51
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Palamarchuk IV, Shulgau ZT, Dautov AY, Sergazy SD, Kulakov IV. Design, synthesis, spectroscopic characterization, computational analysis, and in vitro α-amylase and α-glucosidase evaluation of 3-aminopyridin-2(1 H)-one based novel monothiooxamides and 1,3,4-thiadiazoles. Org Biomol Chem 2022; 20:8962-8976. [DOI: 10.1039/d2ob01772e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
On the basis of biologically active 3-aminopyridin-2(1H)-ones, chemical modification of derivatives of the corresponding monothiooxamides, thiohydrazides, and conjugated 1,3,4-thiadiazole derivatives has been carried out for the first time.
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Affiliation(s)
- Irina V. Palamarchuk
- Tyumen State University, Institute of Chemistry, 15a Perekopskaya St., Tyumen 625003, Russia
| | - Zarina T. Shulgau
- National Center for Biotechnology, 13/5 Kurgalzhynskoe road, Nur-Sultan, 010000, Kazakhstan
| | - Adilet Y. Dautov
- National Center for Biotechnology, 13/5 Kurgalzhynskoe road, Nur-Sultan, 010000, Kazakhstan
| | - Shynggys D. Sergazy
- National Center for Biotechnology, 13/5 Kurgalzhynskoe road, Nur-Sultan, 010000, Kazakhstan
| | - Ivan V. Kulakov
- Tyumen State University, Institute of Chemistry, 15a Perekopskaya St., Tyumen 625003, Russia
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52
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Krishna Deepak RNV, Verma RK, Hartono YD, Yew WS, Fan H. Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery. Pharmaceuticals (Basel) 2021; 15:12. [PMID: 35056070 PMCID: PMC8779880 DOI: 10.3390/ph15010012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 01/01/2023] Open
Abstract
Great progress has been made over the past decade in understanding the structural, functional, and pharmacological diversity of lipid GPCRs. From the first determination of the crystal structure of bovine rhodopsin in 2000, much progress has been made in the field of GPCR structural biology. The extraordinary progress in structural biology and pharmacology of GPCRs, coupled with rapid advances in computational approaches to study receptor dynamics and receptor-ligand interactions, has broadened our comprehension of the structural and functional facets of the receptor family members and has helped usher in a modern age of structure-based drug design and development. First, we provide a primer on lipid mediators and lipid GPCRs and their role in physiology and diseases as well as their value as drug targets. Second, we summarize the current advancements in the understanding of structural features of lipid GPCRs, such as the structural variation of their extracellular domains, diversity of their orthosteric and allosteric ligand binding sites, and molecular mechanisms of ligand binding. Third, we close by collating the emerging paradigms and opportunities in targeting lipid GPCRs, including a brief discussion on current strategies, challenges, and the future outlook.
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Affiliation(s)
- R. N. V. Krishna Deepak
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
| | - Ravi Kumar Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
| | - Yossa Dwi Hartono
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Hao Fan
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore 138671, Singapore; (R.K.V.); (Y.D.H.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore;
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53
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Elisi GM, Scalvini L, Lodola A, Mor M, Rivara S. Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors. J Chem Inf Model 2021; 62:210-222. [PMID: 34932329 PMCID: PMC8757440 DOI: 10.1021/acs.jcim.1c01183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
![]()
The effects of the
neurohormone melatonin are mediated by the activation
of the GPCRs MT1 and MT2 in a variety of tissues.
Crystal structures suggest ligand access to the orthosteric binding
site of MT1 and MT2 receptors through a lateral
channel between transmembrane (TM) helices IV and V. We investigated
the feasibility of this lipophilic entry route for 2-iodomelatonin,
a nonselective agonist with a slower dissociation rate from the MT2 receptor, applying enhanced sampling simulations and free-energy
calculations. 2-Iodomelatonin unbinding was investigated with steered
molecular dynamics simulations which revealed different trajectories
passing through the gap between TM helices IV and V for both receptors.
For one of these unbinding trajectories from the MT1 receptor,
an umbrella-sampling protocol with path-collective variables provided
a calculated energy barrier consistent with the experimental dissociation
rate. The side-chain flexibility of Tyr5.38 was significantly different
in the two receptor subtypes, as assessed by metadynamics simulations,
and during ligand unbinding it frequently assumes an open conformation
in the MT1 but not in the MT2 receptor, favoring
2-iodomelatonin egress. Taken together, our simulations are consistent
with the possibility that the gap between TM IV and V is a way of
connecting the orthosteric binding site and the membrane core for
lipophilic melatonin receptor ligands. Our simulations also suggest
that the open state of Tyr5.38 generates a small pocket on the surface
of MT1 receptor, which could participate in the recognition
of MT1-selective ligands and may be exploited in the design
of new selective compounds.
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Affiliation(s)
- Gian Marco Elisi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy.,Microbiome Research Hub, University of Parma, I-43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
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54
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Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J. Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You? Pharmacol Rev 2021; 73:527-565. [PMID: 34907092 DOI: 10.1124/pharmrev.120.000246] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.
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Affiliation(s)
- Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Albert J Kooistra
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
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55
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Gado F, Ceni C, Ferrisi R, Sbrana G, Stevenson LA, Macchia M, Pertwee RG, Bertini S, Manera C, Ortore G. CB1 receptor binding sites for NAM and PAM: A first approach for studying, new n‑butyl‑diphenylcarboxamides as allosteric modulators. Eur J Pharm Sci 2021; 169:106088. [PMID: 34863873 DOI: 10.1016/j.ejps.2021.106088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 01/01/2023]
Abstract
The development of cannabinoid receptor type-1 (CB1R) modulators has been implicated in multiple pathophysiological events ranging from memory deficits to neurodegenerative disorders among others, even if their central psychiatric side effects such as depression, anxiety, and suicidal tendencies, have limited their clinical use. Thus, the identification of ligands which selectively act on peripheral CB1Rs, is becoming more interesting. A recent study reported a class of peripheral CB1R selective antagonists, characterized by a 5-aryl substituted nicotinamide core. These derivatives have structural similarities with the biphenyl compounds, endowed with CB2R antagonist activity, previously synthesized by our research group. In this work we combined the pharmacophoric portion of both classes, in order to obtain novel CBR antagonists. Among the synthesized compounds rather unexpectedly two compounds of this series, C7 and C10, did not show the radioligand ([3H]CP55940) displacement on CB1R but increased binding (∼ 150%), suggesting a possible allosteric behavior. Computational studies were performed to investigate the role of these compounds in CB1R modulation. The analysis of their binding poses in two different binding cavities of the CB1R surface, revealed a preferred interaction with the experimental binding site for negative allosteric modulators.
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Affiliation(s)
- Francesca Gado
- Department of Pharmacy, University of Pisa, 56126 Pisa Italy
| | - Costanza Ceni
- Department of Pharmacy, University of Pisa, 56126 Pisa Italy; Doctoral school in Life Sciences, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Rebecca Ferrisi
- Department of Pharmacy, University of Pisa, 56126 Pisa Italy
| | - Giulia Sbrana
- Department of Pharmacy, University of Pisa, 56126 Pisa Italy
| | - Lesley A Stevenson
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, AB25 2ZD Aberdeen, Scotland, UK
| | - Marco Macchia
- Department of Pharmacy, University of Pisa, 56126 Pisa Italy
| | - Roger G Pertwee
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, AB25 2ZD Aberdeen, Scotland, UK
| | - Simone Bertini
- Department of Pharmacy, University of Pisa, 56126 Pisa Italy
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56
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Ciancetta A, Gill AK, Ding T, Karlov DS, Chalhoub G, McCormick PJ, Tikhonova IG. Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction. ACS CENTRAL SCIENCE 2021; 7:1847-1862. [PMID: 34841058 PMCID: PMC8614102 DOI: 10.1021/acscentsci.1c00802] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Indexed: 05/06/2023]
Abstract
Targeting G protein-coupled receptors (GPCRs) through allosteric sites offers advantages over orthosteric sites in identifying drugs with increased selectivity and potentially reduced side effects. In this study, we developed a probe confined dynamic mapping protocol that allows the prediction of allosteric sites at both the GPCR extracellular and intracellular sides, as well as at the receptor-lipid interface. The applied harmonic wall potential enhanced sampling of probe molecules in a selected area of a GPCR while preventing membrane distortion in molecular dynamics simulations. The specific probes derived from GPCR allosteric ligand structures performed better in allosteric site mapping compared to commonly used cosolvents. The M2 muscarinic, β2 adrenergic, and P2Y1 purinergic receptors were selected for the protocol's retrospective validation. The protocol was next validated prospectively to locate the binding site of [5-fluoro-4-(hydroxymethyl)-2-methoxyphenyl]-(4-fluoro-1H-indol-1-yl)methanone at the D2 dopamine receptor, and subsequent mutagenesis confirmed the prediction. The protocol provides fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins and facilitates the structure-based design of allosteric modulators.
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Affiliation(s)
- Antonella Ciancetta
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - Amandeep Kaur Gill
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Tianyi Ding
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - Dmitry S. Karlov
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - George Chalhoub
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Peter J. McCormick
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Irina G. Tikhonova
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
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57
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Kricker JA, Page CP, Gardarsson FR, Baldursson O, Gudjonsson T, Parnham MJ. Nonantimicrobial Actions of Macrolides: Overview and Perspectives for Future Development. Pharmacol Rev 2021; 73:233-262. [PMID: 34716226 DOI: 10.1124/pharmrev.121.000300] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Macrolides are among the most widely prescribed broad spectrum antibacterials, particularly for respiratory infections. It is now recognized that these drugs, in particular azithromycin, also exert time-dependent immunomodulatory actions that contribute to their therapeutic benefit in both infectious and other chronic inflammatory diseases. Their increased chronic use in airway inflammation and, more recently, of azithromycin in COVID-19, however, has led to a rise in bacterial resistance. An additional crucial aspect of chronic airway inflammation, such as chronic obstructive pulmonary disease, as well as other inflammatory disorders, is the loss of epithelial barrier protection against pathogens and pollutants. In recent years, azithromycin has been shown with time to enhance the barrier properties of airway epithelial cells, an action that makes an important contribution to its therapeutic efficacy. In this article, we review the background and evidence for various immunomodulatory and time-dependent actions of macrolides on inflammatory processes and on the epithelium and highlight novel nonantibacterial macrolides that are being studied for immunomodulatory and barrier-strengthening properties to circumvent the risk of bacterial resistance that occurs with macrolide antibacterials. We also briefly review the clinical effects of macrolides in respiratory and other inflammatory diseases associated with epithelial injury and propose that the beneficial epithelial effects of nonantibacterial azithromycin derivatives in chronic inflammation, even given prophylactically, are likely to gain increasing attention in the future. SIGNIFICANCE STATEMENT: Based on its immunomodulatory properties and ability to enhance the protective role of the lung epithelium against pathogens, azithromycin has proven superior to other macrolides in treating chronic respiratory inflammation. A nonantibiotic azithromycin derivative is likely to offer prophylactic benefits against inflammation and epithelial damage of differing causes while preserving the use of macrolides as antibiotics.
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Affiliation(s)
- Jennifer A Kricker
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Clive P Page
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Fridrik Runar Gardarsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Olafur Baldursson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Thorarinn Gudjonsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Michael J Parnham
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
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58
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Paternoster S, Simpson PV, Kokh E, Kizilkaya HS, Rosenkilde MM, Mancera RL, Keating DJ, Massi M, Falasca M. Pharmacological and structure-activity relationship studies of oleoyl-lysophosphatidylinositol synthetic mimetics. Pharmacol Res 2021; 172:105822. [PMID: 34411732 DOI: 10.1016/j.phrs.2021.105822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 02/01/2023]
Abstract
Metabolic diseases, such as obesity and type 2 diabetes, are relentlessly spreading worldwide. The beginning of the 21st century has seen the introduction of mechanistically novel types of drugs, aimed primarily at keeping these pathologies under control. In particular, an important family of therapeutics exploits the beneficial physiology of the gut-derived glucagon-like peptide-1 (GLP-1), with important clinical benefits, from glycaemic control to cardioprotection. Nonetheless, these protein-based drugs act systemically as exogenous GLP-1 mimetics and are not exempt from side effects. The food-derived lipid oleoyl-lysophosphatidylinositol (LPI) is a potent GPR119-dependent GLP-1 secreting agent. Here we present a structure-activity relationship (SAR) study of a synthetic library of oleoyl-LPI mimetics capable to induce the physiological release of GLP-1 from gastrointestinal enteroendocrine cells (EECs). The best lead compounds have shown potent and efficient release of GLP-1 in vitro from human and murine cells, and in vivo in diabetic db/db mice. We have also generated a molecular model of oleoyl-LPI, as well as its best performing analogues, interacting with the orthosteric site of GPR119, laying foundational evidence for their pharmacological activity.
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Affiliation(s)
- Silvano Paternoster
- Metabolic Signalling Group, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Peter V Simpson
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Elena Kokh
- Metabolic Signalling Group, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Hüsün Sheyma Kizilkaya
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Marie Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ricardo L Mancera
- Metabolic Signalling Group, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Damien J Keating
- Flinders Health and Medical Research Institute, Flinders University, Adelaide 5042, Australia
| | - Massimiliano Massi
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Marco Falasca
- Metabolic Signalling Group, Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
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59
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Nagasawa T, Horitani M, Kawaguchi SI, Higashiyama S, Hama Y, Mitsutake S. The molecular mechanism of phytosphingosine binding to FFAR4/GPR120 differs from that of other fatty acids. FEBS Open Bio 2021; 11:3081-3089. [PMID: 34535977 PMCID: PMC8564095 DOI: 10.1002/2211-5463.13301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/21/2022] Open
Abstract
Free fatty acid receptor 4 (FFAR4)/GPR120 comprises a receptor for medium‐ and long‐chain fatty acids. We previously identified phytosphingosine (PHS) as a novel ligand of FFAR4. Although many natural FFAR4 ligands have carboxyl groups, PHS does not, thus suggesting that binding to FFAR4 is driven by a completely different mechanism than other natural ligands such as α‐linolenic acid (ALA). To test this hypothesis, we performed docking simulation analysis using a FFAR4 homology model based on a protein model derived from the crystal structure of activated turkey beta‐1 adrenoceptor. The docking simulation revealed that the probable hydrogen bonds to FFAR4 differ between various ligands. In particular, binding was predicted between R264 of the FFAR4 and the oxygen of the carboxylate group in ALA, as well as between E249 of the FFAR4 and the oxygen of the hydroxy group at the C4‐position in PHS. Alanine substitution at E249 (E249A) dramatically reduced PHS‐induced FFAR4 activation but demonstrated a weaker effect on ALA‐induced FFAR4 activation. Kinetic analysis and Km values clearly demonstrated that the E249A substitution resulted in reduced affinity for PHS but not for ALA. Additionally, we observed that sphingosine, lacking a hydroxyl group at C4‐position, could not activate FFAR4. Our data show that E249 of the FFAR4 receptor is crucial for binding to the hydroxy group at the C4‐position in PHS, and this is a completely different molecular mechanism of binding from ALA. Because GPR120 agonists have attracted attention as treatments for type 2 diabetes, our findings may provide new insights into their development.
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Affiliation(s)
- Tomotaka Nagasawa
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Masaki Horitani
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga, Japan
| | - Shin-Ichi Kawaguchi
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Center for Education and Research in Agricultural Innovation, Faculty of Agriculture, Saga University, Saga, Japan
| | - Shigeki Higashiyama
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Matsuyama, Japan.,Department of Molecular and Cellular Biology, Osaka International Cancer Institute, Osaka, Japan
| | - Yoichiro Hama
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga, Japan
| | - Susumu Mitsutake
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Department of Applied Biochemistry and Food Science, Faculty of Agriculture, Saga University, Saga, Japan
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60
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Positive allosteric mechanisms of adenosine A 1 receptor-mediated analgesia. Nature 2021; 597:571-576. [PMID: 34497422 PMCID: PMC8711093 DOI: 10.1038/s41586-021-03897-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
The adenosine A1 receptor (A1R) is a promising therapeutic target for non-opioid analgesic agents to treat neuropathic pain1,2. However, development of analgesic orthosteric A1R agonists has failed because of a lack of sufficient on-target selectivity as well as off-tissue adverse effects3. Here we show that [2-amino-4-(3,5-bis(trifluoromethyl)phenyl)thiophen-3-yl)(4-chlorophenyl)methanone] (MIPS521), a positive allosteric modulator of the A1R, exhibits analgesic efficacy in rats in vivo through modulation of the increased levels of endogenous adenosine that occur in the spinal cord of rats with neuropathic pain. We also report the structure of the A1R co-bound to adenosine, MIPS521 and a Gi2 heterotrimer, revealing an extrahelical lipid-detergent-facing allosteric binding pocket that involves transmembrane helixes 1, 6 and 7. Molecular dynamics simulations and ligand kinetic binding experiments support a mechanism whereby MIPS521 stabilizes the adenosine-receptor-G protein complex. This study provides proof of concept for structure-based allosteric drug design of non-opioid analgesic agents that are specific to disease contexts.
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Mach M, Bazydło-Guzenda K, Buda P, Matłoka M, Dzida R, Stelmach F, Gałązka K, Wąsińska-Kałwa M, Smuga D, Hołowińska D, Dawid U, Gurba-Bryśkiewicz L, Wiśniewski K, Dubiel K, Pieczykolan J, Wieczorek M. Discovery and development of CPL207280 as new GPR40/FFA1 agonist. Eur J Med Chem 2021; 226:113810. [PMID: 34537444 DOI: 10.1016/j.ejmech.2021.113810] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/28/2022]
Abstract
Due to a unique mechanism that limits the possibility of hypoglycemia, the free fatty acid receptor (FFA1) is an attractive target for the treatment of type 2 diabetes. So far, however, none of the promising agonists have been able to enter the market. The most advanced clinical candidate, TAK-875, was withdrawn from phase III clinical trials due to liver safety issues. In this article, we describe the key aspects leading to the discovery of CPL207280 (13), the design of which focused on long-term safety. The introduction of small, nature-inspired acyclic structural fragments resulted in compounds with retained high potency and a satisfactory pharmacokinetic profile. Optimized synthesis and upscaling provided a stable, solid form of CPL207280-51 (45) with the properties required for the toxicology studies and ongoing clinical trials.
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Affiliation(s)
- Mateusz Mach
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland.
| | - Katarzyna Bazydło-Guzenda
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki i Wigury Street, 02-091, Warsaw, Poland
| | - Paweł Buda
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Mikołaj Matłoka
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Radosław Dzida
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Filip Stelmach
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Kinga Gałązka
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | | | - Damian Smuga
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Dagmara Hołowińska
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Urszula Dawid
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | | | | | - Krzysztof Dubiel
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Jerzy Pieczykolan
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
| | - Maciej Wieczorek
- Celon Pharma S.A., R&D Centre, Marymoncka 15, 05-152, Kazun Nowy, Poland
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Burger WAC, Gentry PR, Berizzi AE, Vuckovic Z, van der Westhuizen ET, Thompson G, Yeasmin M, Lindsley CW, Sexton PM, Langmead CJ, Tobin AB, Christopoulos A, Valant C, Thal DM. Identification of a Novel Allosteric Site at the M 5 Muscarinic Acetylcholine Receptor. ACS Chem Neurosci 2021; 12:3112-3123. [PMID: 34351123 PMCID: PMC7616173 DOI: 10.1021/acschemneuro.1c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The M5 muscarinic acetylcholine receptor (mAChR) has emerged as an exciting therapeutic target for the treatment of addiction and behavioral disorders. This has been in part due to promising preclinical studies with the M5 mAChR selective negative allosteric modulator (NAM), ML375. The binding site of ML375 remains unknown, however, making it difficult to develop improved M5 mAChR selective modulators. To determine the possible location of the ML375 binding site, we used radioligand binding and functional assays to show that ML375 does not interact with the well-characterized "common" mAChR allosteric site located in the receptor's extracellular vestibule, nor a previously proposed second allosteric site recognized by the modulator, amiodarone. Molecular docking was used to predict potential allosteric sites within the transmembrane (TM) domain of the M5 mAChR. These predicted sites were assessed using M5-M2 mAChR receptor chimeras and further targeted with site-directed mutagenesis, which enabled the identification of a putative binding site for ML375 at the interface of TMs 2-4. Collectively, these results identify a third allosteric site at the M5 mAChR and highlight the ability of allosteric modulators to selectively target highly conserved proteins.
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Affiliation(s)
- Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Patrick R Gentry
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Alice E Berizzi
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Ziva Vuckovic
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Emma T van der Westhuizen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Mahmuda Yeasmin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Craig W Lindsley
- Department of Pharmacology, Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Christopher J Langmead
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew B Tobin
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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63
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Lu S, He X, Yang Z, Chai Z, Zhou S, Wang J, Rehman AU, Ni D, Pu J, Sun J, Zhang J. Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nat Commun 2021; 12:4721. [PMID: 34354057 PMCID: PMC8342441 DOI: 10.1038/s41467-021-25020-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 07/17/2021] [Indexed: 02/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the most common proteins targeted by approved drugs. A complete mechanistic elucidation of large-scale conformational transitions underlying the activation mechanisms of GPCRs is of critical importance for therapeutic drug development. Here, we apply a combined computational and experimental framework integrating extensive molecular dynamics simulations, Markov state models, site-directed mutagenesis, and conformational biosensors to investigate the conformational landscape of the angiotensin II (AngII) type 1 receptor (AT1 receptor) - a prototypical class A GPCR-activation. Our findings suggest a synergistic transition mechanism for AT1 receptor activation. A key intermediate state is identified in the activation pathway, which possesses a cryptic binding site within the intracellular region of the receptor. Mutation of this cryptic site prevents activation of the downstream G protein signaling and β-arrestin-mediated pathways by the endogenous AngII octapeptide agonist, suggesting an allosteric regulatory mechanism. Together, these findings provide a deeper understanding of AT1 receptor activation at an atomic level and suggest avenues for the design of allosteric AT1 receptor modulators with a broad range of applications in GPCR biology, biophysics, and medicinal chemistry.
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Affiliation(s)
- Shaoyong Lu
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
| | - Xinheng He
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Material Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhao Yang
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Shuhua Zhou
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Junyan Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China
| | - Ashfaq Ur Rehman
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Duan Ni
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jinpeng Sun
- Department of Biochemistry and Molecular Biology, Key Laboratory Experimental Teratology of Chinese Ministry of Education, School of Medicine, Shandong University, Jinan, Shandong, China.
| | - Jian Zhang
- College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region, China.
- State Key Laboratory of Oncogenes and Related Genes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.
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Hansen AH, Christensen HB, Pandey SK, Sergeev E, Valentini A, Dunlop J, Dedeo D, Fratta S, Hudson BD, Milligan G, Ulven T, Rexen Ulven E. Structure-Activity Relationship Explorations and Discovery of a Potent Antagonist for the Free Fatty Acid Receptor 2. ChemMedChem 2021; 16:3326-3341. [PMID: 34288488 DOI: 10.1002/cmdc.202100356] [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: 05/21/2021] [Revised: 07/13/2021] [Indexed: 11/12/2022]
Abstract
Free fatty acid receptor 2 (FFA2) is a sensor for short-chain fatty acids that has been identified as an interesting potential drug target for treatment of metabolic and inflammatory diseases. Although several ligand series are known for the receptor, there is still a need for improved compounds. One of the most potent and frequently used antagonists is the amide-substituted phenylbutanoic acid known as CATPB ( 1 ). We here report the structure-activity relationship exploration of this compound, leading to the identification of homologues with increased potency. The preferred compound 37 (TUG-1958) was found, besides improved potency, to have high solubility and favorable pharmacokinetic properties.
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Affiliation(s)
- Anders Højgaard Hansen
- University of Southern Denmark: Syddansk Universitet, Department of Physics,Chemistry and Pharmacy, DENMARK
| | - Henriette B Christensen
- University of Southern Denmark: Syddansk Universitet, Department of Physics, Chemsitry and Pharmacy, DENMARK
| | - Sunil K Pandey
- University of Southern Denmark: Syddansk Universitet, FKF, DENMARK
| | - Eugenia Sergeev
- University of Glasgow, Center for Translational Pharmacology, UNITED KINGDOM
| | - Alice Valentini
- University of Copenhagen: Kobenhavns Universitet, Department of Drug Design and Pharmacoloy, DENMARK
| | - Julia Dunlop
- University of Glasgow, Center for Translational Medicine, DENMARK
| | - Domonkos Dedeo
- University of Glasgow, Center for Translational Research, DENMARK
| | - Simone Fratta
- University of Copenhagen: Kobenhavns Universitet, Department of Drug Design and Pharmacology, DENMARK
| | - Brian D Hudson
- University of Glasgow, Center for Translational Medicine, DENMARK
| | - Graeme Milligan
- University of Glasgow, Center for Translational Research, DENMARK
| | - Trond Ulven
- University of Copenhagen, Department of Drug Design and Pharmacology, Jagtvej 162, DK-2100, Copenhagen, DENMARK
| | - Elisabeth Rexen Ulven
- University of Copenhagen: Kobenhavns Universitet, Department of Drug Design and Pharmacology, DENMARK
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Caroleo MC, Plastina P, Fazio A, La Torre C, Manetti F, Cione E. Olive Oil Lipophenols Induce Insulin Secretion in 832/13 β-Cell Models. Pharmaceutics 2021; 13:pharmaceutics13071085. [PMID: 34371780 PMCID: PMC8309142 DOI: 10.3390/pharmaceutics13071085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 01/12/2023] Open
Abstract
Glycemic control is a mainstay of type 2 diabetes mellitus (T2DM) clinical management. Despite the continuous improvement in knowledge and progress in terms of treatment, the achievement of the physiologic metabolic profile is still an ongoing challenge in diabetic patients. Pancreatic β-cell line INS-1 832/13 was used to assess the insulin secretagogue activity of hydroxytyrosyl oleate (HtyOle) and tyrosyl oleate (TyOle), two naturally occurring lipophenols deriving from the conjugation of oleic acid (OA) and hydroxytyrosol (Hty) or tyrosol (Ty), respectively. The insulin secretion was determined under a glucose-induced insulin secretion (GSIS) condition by the ELISA method. The potential involvement of G-protein-coupled receptor 40 (GPR40), also known as free fatty acid receptor 1 (FFAR1), was investigated by both molecular docking and functional pharmacological approaches. Herein, we demonstrated that HtyOle and TyOle exerted a facilitatory activity on insulin secretion under the GSIS condition. Moreover, we provided evidence that both lipophenols are natural modulators of FFAR1 receptor. From our results, the anti-diabetes properties associated with olive oil consumption can be partly explained by the HtyOle and TyOle effects.
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Affiliation(s)
- Maria Cristina Caroleo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (M.C.C.); (P.P.); (A.F.); (C.L.T.)
| | - Pierluigi Plastina
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (M.C.C.); (P.P.); (A.F.); (C.L.T.)
| | - Alessia Fazio
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (M.C.C.); (P.P.); (A.F.); (C.L.T.)
| | - Chiara La Torre
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (M.C.C.); (P.P.); (A.F.); (C.L.T.)
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy
- Correspondence: (F.M.); (E.C.)
| | - Erika Cione
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (M.C.C.); (P.P.); (A.F.); (C.L.T.)
- Correspondence: (F.M.); (E.C.)
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66
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Ligand binding at the protein-lipid interface: strategic considerations for drug design. Nat Rev Drug Discov 2021; 20:710-722. [PMID: 34257432 DOI: 10.1038/s41573-021-00240-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Many drug targets are embedded within the phospholipid bilayer of cellular membranes, including G protein-coupled receptors, ion channels, transporters and membrane-bound enzymes. Increasing evidence from biophysical and structural studies suggests that many small-molecule drugs commonly associate with these targets at binding sites at the protein-phospholipid interface. Without a direct path from bulk solvent to a binding site, a drug must first partition in the phospholipid membrane before interacting with the protein target. This membrane access mechanism necessarily affects the interpretation of potency data, structure-activity relationships, pharmacokinetics and physicochemical properties for drugs that target these sites. With an increasing number of small-molecule intramembrane binding sites revealed through X-ray crystallography and cryogenic electron microscopy, we suggest that ligand-lipid interactions likely play a larger role in small-molecule drug action than commonly appreciated. This Perspective introduces key concepts and drug design considerations to aid discovery teams operating within this target space, and discusses challenges and future opportunities in the field.
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An X, Bai Q, Bing Z, Liu H, Yao X. Insights into the molecular mechanism of positive cooperativity between partial agonist MK-8666 and full allosteric agonist AP8 of hGPR40 by Gaussian accelerated molecular dynamics (GaMD) simulations. Comput Struct Biotechnol J 2021; 19:3978-3989. [PMID: 34377364 PMCID: PMC8313488 DOI: 10.1016/j.csbj.2021.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 10/29/2022] Open
Abstract
Activation of human free fatty acid receptor 1 (FFAR1, also called hGPR40) enhances insulin secretion in a glucose-dependent manner. Hence, the development of selective agonist targeting hGPR40 has been proposed as a therapeutic strategy of type 2 diabetes mellitus. Some agonists targeting hGPR40 were reported. The radioligand-binding studies and the crystal structures reveal that there are multiple sites on GPR40, and there exists positive binding cooperativity between the partial agonist MK-8666 and full allosteric agonist (AgoPAM) AP8. In this work, we carried out long-time Gaussian accelerated molecular dynamics (GaMD) simulations on hGPR40 to shed light on the mechanism of the cooperativity between the two agonists at different sites. Our results reveal that the induced-fit conformational coupling is bidirectional between the two sites. The movements and rotations of TM3, TM4, TM5 and TM6 due to their inherent flexibility are crucial in coupling the conformational changes of the two agonists binding sites. These helices adopt similar conformational states upon alternative ligand or both ligands binding. The Leu1384.57, Leu1865.42 and Leu1905.46 play roles in coordinating the rearrangements of residues in the two pockets, which makes the movements of residues in the two sites like gear movements. These results provide detailed information at the atomic level about the conformational coupling between different sites of GPR40, and also provide the structural information for further design of new agonists of GPR40. In addition, these results suggest that it is necessary by considering the effect of other site bound in structure-based ligands discovery.
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Affiliation(s)
- Xiaoli An
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Qifeng Bai
- School of Basic Medical Science, Lanzhou University, Lanzhou, China
| | - Zhitong Bing
- Institute of Modern Physics of Chinese Academy of Sciences, Gansu Province, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China.,State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
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68
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Rani L, Grewal AS, Sharma N, Singh S. Recent Updates on Free Fatty Acid Receptor 1 (GPR-40) Agonists for the Treatment of Type 2 Diabetes Mellitus. Mini Rev Med Chem 2021; 21:426-470. [PMID: 33100202 DOI: 10.2174/1389557520666201023141326] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/09/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The global incidence of type 2 diabetes mellitus (T2DM) has enthused the development of new antidiabetic targets with low toxicity and long-term stability. In this respect, free fatty acid receptor 1 (FFAR1), which is also recognized as a G protein-coupled receptor 40 (GPR40), is a novel target for the treatment of T2DM. FFAR1/GPR40 has a high level of expression in β-cells of the pancreas, and the requirement of glucose for stimulating insulin release results in immense stimulation to utilise this target in the medication of T2DM. METHODS The data used for this review is based on the search of several scienctific databases as well as various patent databases. The main search terms used were free fatty acid receptor 1, FFAR1, FFAR1 agonists, diabetes mellitus, G protein-coupled receptor 40 (GPR40), GPR40 agonists, GPR40 ligands, type 2 diabetes mellitus and T2DM. RESULTS The present review article gives a brief overview of FFAR1, its role in T2DM, recent developments in small molecule FFAR1 (GPR40) agonists reported till now, compounds of natural/plant origin, recent patents published in the last few years, mechanism of FFAR1 activation by the agonists, and clinical status of the FFAR1/GPR40 agonists. CONCLUSION The agonists of FFAR1/GRP40 showed considerable potential for the therapeutic control of T2DM. Most of the small molecule FFAR1/GPR40 agonists developed were aryl alkanoic acid derivatives (such as phenylpropionic acids, phenylacetic acids, phenoxyacetic acids, and benzofuran acetic acid derivatives) and thiazolidinediones. Some natural/plant-derived compounds, including fatty acids, sesquiterpenes, phenolic compounds, anthocyanins, isoquinoline, and indole alkaloids, were also reported as potent FFAR1 agonists. The clinical investigations of the FFAR1 agonists demonstrated their probable role in the improvement of glucose control. Though, there are some problems still to be resolved in this field as some FFAR1 agonists terminated in the late phase of clinical studies due to "hepatotoxicity." Currently, PBI-4050 is under clinical investigation by Prometic. Further investigation of pharmacophore scaffolds for FFAR1 full agonists as well as multitargeted modulators and corresponding clinical investigations will be anticipated, which can open up new directions in this area.
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Affiliation(s)
- Lata Rani
- Chitkara University School of Basic Sciences, Chitkara University, Himachal Pradesh, India
| | - Ajmer Singh Grewal
- Chitkara University School of Basic Sciences, Chitkara University, Himachal Pradesh, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
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69
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Wu Y, Zeng L, Zhao S. Ligands of Adrenergic Receptors: A Structural Point of View. Biomolecules 2021; 11:biom11070936. [PMID: 34202543 PMCID: PMC8301793 DOI: 10.3390/biom11070936] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 01/14/2023] Open
Abstract
Adrenergic receptors are G protein-coupled receptors for epinephrine and norepinephrine. They are targets of many drugs for various conditions, including treatment of hypertension, hypotension, and asthma. Adrenergic receptors are intensively studied in structural biology, displayed for binding poses of different types of ligands. Here, we summarized molecular mechanisms of ligand recognition and receptor activation exhibited by structure. We also reviewed recent advances in structure-based ligand discovery against adrenergic receptors.
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Affiliation(s)
- Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (Y.W.); (L.Z.)
| | - Liting Zeng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (Y.W.); (L.Z.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (Y.W.); (L.Z.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Correspondence:
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Abstract
RORγt is a nuclear receptor associated with several diseases. Various synthetic ligands have been developed that target the canonical orthosteric or a second, allosteric pocket of RORγt. We show that orthosteric and allosteric ligands can simultaneously bind to RORγt and that their potency is positively influenced by the other ligand, a phenomenon called cooperative dual ligand binding. The mechanism behind cooperative binding in proteins is poorly understood, primarily due to the lack of structural data. We solved 12 crystal structures of RORγt, simultaneously bound to various orthosteric and allosteric ligands. In combination with molecular dynamics, we reveal a mechanism responsible for the cooperative binding behavior. Our comprehensive structural studies provide unique insights into how cooperative binding occurs in proteins. Cooperative ligand binding is an important phenomenon in biological systems where ligand binding influences the binding of another ligand at an alternative site of the protein via an intramolecular network of interactions. The underlying mechanisms behind cooperative binding remain poorly understood, primarily due to the lack of structural data of these ternary complexes. Using time-resolved fluorescence resonance energy transfer (TR-FRET) studies, we show that cooperative ligand binding occurs for RORγt, a nuclear receptor associated with the pathogenesis of autoimmune diseases. To provide the crucial structural insights, we solved 12 crystal structures of RORγt simultaneously bound to various orthosteric and allosteric ligands. The presence of the orthosteric ligand induces a clamping motion of the allosteric pocket via helices 4 to 5. Additional molecular dynamics simulations revealed the unusual mechanism behind this clamping motion, with Ala355 shifting between helix 4 and 5. The orthosteric RORγt agonists regulate the conformation of Ala355, thereby stabilizing the conformation of the allosteric pocket and cooperatively enhancing the affinity of the allosteric inverse agonists.
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71
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Sun B, Feng D, Chu MLH, Fish I, Lovera S, Sands ZA, Kelm S, Valade A, Wood M, Ceska T, Kobilka TS, Lebon F, Kobilka BK. Crystal structure of dopamine D1 receptor in complex with G protein and a non-catechol agonist. Nat Commun 2021; 12:3305. [PMID: 34083522 PMCID: PMC8175458 DOI: 10.1038/s41467-021-23519-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Dopamine D1 receptor (D1R) is an important drug target implicated in many psychiatric and neurological disorders. Selective agonism of D1R are sought to be the therapeutic strategy for these disorders. Most selective D1R agonists share a dopamine-like catechol moiety in their molecular structure, and their therapeutic potential is therefore limited by poor pharmacological properties in vivo. Recently, a class of non-catechol D1R selective agonists with a distinct scaffold and pharmacological properties were reported. Here, we report the crystal structure of D1R in complex with stimulatory G protein (Gs) and a non-catechol agonist Compound 1 at 3.8 Å resolution. The structure reveals the ligand bound to D1R in an extended conformation, spanning from the orthosteric site to extracellular loop 2 (ECL2). Structural analysis reveals that the unique features of D1R ligand binding pocket explains the remarkable selectivity of this scaffold for D1R over other aminergic receptors, and sheds light on the mechanism for D1R activation by the non-catechol agonist.
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Affiliation(s)
| | - Dan Feng
- ConfometRx, Inc., Santa Clara, CA, USA
| | | | | | | | - Zara A Sands
- UCB Pharma, Braine-l'Alleud, Belgium
- Confo Therapeutics, Zwijnaarde, Belgium
| | | | | | | | | | | | | | - Brian K Kobilka
- ConfometRx, Inc., Santa Clara, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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72
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Zhao X, Yoon DO, Yoo J, Park HJ. Structure-Activity Relationship Study and Biological Evaluation of 2-(Disubstituted phenyl)-indole-5-propanoic Acid Derivatives as GPR40 Full Agonists. J Med Chem 2021; 64:4130-4149. [PMID: 33769827 DOI: 10.1021/acs.jmedchem.1c00031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
G-protein-coupled receptor 40 (GPR40) is considered as an attractive drug target for treating type 2 diabetes, owing to its role in the free fatty acid-mediated increase in glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells. To identify a new chemotype of GPR40 agonist, a series of 2-aryl-substituted indole-5-propanoic acid derivatives were designed and synthesized. We identified two GPR40 agonist lead compounds-4k (3-[2-(4-fluoro-2-methylphenyl)-1H-indol-5-yl]propanoic acid) and 4o (3-[2-(2,5-dimethylphenyl)-1H-indol-5-yl]propanoic acid), having GSIS and glucagon-like peptide 1 secretory effects. Unlike previously reported GPR40 partial agonists that only activate the Gq pathway, 4k and 4o activated both the Gq and Gs signaling pathways and were characterized as GPR40 full agonists. In in vivo efficacy studies, 4o significantly improved glycemic control in both C57BL/6J and db/db mice and increased plasma-active GLP-1 in C57BL/6J mice. Thus, 4o represents a promising lead for further development as a novel GPR40 full agonist against type 2 diabetes.
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Affiliation(s)
- Xiaodi Zhao
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dong-Oh Yoon
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jaeho Yoo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hyun-Ju Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
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73
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Governa P, Caroleo MC, Carullo G, Aiello F, Cione E, Manetti F. FFAR1/GPR40: One target, different binding sites, many agonists, no drugs, but a continuous and unprofitable tug-of-war between ligand lipophilicity, activity, and toxicity. Bioorg Med Chem Lett 2021; 41:127969. [PMID: 33771587 DOI: 10.1016/j.bmcl.2021.127969] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/31/2022]
Abstract
The progress made so far in the elucidation of the structure of free fatty acid receptor 1 (FFAR1) and its secondary and ternary complexes with partial and full allosteric ligands led to the discovery of various putative binding regions on the FFAR1 surface. Attempts to develop FFAR1 agonists culminated with the identification of TAK-875 (1), whose phase 3 clinical trials were terminated due to potential liver toxicity. In the search of safer agonists, numerous classes of new compounds were designed, synthesized, and tested. Chemical decoration of the scaffolds was rationalized to reach a good balance between lipophilicity, activity, and toxicity. Today, targeting FFAR1 with positive modulators represents an attractive pharmacological tool for the treatment of type 2 diabetes mellitus (T2DM), mainly because of the lack of hypoglycaemic side effects associated with several antidiabetic drugs currently available. Moreover, considering the involvement of FFAR1 in many physio-pathological processes, its agonists are also emerging as possible therapeutic tools for alleviating organ inflammation and fibrosis, as well as for the treatment of CNS disorders, such as Alzheimer's disease and dementia.
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Affiliation(s)
- Paolo Governa
- Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Maria Cristina Caroleo
- Department of Pharmacy, Health and Nutritional Sciences-Department of Excellence 2018-2022, University of Calabria, Ed. Polifunzionale, I-87036 Arcavacata di Rende, CS, Italy
| | - Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - Francesca Aiello
- Department of Pharmacy, Health and Nutritional Sciences-Department of Excellence 2018-2022, University of Calabria, Ed. Polifunzionale, I-87036 Arcavacata di Rende, CS, Italy.
| | - Erika Cione
- Department of Pharmacy, Health and Nutritional Sciences-Department of Excellence 2018-2022, University of Calabria, Ed. Polifunzionale, I-87036 Arcavacata di Rende, CS, Italy.
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy.
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74
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Ghislain J, Poitout V. Targeting lipid GPCRs to treat type 2 diabetes mellitus - progress and challenges. Nat Rev Endocrinol 2021; 17:162-175. [PMID: 33495605 DOI: 10.1038/s41574-020-00459-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/04/2020] [Indexed: 02/07/2023]
Abstract
Therapeutic approaches to the treatment of type 2 diabetes mellitus that are designed to increase insulin secretion either directly target β-cells or indirectly target gastrointestinal enteroendocrine cells (EECs), which release hormones that modulate insulin secretion (for example, incretins). Given that β-cells and EECs both express a large array of G protein-coupled receptors (GPCRs) that modulate insulin secretion, considerable research and development efforts have been undertaken to design therapeutic drugs targeting these GPCRs. Among them are GPCRs specific for free fatty acid ligands (lipid GPCRs), including free fatty acid receptor 1 (FFA1, otherwise known as GPR40), FFA2 (GPR43), FFA3 (GPR41) and FFA4 (GPR120), as well as the lipid metabolite binding glucose-dependent insulinotropic receptor (GPR119). These lipid GPCRs have demonstrated important roles in the control of islet and gut hormone secretion. Advances in lipid GPCR pharmacology have led to the identification of a number of synthetic agonists that exert beneficial effects on glucose homeostasis in preclinical studies. Yet, translation of these promising results to the clinic has so far been disappointing. In this Review, we present the physiological roles, pharmacology and clinical studies of these lipid receptors and discuss the challenges associated with their clinical development for the treatment of type 2 diabetes mellitus.
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Affiliation(s)
- Julien Ghislain
- Montreal Diabetes Research Center, Centre Hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Vincent Poitout
- Montreal Diabetes Research Center, Centre Hospitalier de l'Université de Montréal, Montréal, QC, Canada.
- Department of Medicine, Université de Montréal, Montréal, QC, Canada.
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75
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Grundmann M, Bender E, Schamberger J, Eitner F. Pharmacology of Free Fatty Acid Receptors and Their Allosteric Modulators. Int J Mol Sci 2021; 22:ijms22041763. [PMID: 33578942 PMCID: PMC7916689 DOI: 10.3390/ijms22041763] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
The physiological function of free fatty acids (FFAs) has long been regarded as indirect in terms of their activities as educts and products in metabolic pathways. The observation that FFAs can also act as signaling molecules at FFA receptors (FFARs), a family of G protein-coupled receptors (GPCRs), has changed the understanding of the interplay of metabolites and host responses. Free fatty acids of different chain lengths and saturation statuses activate FFARs as endogenous agonists via binding at the orthosteric receptor site. After FFAR deorphanization, researchers from the pharmaceutical industry as well as academia have identified several ligands targeting allosteric sites of FFARs with the aim of developing drugs to treat various diseases such as metabolic, (auto)inflammatory, infectious, endocrinological, cardiovascular, and renal disorders. GPCRs are the largest group of transmembrane proteins and constitute the most successful drug targets in medical history. To leverage the rich biology of this target class, the drug industry seeks alternative approaches to address GPCR signaling. Allosteric GPCR ligands are recognized as attractive modalities because of their auspicious pharmacological profiles compared to orthosteric ligands. While the majority of marketed GPCR drugs interact exclusively with the orthosteric binding site, allosteric mechanisms in GPCR biology stay medically underexploited, with only several allosteric ligands currently approved. This review summarizes the current knowledge on the biology of FFAR1 (GPR40), FFAR2 (GPR43), FFAR3 (GPR41), FFAR4 (GPR120), and GPR84, including structural aspects of FFAR1, and discusses the molecular pharmacology of FFAR allosteric ligands as well as the opportunities and challenges in research from the perspective of drug discovery.
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Affiliation(s)
- Manuel Grundmann
- Research and Early Development, Bayer Pharmaceuticals, Bayer AG, 42096 Wuppertal, Germany;
- Correspondence:
| | - Eckhard Bender
- Drug Discovery Sciences, Bayer Pharmaceuticals, Bayer AG, 42096 Wuppertal, Germany; (E.B.); (J.S.)
| | - Jens Schamberger
- Drug Discovery Sciences, Bayer Pharmaceuticals, Bayer AG, 42096 Wuppertal, Germany; (E.B.); (J.S.)
| | - Frank Eitner
- Research and Early Development, Bayer Pharmaceuticals, Bayer AG, 42096 Wuppertal, Germany;
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76
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Koyama R, Ookawara M, Watanabe M, Moritoh Y. Chronic Exposure to SCO-267, an Allosteric GPR40 Full Agonist, Is Effective in Improving Glycemic Control in Rats. Mol Pharmacol 2021; 99:286-293. [PMID: 33547250 DOI: 10.1124/molpharm.120.000168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/15/2021] [Indexed: 11/22/2022] Open
Abstract
Full agonist-mediated activation of free fatty acid receptor 1 (FFAR1/GPR40) alleviates diabetes in rodents. Considering that diabetes is a chronic disease, assessment of treatment durability of chronic exposure to a GPR40 full agonist is pivotal for treating patients with diabetes. However, the physiologic significance of chronic in vitro and in vivo exposure to GPR40 full agonists is largely unclear. Here, we evaluated the in vitro and in vivo effects of chronic treatment with SCO-267, a GPR40 full agonist, on signal transduction and glucose control. In vitro experiments showed that SCO-267 is an allosteric full agonist for GPR40, which activates the Gα q, Gα s, and Gα 12/13 pathways and β-arrestin recruitment. The calcium signal response was largely sustained in GPR40-overexpressing CHO cells even after prolonged incubation with SCO-267. To evaluate the in vivo relevance of chronic exposure to GPR40 full agonists, SCO-267 (1 and 10 mg/kg) was administered once daily to neonatally streptozotocin-induced diabetic rats for 15-33 days, and glucose control was evaluated. After 15 days of dosing followed by the drug washout period, SCO-267 improved glucose tolerance, most likely by increasing insulin sensitivity in rats. After 33 days, repeated exposure to SCO-267 was highly effective in improving glucose tolerance in rats. Furthermore, chronic exposure to SCO-267 increased pancreatic insulin content. These results demonstrated that even after chronic exposure, SCO-267 effectively activates GPR40 in cells and rats, suggesting the clinical application of SCO-267 in treating chronic diseases including diabetes. SIGNIFICANCE STATEMENT: GPR40 is a validated therapeutic target for diabetes. This study showed that even after chronic exposure, SCO-267, an allosteric GPR40 full agonist, effectively activates GPR40 in cells and rats; these results suggest a durable efficacy of SCO-267 in patients.
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Affiliation(s)
- Ryokichi Koyama
- Research Division, SCOHIA PHARMA, Inc., Fujisawa, Kanagawa, Japan
| | - Mitsugi Ookawara
- Research Division, SCOHIA PHARMA, Inc., Fujisawa, Kanagawa, Japan
| | | | - Yusuke Moritoh
- Research Division, SCOHIA PHARMA, Inc., Fujisawa, Kanagawa, Japan
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78
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Kuranov SO, Luzina OA, Salakhutdinov NF. FFA1 (GPR40) Receptor Agonists Based on Phenylpropanoic Acid as Hypoglycemic Agents: Structure–Activity Relationship. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020060151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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79
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Wang Y, Yu Z, Xiao W, Lu S, Zhang J. Allosteric binding sites at the receptor-lipid bilayer interface: novel targets for GPCR drug discovery. Drug Discov Today 2020; 26:690-703. [PMID: 33301977 DOI: 10.1016/j.drudis.2020.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023]
Abstract
As a superfamily of membrane receptors, G-protein-coupled receptors (GPCRs) have significant roles in human physiological processes, including cell proliferation, metabolism, and neuromodulation. GPCRs are vital targets of therapeutic drugs, and their allosteric regulation represents a novel direction for drug discovery. Given the numerous breakthroughs in structural biology, diverse allosteric sites on GPCRs have been identified within the extracellular and intracellular loops, and the seven core transmembrane helices. However, a unique type of allosteric site has also been discovered at the interface of the receptor-lipid bilayer, similar to the β2-adrenergic receptor. Here, we review recent identifications of these allosteric sites and the detailed modulator-target interactions within the interface for each modulator to highlight the role of lipids in GPCR allosteric drug discovery.
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Affiliation(s)
- Ying Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Zhengtian Yu
- Nutshell Biotechnology Co., Ltd., Shanghai, China
| | - Wen Xiao
- Nutshell Biotechnology Co., Ltd., Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
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80
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Husted AS, Ekberg JH, Tripp E, Nissen TAD, Meijnikman S, O'Brien SL, Ulven T, Acherman Y, Bruin SC, Nieuwdorp M, Gerhart-Hines Z, Calebiro D, Dragsted LO, Schwartz TW. Autocrine negative feedback regulation of lipolysis through sensing of NEFAs by FFAR4/GPR120 in WAT. Mol Metab 2020; 42:101103. [PMID: 33091626 PMCID: PMC7683346 DOI: 10.1016/j.molmet.2020.101103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES Long-chain fatty acids (LCFAs) released from adipocytes inhibit lipolysis through an unclear mechanism. We hypothesized that the LCFA receptor, FFAR4 (GPR120), which is highly expressed in adipocytes, may be involved in this feedback regulation. METHODS AND RESULTS Liquid chromatography mass spectrometry (LC-MS) analysis of conditioned media from isoproterenol-stimulated primary cultures of murine and human adipocytes demonstrated that most of the released non-esterified free fatty acids (NEFAs) are known agonists for FFAR4. In agreement with this, conditioned medium from isoproterenol-treated adipocytes stimulated signaling strongly in FFAR4 transfected COS-7 cells as opposed to non-transfected control cells. In transfected 3T3-L1 cells, FFAR4 agonism stimulated Gi- and Go-mini G protein binding more strongly than Gq, effects which were blocked by the selective FFAR4 antagonist AH7614. In primary cultures of murine white adipocytes, the synthetic, selective FFAR4 agonist CpdA inhibited isoproterenol-induced intracellular cAMP accumulation in a manner similar to the antilipolytic control agent nicotinic acid acting through another receptor, HCAR2. In vivo, oral gavage with the synthetic, specific FFAR4 agonist CpdB decreased the level of circulating NEFAs in fasting lean mice to a similar degree as nicotinic acid. In agreement with the identified anti-lipolytic effect of FFAR4, plasma NEFAs and glycerol were increased in FFAR4-deficient mice as compared to littermate controls despite having elevated insulin levels, and cAMP accumulation in primary adipocyte cultures was augmented by treatment with the FFAR4 antagonist conceivably by blocking the stimulatory tone of endogenous NEFAs on FFAR4. CONCLUSIONS In white adipocytes, FFAR4 functions as an NEFA-activated, autocrine, negative feedback regulator of lipolysis by decreasing cAMP though Gi-mediated signaling.
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Affiliation(s)
- Anna Sofie Husted
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
| | - Jeppe H Ekberg
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
| | - Emma Tripp
- Institute of Metabolism and Systems Research and Center of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TT, United Kingdom.
| | - Tinne A D Nissen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
| | - Stijn Meijnikman
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands.
| | - Shannon L O'Brien
- Institute of Metabolism and Systems Research and Center of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TT, United Kingdom.
| | - Trond Ulven
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
| | - Yair Acherman
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands.
| | - Sjoerd C Bruin
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands.
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, the Netherlands.
| | - Zach Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
| | - Davide Calebiro
- Institute of Metabolism and Systems Research and Center of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham B15 2TT, United Kingdom.
| | - Lars O Dragsted
- Department of Nutrition, Exercise, and Sports, Section of Preventive and Clinical Nutrition, University of Copenhagen, Rolighedsvej 30, Frederiksberg C, 1958, Denmark.
| | - Thue W Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
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81
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Bian Y, Jun JJ, Cuyler J, Xie XQ. Covalent allosteric modulation: An emerging strategy for GPCRs drug discovery. Eur J Med Chem 2020; 206:112690. [PMID: 32818870 PMCID: PMC9948676 DOI: 10.1016/j.ejmech.2020.112690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 12/13/2022]
Abstract
Designing covalent allosteric modulators brings new opportunities to the field of drug discovery towards G-protein-coupled receptors (GPCRs). Targeting an allosteric binding pocket can allow a modulator to have protein subtype selectivity and low drug resistance. Utilizing covalent warheads further enables the modulator to increase the binding potency and extend the duration of action. This review starts with GPCR allosteric modulation to discuss the structural biology of allosteric binding pockets, the different types of allosteric modulators, as well as the advantages of employing allosteric modulation. This is followed by a discussion on covalent modulators to clarify how covalent ligands can benefit the receptor modulation and to illustrate moieties that can commonly be used as covalent warheads. Finally, case studies are presented on designing class A, B, and C GPCR covalent allosteric modulators to demonstrate successful stories on combining allosteric modulation and covalent binding. Limitations and future perspectives are also covered.
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Affiliation(s)
- Yuemin Bian
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy,NIH National Center of Excellence for Computational Drug Abuse Research
| | - Jaden Jungho Jun
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy,NIH National Center of Excellence for Computational Drug Abuse Research
| | - Jacob Cuyler
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy,NIH National Center of Excellence for Computational Drug Abuse Research
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, Pittsburgh, PA, 15261, United States; NIH National Center of Excellence for Computational Drug Abuse Research, Pittsburgh, PA, 15261, United States; Drug Discovery Institute, Pittsburgh, PA, 15261, United States; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, United States.
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82
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Burggraaff L, van Veen A, Lam CC, van Vlijmen HWT, IJzerman AP, van Westen GJP. Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. J Chem Inf Model 2020; 60:4664-4672. [PMID: 32931270 PMCID: PMC7592116 DOI: 10.1021/acs.jcim.0c00695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 02/06/2023]
Abstract
Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to a protein noncompetitively with its endogenous ligand or substrate. The growing interest in allosteric modulators has resulted in a substantial increase of these entities and their features such as binding data in chemical libraries and databases. Although this data surge fuels research focused on allosteric modulators, binding data is unfortunately not always clearly indicated as being allosteric or orthosteric. Therefore, allosteric binding data is difficult to retrieve from databases that contain a mixture of allosteric and orthosteric compounds. This decreases model performance when statistical methods, such as machine learning models, are applied. In previous work we generated an allosteric data subset of ChEMBL release 14. In the current study an improved text mining approach is used to retrieve the allosteric and orthosteric binding types from the literature in ChEMBL release 22. Moreover, convolutional deep neural networks were constructed to predict the binding types of compounds for class A G protein-coupled receptors (GPCRs). Temporal split validation showed the model predictiveness with Matthews correlation coefficient (MCC) = 0.54, sensitivity allosteric = 0.54, and sensitivity orthosteric = 0.94. Finally, this study shows that the inclusion of accurate binding types increases binding predictions by including them as descriptor (MCC = 0.27 improved to MCC = 0.34; validated for class A GPCRs, trained on all GPCRs). Although the focus of this study is mainly on class A GPCRs, binding types for all protein classes in ChEMBL were obtained and explored. The data set is included as a supplement to this study, allowing the reader to select the compounds and binding types of interest.
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Affiliation(s)
- Lindsey Burggraaff
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC, Leiden, The Netherlands
| | - Amber van Veen
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC, Leiden, The Netherlands
| | - Chi Chung Lam
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC, Leiden, The Netherlands
| | - Herman W. T. van Vlijmen
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC, Leiden, The Netherlands
- Janssen
Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Adriaan P. IJzerman
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC, Leiden, The Netherlands
| | - Gerard J. P. van Westen
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC, Leiden, The Netherlands
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83
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Feng Z, Liang T, Wang S, Chen M, Hou T, Zhao J, Chen H, Zhou Y, Xie XQ. Binding Characterization of GPCRs-Modulator by Molecular Complex Characterizing System (MCCS). ACS Chem Neurosci 2020; 11:3333-3345. [PMID: 32941011 PMCID: PMC10063373 DOI: 10.1021/acschemneuro.0c00457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Increasing attention has been devoted to allosteric modulators as the preferred therapeutic agents for their colossal advantages such as higher selectivity, fewer side effects, and lower toxicity since they bind at allosteric sites that are topographically distinct from the classic orthosteric sites. However, the allosteric binding pockets are not conserved and there are no cogent methods to comprehensively characterize the features of allosteric sites with the binding of modulators. To overcome this limitation, our lab has developed a novel algorithm that can quantitatively characterize the receptor-ligand binding feature named Molecular Complex Characterizing System (MCCS). To illustrate the methodology and application of MCCS, we take G protein coupled receptors (GPCRs) as an example. First, we summarized and analyzed the reported allosteric binding pockets of class A GPCRs using MCCS. Sequentially, a systematic study was conducted between cannabinoid receptor type 1 (CB1) and its allosteric modulators, where we used MCCS to analyze the residue energy contribution and the interaction pattern. Finally, we validated the predicted allosteric binding site in CB2 via MCCS in combination with molecular dynamics (MD) simulation. Our results demonstrate that the MCCS program is advantageous in recapitulating the allosteric regulation pattern of class A GPCRs of the reported pockets as well as in predicting potential allosteric binding pockets. This MCCS program can serve as a valuable tool for the discovery of small-molecule allosteric modulators for class A GPCRs.
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Affiliation(s)
- Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Tianjian Liang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Siyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Maozi Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Tianling Hou
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Jack Zhao
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Hui Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Yuehan Zhou
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy; National Center of Excellence for Computational Drug Abuse Research; Drug Discovery Institute; Departments of Computational Biology and Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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84
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Chitre NM, Moniri NH, Murnane KS. Omega-3 Fatty Acids as Druggable Therapeutics for Neurodegenerative Disorders. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2020; 18:735-749. [PMID: 31724519 DOI: 10.2174/1871527318666191114093749] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/07/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022]
Abstract
Neurodegenerative disorders are commonly associated with a complex pattern of pathophysiological hallmarks, including increased oxidative stress and neuroinflammation, which makes their treatment challenging. Omega-3 Fatty Acids (O3FA) are natural products with reported neuroprotective, anti-inflammatory, and antioxidant effects. These effects have been attributed to their incorporation into neuronal membranes or through the activation of intracellular or recently discovered cell-surface receptors (i.e., Free-Fatty Acid Receptors; FFAR). Molecular docking studies have investigated the roles of O3FA as agonists of FFAR and have led to the development of receptor-specific targeted agonists for therapeutic purposes. Moreover, novel formulation strategies for targeted delivery of O3FA to the brain have supported their development as therapeutics for neurodegenerative disorders. Despite the compelling evidence of the beneficial effects of O3FA for several neuroprotective functions, they are currently only available as unregulated dietary supplements, with only a single FDA-approved prescription product, indicated for triglyceride reduction. This review highlights the relative safety and efficacy of O3FA, their drug-like properties, and their capacity to be formulated in clinically viable drug delivery systems. Interestingly, the presence of cardiac conditions such as hypertriglyceridemia is associated with brain pathophysiological hallmarks of neurodegeneration, such as neuroinflammation, thereby further suggesting potential therapeutic roles of O3FA for neurodegenerative disorders. Taken together, this review article summarizes and integrates the compelling evidence regarding the feasibility of developing O3FA and their synthetic derivatives as potential drugs for neurodegenerative disorders.
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Affiliation(s)
- Neha M Chitre
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA, United States
| | - Nader H Moniri
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA, United States
| | - Kevin S Murnane
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA, United States
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85
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Mizuno H, Kihara Y. Druggable Lipid GPCRs: Past, Present, and Prospects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1274:223-258. [PMID: 32894513 DOI: 10.1007/978-3-030-50621-6_10] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) have seven transmembrane spanning domains and comprise the largest superfamily with ~800 receptors in humans. GPCRs are attractive targets for drug discovery because they transduce intracellular signaling in response to endogenous ligands via heterotrimeric G proteins or arrestins, resulting in a wide variety of physiological and pathophysiological responses. The endogenous ligands for GPCRs are highly chemically diverse and include ions, biogenic amines, nucleotides, peptides, and lipids. In this review, we follow the KonMari method to better understand druggable lipid GPCRs. First, we have a comprehensive tidying up of lipid GPCRs including receptors for prostanoids, leukotrienes, specialized pro-resolving mediators (SPMs), lysophospholipids, sphingosine 1-phosphate (S1P), cannabinoids, platelet-activating factor (PAF), free fatty acids (FFAs), and sterols. This tidying up consolidates 46 lipid GPCRs and declutters several perplexing lipid GPCRs. Then, we further tidy up the lipid GPCR-directed drugs from the literature and databases, which identified 24 clinical drugs targeting 16 unique lipid GPCRs available in the market and 44 drugs under evaluation in more than 100 clinical trials as of 2019. Finally, we introduce drug designs for GPCRs that spark joy, such as positive or negative allosteric modulators (PAM or NAM), biased agonism, functional antagonism like fingolimod, and monoclonal antibodies (MAbs). These strategic drug designs may increase the efficacy and specificity of drugs and reduce side effects. Technological advances will help to discover more endogenous lipid ligands from the vast number of remaining orphan GPCRs and will also lead to the development novel lipid GPCR drugs to treat various diseases.
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Affiliation(s)
| | - Yasuyuki Kihara
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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86
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Yan Y, Xu Q, Zhao C, Dong H, Xu W, Zhang Y. In vivo pharmacokinetic study and oral glucose tolerance test of sulfoxide analogs of GPR40 agonist TAK-875. Drug Dev Res 2020; 81:708-715. [PMID: 32359092 DOI: 10.1002/ddr.21675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/25/2020] [Accepted: 04/11/2020] [Indexed: 10/31/2023]
Abstract
TAK-875 (compound 1) was the only GPR40 agonist with promising oral glucose-lowering effect, which entered phase III clinical trials. In previous studies, we successfully synthesized the TAK-875 sulfoxide analog 2, which was further separated to optically pure compounds 3 (S, S, 100.0% de) and 4 (R, S, 100.0% de). In vitro biological evaluation revealed that the sulfoxide analogs 3 and 4 possessed comparable GPR40 agonist activity to TAK-875. Herein, in order to further evaluate the druglikeness of TAK-875 sulfoxide analogs, the pharmacokinetic properties of compounds 2, 3, and 4 in rats were investigated and compared with that of TAK-875. The results showed that sulfoxide (2, 3, and 4) and sulfone (TAK-875) could be converted into each other in different degrees in vivo. Interestingly, compound 3 showed higher drug exposure calculated by the AUC sum of sulfoxide and sulfone in plasma than TAK-875, 2 and 4. In order to further investigate the in vivo glucose-lowering potency of sulfoxide analogs, asymmetric synthesis was carried out and led to two sulfoxides with moderate de values, 5 (S, S, 66.4% de) and 6 (R, S, 71.0% de). The following oral glucose tolerance test (OGTT) in rats showed that 5 (S, S, 66.4% de) had stronger glucose-lowering effect in vivo than 6 (R, S, 71.0% de) and TAK-875, which could be partly rationalized by the superior pharmacokinetic property of sulfoxide 3 (the main component of 5) relative to sulfoxide 4 (the main component of 6) and TAK-875.
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Affiliation(s)
- Yugang Yan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, China
- School of Medical Engineering, Jining Medical University, Jining, China
| | - Qifu Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Chunlong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Hang Dong
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Wenfang Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Yingjie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, China
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87
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Atanasio S, Deganutti G, Reynolds CA. Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics. J Comput Aided Mol Des 2020; 34:1181-1193. [PMID: 32851580 DOI: 10.1007/s10822-020-00338-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/18/2020] [Indexed: 01/12/2023]
Abstract
The free fatty acid receptor 1 (FFAR1, formerly GPR40), is a potential G protein-coupled receptor (GPCR) target for the treatment of type 2 diabetes mellitus (T2DM), as it enhances glucose-dependent insulin secretion upon activation by endogenous long-chain free fatty acids. The presence of two allosterically communicating binding sites and the lack of the conserved GPCR structural motifs challenge the general knowledge of its activation mechanism. To date, four X-ray crystal structures are available for computer-aided drug design. In this study, we employed molecular dynamics (MD) and supervised molecular dynamics (SuMD) to deliver insights into the (un)binding mechanism of the agonist MK-8666, and the allosteric communications between the two experimentally determined FFAR1 binding sites. We found that FFAR1 extracellular loop 2 (ECL2) mediates the binding of the partial agonist MK-8666. Moreover, simulations showed that the agonists MK-8666 and AP8 are reciprocally stabilized and that AP8 influences MK-8666 unbinding from FFAR1.
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Affiliation(s)
- Silvia Atanasio
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Giuseppe Deganutti
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK. .,Centre for Sport, Exercise and Life Sciences, Coventry University, Alison Gingell Building, Coventry, CV1 5FB, UK.
| | - Christopher A Reynolds
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.,Centre for Sport, Exercise and Life Sciences, Coventry University, Alison Gingell Building, Coventry, CV1 5FB, UK
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88
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Dijkman PM, Muñoz-García JC, Lavington SR, Kumagai PS, dos Reis RI, Yin D, Stansfeld PJ, Costa-Filho AJ, Watts A. Conformational dynamics of a G protein-coupled receptor helix 8 in lipid membranes. SCIENCE ADVANCES 2020; 6:eaav8207. [PMID: 32851152 PMCID: PMC7428336 DOI: 10.1126/sciadv.aav8207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 07/02/2020] [Indexed: 05/21/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest and pharmaceutically most important class of membrane proteins encoded in the human genome, characterized by a seven-transmembrane helix architecture and a C-terminal amphipathic helix 8 (H8). In a minority of GPCR structures solved to date, H8 either is absent or adopts an unusual conformation. The controversial existence of H8 of the class A GPCR neurotensin receptor 1 (NTS1) has been examined here for the nonthermostabilized receptor in a functionally supporting membrane environment using electron paramagnetic resonance, molecular dynamics simulations, and circular dichroism. Lipid-protein interactions with phosphatidylserine and phosphatidylethanolamine lipids, in particular, stabilize the residues 374 to 390 of NTS1 into forming a helix. Furthermore, introduction of a helix-breaking proline residue in H8 elicited an increase in ß-arrestin-NTS1 interactions observed in pull-down assays, suggesting that the structure and/or dynamics of H8 might play an important role in GPCR signaling.
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Affiliation(s)
- Patricia M. Dijkman
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Juan C. Muñoz-García
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Steven R. Lavington
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Patricia Suemy Kumagai
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, C.P. 369, São Carlos SP 13560-970, Brazil
| | - Rosana I. dos Reis
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Daniel Yin
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Antonio José Costa-Filho
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto SP 14040-901, Brazil
| | - Anthony Watts
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Corresponding author.
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89
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Benchmarking GPCR homology model template selection in combination with de novo loop generation. J Comput Aided Mol Des 2020; 34:1027-1044. [PMID: 32737667 DOI: 10.1007/s10822-020-00325-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/16/2020] [Indexed: 01/08/2023]
Abstract
G protein-coupled receptors (GPCR) comprise the largest family of membrane proteins and are of considerable interest as targets for drug development. However, many GPCR structures remain unsolved. To address the structural ambiguity of these receptors, computational tools such as homology modeling and loop modeling are often employed to generate predictive receptor structures. Here we combined both methods to benchmark a protocol incorporating homology modeling based on a locally selected template and extracellular loop modeling that additionally evaluates the presence of template ligands during these modeling steps. Ligands were also docked using three docking methods and two pose selection methods to elucidate an optimal ligand pose selection method. Results suggest that local template-based homology models followed by loop modeling produce more accurate and predictive receptor models than models produced without loop modeling, with decreases in average receptor and ligand RMSD of 0.54 Å and 2.91 Å, respectively. Ligand docking results showcased the ability of MOE induced fit docking to produce ligand poses with atom root-mean-square deviation (RMSD) values at least 0.20 Å lower (on average) than the other two methods benchmarked in this study. In addition, pose selection methods (software-based scoring, ligand complementation) selected lower RMSD poses with MOE induced fit docking than either of the other methods (averaging at least 1.57 Å lower), indicating that MOE induced fit docking is most suited for docking into GPCR homology models in our hands. In addition, target receptor models produced with a template ligand present throughout the modeling process most often produced target ligand poses with RMSD values ≤ 4.5 Å and Tanimoto coefficients > 0.6 after selection based on ligand complementation than target receptor models produced in the absence of template ligands. Overall, the findings produced by this study support the use of local template homology modeling in combination with de novo ECL2 modeling in the presence of a ligand from the template crystal structure to generate GPCR models intended to study ligand binding interactions.
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90
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Structural basis of GPBAR activation and bile acid recognition. Nature 2020; 587:499-504. [PMID: 32698187 DOI: 10.1038/s41586-020-2569-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/10/2020] [Indexed: 02/08/2023]
Abstract
The G-protein-coupled bile acid receptor (GPBAR) conveys the cross-membrane signalling of a vast variety of bile acids and is a signalling hub in the liver-bile acid-microbiota-metabolism axis1-3. Here we report the cryo-electron microscopy structures of GPBAR-Gs complexes stabilized by either the high-affinity P3954 or the semisynthesized bile acid derivative INT-7771,3 at 3 Å resolution. These structures revealed a large oval pocket that contains several polar groups positioned to accommodate the amphipathic cholic core of bile acids, a fingerprint of key residues to recognize diverse bile acids in the orthosteric site, a putative second bile acid-binding site with allosteric properties and structural features that contribute to bias properties. Moreover, GPBAR undertakes an atypical mode of activation and G protein coupling that features a different set of key residues connecting the ligand-binding pocket to the Gs-coupling site, and a specific interaction motif that is localized in intracellular loop 3. Overall, our study not only reveals unique structural features of GPBAR that are involved in bile acid recognition and allosteric effects, but also suggests the presence of distinct connecting mechanisms between the ligand-binding pocket and the G-protein-binding site in the G-protein-coupled receptor superfamily.
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91
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Bartuzi D, Wróbel TM, Kaczor AA, Matosiuk D. Tuning Down the Pain - An Overview of Allosteric Modulation of Opioid Receptors: Mechanisms of Modulation, Allosteric Sites, Modulator Syntheses. Curr Top Med Chem 2020; 20:2852-2865. [PMID: 32479245 DOI: 10.2174/1568026620666200601155451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 01/09/2023]
Abstract
Opioid signaling plays a central role in pain perception. As such, it remains the main target in the development of antinociceptive agents, despite serious side effects involved. In recent years, hopes for improved opioid painkillers are rising, together with our understanding of allosterism and biased signaling mechanisms. In this review, we focus on recently discovered allosteric modulators of opioid receptors, insights into phenomena underlying their action, as well as on how they extend our understanding of mechanisms of previously known compounds. A brief overlook of their synthesis is also presented.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
| | - Tomasz M Wróbel
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, Lublin, Poland
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92
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Chabowski DS, Cohen KE, Abu-Hatoum O, Gutterman DD, Freed JK. Crossing signals: bioactive lipids in the microvasculature. Am J Physiol Heart Circ Physiol 2020; 318:H1185-H1197. [PMID: 32243770 PMCID: PMC7541955 DOI: 10.1152/ajpheart.00706.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The primary function of the arterial microvasculature is to ensure that regional perfusion of blood flow is matched to the needs of the tissue bed. This critical physiological mechanism is tightly controlled and regulated by a variety of vasoactive compounds that are generated and released from the vascular endothelium. Although these substances are required for modulating vascular tone, they also influence the surrounding tissue and have an overall effect on vascular, as well as parenchymal, homeostasis. Bioactive lipids, fatty acid derivatives that exert their effects through signaling pathways, are included in the list of vasoactive compounds that modulate the microvasculature. Although lipids were identified as important vascular messengers over three decades ago, their specific role within the microvascular system is not well defined. Thorough understanding of these pathways and their regulation is not only essential to gain insight into their role in cardiovascular disease but is also important for preventing vascular dysfunction following cancer treatment, a rapidly growing problem in medical oncology. The purpose of this review is to discuss how biologically active lipids, specifically prostanoids, epoxyeicosatrienoic acids, sphingolipids, and lysophospholipids, contribute to vascular function and signaling within the endothelium. Methods for quantifying lipids will be briefly discussed, followed by an overview of the various lipid families. The cross talk in signaling between classes of lipids will be discussed in the context of vascular disease. Finally, the potential clinical implications of these lipid families will be highlighted.
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Affiliation(s)
- Dawid S. Chabowski
- 1Division of Cardiology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin,2Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Katie E. Cohen
- 1Division of Cardiology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin,2Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ossama Abu-Hatoum
- 4Department of Surgery, HaEmek Medical Center, Technion Medical School, Haifa, Israel
| | - David D. Gutterman
- 1Division of Cardiology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin,2Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Julie K. Freed
- 2Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin,3Department of Anesthesiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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93
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Teng D, Chen J, Li D, Wu Z, Li W, Tang Y, Liu G. Computational Insights into Molecular Activation and Positive Cooperative Mechanisms of FFAR1 Modulators. J Chem Inf Model 2020; 60:3214-3230. [DOI: 10.1021/acs.jcim.0c00030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Dan Teng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jianhui Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Dongping Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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94
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Ulven ER, Quon T, Sergeev E, Barki N, Brvar M, Hudson BD, Dutta P, Hansen AH, Bielefeldt LØ, Tobin AB, McKenzie CJ, Milligan G, Ulven T. Structure-Activity Relationship Studies of Tetrahydroquinolone Free Fatty Acid Receptor 3 Modulators. J Med Chem 2020; 63:3577-3595. [PMID: 32141297 PMCID: PMC7307922 DOI: 10.1021/acs.jmedchem.9b02036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Indexed: 12/27/2022]
Abstract
Free fatty acid receptor 3 (FFA3, previously GPR41) is activated by short-chain fatty acids, mediates health effects of the gut microbiota, and is a therapeutic target for metabolic and inflammatory diseases. The shortage of well-characterized tool compounds has however impeded progress. Herein, we report structure-activity relationship of an allosteric modulator series and characterization of physicochemical and pharmacokinetic properties of selected compounds, including previous and new tools. Two representatives, 57 (TUG-1907) and 63 (TUG-2015), showed improved solubility and preserved potency. Of these, 57, with EC50 = 145 nM and a solubility of 33 μM, showed high clearance in vivo but is a preferred tool in vitro. In contrast, 63, with EC50 = 162 nM and a solubility of 9 μM, showed lower clearance and seems better suited for in vivo studies. Using 57, we demonstrate for the first time that FFA3 activation leads to calcium mobilization in murine dorsal root ganglia.
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Affiliation(s)
- Elisabeth Rexen Ulven
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Tezz Quon
- Centre
for Translational Pharmacology, Institute of Molecular, Cell and Systems
Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, Scotland, U.K.
| | - Eugenia Sergeev
- Centre
for Translational Pharmacology, Institute of Molecular, Cell and Systems
Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, Scotland, U.K.
| | - Natasja Barki
- Centre
for Translational Pharmacology, Institute of Molecular, Cell and Systems
Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, Scotland, U.K.
| | - Matjaz Brvar
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Brian D. Hudson
- Centre
for Translational Pharmacology, Institute of Molecular, Cell and Systems
Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, Scotland, U.K.
| | - Palash Dutta
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anders Højgaard Hansen
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Line Ø. Bielefeldt
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Andrew B. Tobin
- Centre
for Translational Pharmacology, Institute of Molecular, Cell and Systems
Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, Scotland, U.K.
| | - Christine J. McKenzie
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Graeme Milligan
- Centre
for Translational Pharmacology, Institute of Molecular, Cell and Systems
Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ Glasgow, Scotland, U.K.
| | - Trond Ulven
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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95
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Gimeno RE, Briere DA, Seeley RJ. Leveraging the Gut to Treat Metabolic Disease. Cell Metab 2020; 31:679-698. [PMID: 32187525 PMCID: PMC7184629 DOI: 10.1016/j.cmet.2020.02.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/23/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023]
Abstract
25 years ago, the future of treating obesity and diabetes focused on end organs known to be involved in energy balance and glucose regulation, including the brain, muscle, adipose tissue, and pancreas. Today, the most effective therapies are focused around the gut. This includes surgical options, such as vertical sleeve gastrectomy and Roux-en-Y gastric bypass, that can produce sustained weight loss and diabetes remission but also extends to pharmacological treatments that simulate or amplify various signals that come from the gut. The purpose of this Review is to discuss the wealth of approaches currently under development that seek to further leverage the gut as a source of novel therapeutic opportunities with the hope that we can achieve the effects of surgical interventions with less invasive and more scalable solutions.
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Affiliation(s)
- Ruth E Gimeno
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46225, USA
| | - Daniel A Briere
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46225, USA
| | - Randy J Seeley
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA.
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96
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Sayama M, Uwamizu A, Otani Y, Inoue A, Aoki J, Sekijima M, Ohwada T. Membrane Phospholipid Analogues as Molecular Rulers to Probe the Position of the Hydrophobic Contact Point of Lysophospholipid Ligands on the Surface of G-Protein-Coupled Receptor during Membrane Approach. Biochemistry 2020; 59:1173-1201. [PMID: 32124599 DOI: 10.1021/acs.biochem.0c00061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
When lipid mediators bind to G-protein-coupled receptors (GPCRs), the ligand first enters the lipid bilayer, then diffuses laterally in the cell membrane to make hydrophobic contact with the receptor protein, and finally enters the receptor's binding pocket. In this process, the location of the hydrophobic contact point on the surface of the receptor has been little discussed even in cases in which the crystal structure has been determined, because the ligand binding pocket is buried inside the transmembrane (TM) domains. Here, we coupled an activator ligand to a series of membrane phospholipid surrogates, which constrain the depth of entry of the ligand into the lipid bilayer. Consequently, via measurement of the receptor-activating activity as a function of the depth of entry into the membrane, these surrogates can be used as molecular rulers to estimate the location of the hydrophobic contact point on the surface of GPCR. We focused on lysophosphatidylserine (LysoPS) receptor GPR34 and prepared a series of simplified membrane-lipid-surrogate-conjugated lysophospholipid analogues by attaching alkoxy amine chains of varying lengths to the hydrophobic tail of a potent GPR34 agonist. As expected, the activity of these lipid-conjugated LysoPS analogues was dependent on chain length. The predicted contact position matches the position of the terminal benzene ring of a nonlipidic ligand that protrudes between TMs 4 and 5 of the receptor. We further found that the nature of the terminal hydrophilic functional group of the conjugated membrane lipid surrogate strongly influences the activity, suggesting that lateral hydrophilic contact of LysoPS analogues with the receptor's surface is also crucial for ligand-GPCR binding.
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Affiliation(s)
- Misa Sayama
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akiharu Uwamizu
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yuko Otani
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asuka Inoue
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,AMED-PRIME, Japan Science and Technology Corporation, Kawaguchi 332-0012, Japan.,AMED-LEAP, Japan Science and Technology Corporation, Kawaguchi 332-0012, Japan
| | - Junken Aoki
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,AMED-LEAP, Japan Science and Technology Corporation, Kawaguchi 332-0012, Japan.,AMED-CREST, Japan Science and Technology Corporation, Kawaguchi 332-0012, Japan
| | - Masakazu Sekijima
- Department of Computer Science, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Tomohiko Ohwada
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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97
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Thomas-Fowlkes B, Cifelli S, Souza S, Visconti R, Struck A, Weinglass A, Wildey MJ. Cell-Based In Vitro Assay Automation: Balancing Technology and Data Reproducibility/Predictability. SLAS Technol 2020; 25:276-285. [PMID: 32003291 DOI: 10.1177/2472630320902095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
G-protein-coupled receptors (GPCRs) are modulated by many marketed drugs, and as such, they continue to be key targets for drug discovery and development. Many GPCR targets at Merck Research Laboratories (MRL) are profiled using homogenous time-resolved fluorescence (HTRF) inositol monophosphate (IP-1) cell-based functional assays using adherent cells in 384-well microplates. Due to discrepancies observed across several in vitro assays supporting lead optimization structure-activity relationship (SAR) efforts, different assay paradigms were evaluated for removing growth medium from the assay plates prior to compound addition and determination of IP-1 accumulation. Remarkably, employing the noncontact centrifugation BlueWasher method leads to left-shifted potencies across multiple structural classes and rescues "false negatives" relative to the traditional manual evacuation method. Further, assay performance is improved, with the minimum significant ratio of challenging chemotypes dropping from ~5-6 to <3. While the impact of BlueWasher on a broad range of our GPCR targets remains to be determined, for highly protein-bound small molecules, it provides a path toward improving assay reproducibility across scientists and sites as well as reducing replicates in SAR assay support.
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Affiliation(s)
- Brande Thomas-Fowlkes
- Screening, Target and Compound Profiling, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ, USA.,Global Clinical Trials Operations, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Steven Cifelli
- Screening, Target and Compound Profiling, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Sarah Souza
- In Vitro Pharmacology, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ, USA.,Evotec AG, Princeton Junction, NJ, USA
| | - Richard Visconti
- In Vitro Pharmacology, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ, USA.,Celgene Corporation, Summit, NJ, USA
| | - Alice Struck
- Screening, Target and Compound Profiling, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Adam Weinglass
- Screening, Target and Compound Profiling, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Mary Jo Wildey
- Screening, Target and Compound Profiling, Merck Research Labs, Merck & Co., Inc., Kenilworth, NJ, USA
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98
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Pioszak AA, Hay DL. RAMPs as allosteric modulators of the calcitonin and calcitonin-like class B G protein-coupled receptors. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2020; 88:115-141. [PMID: 32416865 DOI: 10.1016/bs.apha.2020.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Receptor activity-modifying proteins (RAMPs) are a family of three single span transmembrane proteins in humans that interact with many GPCRs and can modulate their function. RAMPs were discovered as key components of the calcitonin gene-related peptide and adrenomedullin receptors. They are required for transport of this class B GPCR, calcitonin receptor-like receptor (CLR), to the cell surface and determine its peptide ligand binding preferences. Soon thereafter RAMPs were shown to modulate the binding of calcitonin and amylin peptides to the related calcitonin receptor (CTR) and in the years since an ever-growing number of RAMP-interacting receptors have been identified including most if not all of the 15 class B GPCRs and several GPCRs from other families. Studies of CLR, CTR, and a handful of other GPCRs revealed that RAMPs are able to modulate various aspects of receptor function including trafficking, ligand binding, and signaling. Here, we review RAMP interactions and functions with an emphasis on class B receptors for which our understanding is most advanced. A key focus is to discuss recent evidence that RAMPs serve as endogenous allosteric modulators of CLR and CTR. We discuss structural studies of RAMP-CLR complexes and CTR and biochemical and pharmacological studies that collectively have significantly expanded our understanding of the mechanistic basis for RAMP modulation of these class B GPCRs. Last, we consider the implications of these findings for drug development targeting RAMP-CLR/CTR complexes.
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Affiliation(s)
- Augen A Pioszak
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.
| | - Debbie L Hay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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99
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MacKerell AD, Jo S, Lakkaraju SK, Lind C, Yu W. Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots). Biochim Biophys Acta Gen Subj 2020; 1864:129519. [PMID: 31911242 DOI: 10.1016/j.bbagen.2020.129519] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/21/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. METHODS The site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. RESULTS The SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. GENERAL SIGNIFICANCE The present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.
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Affiliation(s)
- Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America.
| | - Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, MD 21202, United States of America
| | | | - Christoffer Lind
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD 21201, United States of America
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100
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Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions. Comput Struct Biotechnol J 2020; 18:1577-1586. [PMID: 32637054 PMCID: PMC7330491 DOI: 10.1016/j.csbj.2020.06.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022] Open
Abstract
Despite the wealth of methods developed for exploring the molecular basis of allostery in biomolecular systems, there is still a need for structure-based predictive tools that can efficiently detect susceptible sites for triggering allosteric responses. Toward this goal, we introduce here an elastic network model (ENM)-based method, Essential Site Scanning Analysis (ESSA). Essential sites are here defined as residues that would significantly alter the protein's global dynamics if bound to a ligand. To mimic the crowding induced upon substrate binding, the heavy atoms of each residue are incorporated as additional network nodes into the α-carbon-based ENM, and the resulting shifts in soft mode frequencies are used as a metric for evaluating the essentiality of each residue. Results on a dataset of monomeric proteins indicate the enrichment of allosteric and orthosteric binding sites, as well as global hinge regions among essential residues, highlighting the significant role of these sites in controlling the overall structural dynamics. Further integration of ESSA with information on predicted pockets and their local hydrophobicity density enables successful predictions of allosteric pockets for both ligand-bound and -unbound structures. ESSA can be efficiently applied to large multimeric systems. Three case studies, namely (i) G-protein binding to a GPCR, (ii) heterotrimeric assembly of the Ser/Thr protein phosphatase PP2A, and (iii) allo-targeting of AMPA receptor, demonstrate the utility of ESSA for identifying essential sites and narrowing down target allosteric sites identified by druggability simulations.
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