place on the SPring-8 microbeam beamline BL32XU are described and the major advantages of this system are outlined. The ZOO system will be a major driving force in the evolution of the macromolecular crystallography beamlines at SPring-8.
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Affiliation(s)
- Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Kazuya Hasegawa
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo 679-5198, Hyogo, Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo 679-5198, Hyogo, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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46
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Schöppe J, Ehrenmann J, Klenk C, Rucktooa P, Schütz M, Doré AS, Plückthun A. Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Nat Commun 2019; 10:17. [PMID: 30604743 PMCID: PMC6318301 DOI: 10.1038/s41467-018-07939-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
Neurokinins (or tachykinins) are peptides that modulate a wide variety of human physiology through the neurokinin G protein-coupled receptor family, implicated in a diverse array of pathological processes. Here we report high-resolution crystal structures of the human NK1 receptor (NK1R) bound to two small-molecule antagonist therapeutics – aprepitant and netupitant and the progenitor antagonist CP-99,994. The structures reveal the detailed interactions between clinically approved antagonists and NK1R, which induce a distinct receptor conformation resulting in an interhelical hydrogen-bond network that cross-links the extracellular ends of helices V and VI. Furthermore, the high-resolution details of NK1R bound to netupitant establish a structural rationale for the lack of basal activity in NK1R. Taken together, these co-structures provide a comprehensive structural basis of NK1R antagonism and will facilitate the design of new therapeutics targeting the neurokinin receptor family. Neurokinin receptors are G protein-coupled receptors. Here the authors present three crystal structures of the neurokinin 1 receptor (NK1R) in complex with small-molecule antagonists including aprepitant and netupitant and observe that these clinically approved compounds induce a conformational change in the receptor.
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Affiliation(s)
- Jendrik Schöppe
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Janosch Ehrenmann
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Christoph Klenk
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Prakash Rucktooa
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Marco Schütz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.,Heptares Therapeutics Zürich AG, Grabenstrasse 11a, 8952, Zürich, Switzerland
| | - Andrew S Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
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47
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Wang C, Ralko A, Ren Z, Rosenhouse-Dantsker A, Yang X. Modes of Cholesterol Binding in Membrane Proteins: A Joint Analysis of 73 Crystal Structures. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1135:67-86. [PMID: 31098811 DOI: 10.1007/978-3-030-14265-0_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cholesterol is a highly asymmetric lipid molecule. As an essential constituent of the cell membrane, cholesterol plays important structural and signaling roles in various biological processes. The first high-resolution crystal structure of a transmembrane protein in complex with cholesterol was a human β2-adrenergic receptor structure deposited to the Protein Data Bank in 2007. Since then, the number of the cholesterol-bound crystal structures has grown considerably providing an invaluable resource for obtaining insights into the structural characteristics of cholesterol binding. In this work, we examine the spatial and orientation distributions of cholesterol relative to the protein framework in a collection of 73 crystal structures of membrane proteins. To characterize the cholesterol-protein interactions, we apply singular value decomposition to an array of interatomic distances, which allows us to systematically assess the flexibility and variability of cholesterols in transmembrane proteins. Together, this joint analysis reveals the common characteristics among the observed cholesterol structures, thereby offering important guidelines for prediction and modification of potential cholesterol binding sites in transmembrane proteins.
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Affiliation(s)
- Cong Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Arthur Ralko
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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48
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A Critical Analysis of Molecular Mechanisms Underlying Membrane Cholesterol Sensitivity of GPCRs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1115:21-52. [PMID: 30649754 DOI: 10.1007/978-3-030-04278-3_2] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest and a diverse family of proteins involved in signal transduction across biological membranes. GPCRs mediate a wide range of physiological processes and have emerged as major targets for the development of novel drug candidates in all clinical areas. Since GPCRs are integral membrane proteins, regulation of their organization, dynamics, and function by membrane lipids, in particular membrane cholesterol, has emerged as an exciting area of research. Cholesterol sensitivity of GPCRs could be due to direct interaction of cholesterol with the receptor (specific effect). Alternately, GPCR function could be influenced by the effect of cholesterol on membrane physical properties (general effect). In this review, we critically analyze the specific and general mechanisms of the modulation of GPCR function by membrane cholesterol, taking examples from representative GPCRs. While evidence for both the proposed mechanisms exists, there appears to be no clear-cut distinction between these two mechanisms, and a combination of these mechanisms cannot be ruled out in many cases. We conclude that classifying the mechanism underlying cholesterol sensitivity of GPCR function merely into these two mutually exclusive classes could be somewhat arbitrary. A more holistic approach could be suitable for analyzing GPCR-cholesterol interaction.
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49
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Shihoya W, Izume T, Inoue A, Yamashita K, Kadji FMN, Hirata K, Aoki J, Nishizawa T, Nureki O. Crystal structures of human ET B receptor provide mechanistic insight into receptor activation and partial activation. Nat Commun 2018; 9:4711. [PMID: 30413709 PMCID: PMC6226434 DOI: 10.1038/s41467-018-07094-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 10/14/2018] [Indexed: 12/16/2022] Open
Abstract
Endothelin receptors (ETA and ETB) are class A GPCRs activated by vasoactive peptide endothelins, and are involved in blood pressure regulation. ETB-selective signalling induces vasorelaxation, and thus selective ETB agonists are expected to be utilized for improved anti-tumour drug delivery and neuroprotection. Here, we report the crystal structures of human ETB receptor in complex with ETB-selective agonist, endothelin-3 and an ETB-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 ETB.
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Affiliation(s)
- Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Tamaki Izume
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.,RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Francois Marie Ngako Kadji
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | | | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, 100-0004, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan.
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Dong F, Rues RB, Kazemi S, Dötsch V, Bernhard F. Molecular Determinants for Ligand Selectivity of the Cell-Free Synthesized Human Endothelin B Receptor. J Mol Biol 2018; 430:5105-5119. [PMID: 30342934 DOI: 10.1016/j.jmb.2018.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/02/2018] [Accepted: 10/12/2018] [Indexed: 01/14/2023]
Abstract
Extracellular domains of G-protein-coupled receptors act as initial molecular selectivity filters for subtype specific ligands and drugs. Chimeras of the human endothelin-B receptor containing structural units from the extracellular domains of the endothelin-A receptor were analyzed after their co-translational insertion into preformed nanodiscs. A short β-strand and a linker region in the second extracellular loop as well as parts of the extracellular N-terminal domain were identified as molecular discrimination sites for the endothelin-B receptor-selective agonists IRL1620, sarafotoxin 6c, 4Ala-ET-1 and ET-3, but not for the non-selective agonist ET-1 recognized by both endothelin receptors. A proposed second disulfide bridge in the endothelin-B receptor tethering the N-terminal domain with the third extracellular loop was not essential for ET-1 recognition and binding, but increased the receptor thermostability. We further demonstrate an experimental approach with cell-free synthesized engineered agonists to analyze the differential discrimination of peptide ligand topologies by the two endothelin receptors. The study is based on the engineering and cell-free insertion of G-protein-coupled receptors into defined membranes and may become interesting also for other targets as an alternative platform to reveal molecular details of ligand selectivity and ligand binding mechanisms.
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Affiliation(s)
- Fang Dong
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Ralf B Rues
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Sina Kazemi
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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