1
|
Szwabowski GL, Griffing M, Mugabe EJ, O’Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
Collapse
Affiliation(s)
| | | | | | | | | | - Daniel L. Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
| | - Abby L. Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
| |
Collapse
|
2
|
Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
Collapse
Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
| |
Collapse
|
3
|
El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner A. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Commun Chem 2023; 6:219. [PMID: 37828292 PMCID: PMC10570326 DOI: 10.1038/s42004-023-01014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.
Collapse
Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Christian M Orr
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | | | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Vinay Grama
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Feng Qu
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hok Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosana I Reis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Lutz Vogeley
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Raymond J Owens
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David G Brown
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
| |
Collapse
|
4
|
Birch J, Kwan TOC, Judge PJ, Axford D, Aller P, Butryn A, Reis RI, Bada Juarez JF, Vinals J, Owen RL, Nango E, Tanaka R, Tono K, Joti Y, Tanaka T, Owada S, Sugahara M, Iwata S, Orville AM, Watts A, Moraes I. A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography. J Appl Crystallogr 2023; 56:1361-1370. [PMID: 37791355 PMCID: PMC10543674 DOI: 10.1107/s1600576723006428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/24/2023] [Indexed: 10/05/2023] Open
Abstract
Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.
Collapse
Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
| | - Tristan O. C. Kwan
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Peter J. Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Pierre Aller
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Agata Butryn
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Rosana I. Reis
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Juan F. Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, Lausanne, CH-1015, Switzerland
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Michihiro Sugahara
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Allen M. Orville
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Isabel Moraes
- ChemBio, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| |
Collapse
|
5
|
Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
Collapse
Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| |
Collapse
|
6
|
Claff T, Schlegel JG, Voss JH, Vaaßen VJ, Weiße RH, Cheng RKY, Markovic-Mueller S, Bucher D, Sträter N, Müller CE. Crystal structure of adenosine A 2A receptor in complex with clinical candidate Etrumadenant reveals unprecedented antagonist interaction. Commun Chem 2023; 6:106. [PMID: 37264098 DOI: 10.1038/s42004-023-00894-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/04/2023] [Indexed: 06/03/2023] Open
Abstract
The Gs protein-coupled adenosine A2A receptor (A2AAR) represents an emerging drug target for cancer immunotherapy. The clinical candidate Etrumadenant was developed as an A2AAR antagonist with ancillary blockade of the A2BAR subtype. It constitutes a unique chemotype featuring a poly-substituted 2-amino-4-phenyl-6-triazolylpyrimidine core structure. Herein, we report two crystal structures of the A2AAR in complex with Etrumadenant, obtained with differently thermostabilized A2AAR constructs. This led to the discovery of an unprecedented interaction, a hydrogen bond of T883.36 with the cyano group of Etrumadenant. T883.36 is mutated in most A2AAR constructs used for crystallization, which has prevented the discovery of its interactions. In-vitro characterization of Etrumadenant indicated low selectivity versus the A1AR subtype, which can be rationalized by the structural data. These results will facilitate the future design of AR antagonists with desired selectivity. Moreover, they highlight the advantages of the employed A2AAR crystallization construct that is devoid of ligand binding site mutations.
Collapse
Affiliation(s)
- Tobias Claff
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113, Bonn, Germany.
| | - Jonathan G Schlegel
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113, Bonn, Germany
| | - Jan H Voss
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113, Bonn, Germany
| | - Victoria J Vaaßen
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113, Bonn, Germany
| | - Renato H Weiße
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany
| | | | | | - Denis Bucher
- leadXpro AG, PARK InnovAARE, 5234, Villigen, Switzerland
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Christa E Müller
- PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53113, Bonn, Germany.
| |
Collapse
|
7
|
Tzortzini E, Corey RA, Kolocouris A. Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A 2A and A 1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:928-949. [PMID: 36637988 DOI: 10.1021/acs.jcim.2c01181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A2A adenosine receptor (A2AR) and the A1 adenosine receptor (A1R) and predict new cholesterol binding sites indicating amino acid residues with a high residence time in three biologically relevant membranes. Compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-cholesterol and POPC-phosphatidylinositol-bisphosphate (PIP2)-cholesterol, the plasma mimetic membrane best described the cholesterol binding sites previously detected for the inactive state of A2AR and revealed the binding sites with long-lasting amino acid residues. We observed that using the plasma mimetic membrane and plotting residues with cholesterol residence time ≥2 μs, our CG MD simulations captured most obviously the cholesterol-protein interactions. For the inactive A2AR, we identified one more binding site in which cholesterol is bound to residues with a long residence time compared to the previously detected, for the active A1R, three binding sites, and for the inactive A1R, two binding sites. We calculated that for the active states, cholesterol binds to residues with a much longer residence time compared to the inactive state for both A2AR and A1R. The stability of the identified binding sites to A1R or A2AR with CG MD simulations was additionally investigated with potential of mean force calculations using umbrella sampling. We observed that the binding sites with residues to which cholesterol has a long residence time in A2AR have shallow binding free energy minima compared to the related binding sites in A1R, suggesting a stronger binding for cholesterol to A1R. The differences in binding sites in which cholesterol is stabilized and interacts with residues with a long residence time between active and inactive states of A1R and A2AR can be important for differences in functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators, which can bind through lipid pathways. We observed a stronger binding for cholesterol to A1R (i.e., generally higher association rates) compared to A2AR, which remains to be demonstrated. For the active states, cholesterol binds to residues with much longer residence times compared to the inactive state for both A2AR and A1R. Taken together, binding sites of active A1R may be considered as promising allosteric targets.
Collapse
Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
| |
Collapse
|
8
|
Han R, Yoon H, Yoo J, Lee Y. Systematic analyses of the sequence conservation and ligand interaction patterns of purinergic P1 and P2Y receptors provide a structural basis for receptor selectivity. Comput Struct Biotechnol J 2023; 21:889-898. [PMID: 36698973 PMCID: PMC9860165 DOI: 10.1016/j.csbj.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023] Open
Abstract
Purinergic receptors are membrane proteins that regulate numerous cellular functions by catalyzing reactions involving purine nucleotides or nucleosides. Among the three receptor families, i.e., P1, P2X, and P2Y, the P1 and P2Y receptors share common structural features of class A GPCR. Comprehensive sequence and structural analysis revealed that the P1 and P2Y receptors belong to two distinct groups. They exhibit different ligand-binding site features that can distinguish between specific activators. These specific amino acid residues in the binding cavity may be involved in the selectivity and unique pharmacological behavior of each subtype. In this study, we conducted a structure-based analysis of purinergic P1 and P2Y receptors to identify their evolutionary signature and obtain structural insights into ligand recognition and selectivity. The structural features of the P1 and P2Y receptor classes were compared based on sequence conservation and ligand interaction patterns. Orthologous protein sequences were collected for the P1 and P2Y receptors, and sequence conservation was calculated based on Shannon entropy to identify highly conserved residues. To analyze the ligand interaction patterns, we performed docking studies on the P1 and P2Y receptors using known ligand information extracted from the ChEMBL database. We analyzed how the conserved residues are related to ligand-binding sites and how the key interacting residues differ between P1 and P2Y receptors, or between agonists and antagonists. We extracted new similarities and differences between the receptor subtypes, and the results can be used for designing new ligands by predicting hotspot residues that are important for functional selectivity.
Collapse
|
9
|
GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A 2A Adenosine Receptor. J Med Chem 2022; 65:11648-11657. [PMID: 35977382 PMCID: PMC9469204 DOI: 10.1021/acs.jmedchem.2c00462] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Modulators of the G protein-coupled A2A adenosine
receptor
(A2AAR) have been considered promising agents to treat
Parkinson’s disease, inflammation, cancer, and central nervous
system disorders. Herein, we demonstrate that a thiophene modification
at the C8 position in the common adenine scaffold converted an A2AAR agonist into an antagonist. We synthesized and characterized
a novel A2AAR antagonist, 2 (LJ-4517), with Ki = 18.3 nM. X-ray crystallographic structures
of 2 in complex with two thermostabilized A2AAR constructs were solved at 2.05 and 2.80 Å resolutions. In
contrast to A2AAR agonists, which simultaneously interact
with both Ser2777.42 and His2787.43, 2 only transiently contacts His2787.43, which can be direct
or water-mediated. The n-hexynyl group of 2 extends into an A2AAR exosite. Structural analysis revealed
that the introduced thiophene modification restricted receptor conformational
rearrangements required for subsequent activation. This approach can
expand the repertoire of adenosine receptor antagonists that can be
designed based on available agonist scaffolds.
Collapse
|
10
|
Jacobson KA, Gao ZG, Matricon P, Eddy MT, Carlsson J. Adenosine A 2A receptor antagonists: from caffeine to selective non-xanthines. Br J Pharmacol 2022; 179:3496-3511. [PMID: 32424811 PMCID: PMC9251831 DOI: 10.1111/bph.15103] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 12/12/2022] Open
Abstract
A long evolution of knowledge of the psychostimulant caffeine led in the 1960s to another purine natural product, adenosine and its A2A receptor. Adenosine is a short-lived autocrine/paracrine mediator that acts pharmacologically at four different adenosine receptors in a manner opposite to the pan-antagonist caffeine and serves as an endogenous allostatic regulator. Although detrimental in the developing brain, caffeine appears to be cerebroprotective in aging. Moderate caffeine consumption in adults, except in pregnancy, may also provide benefit in pain, diabetes, and kidney and liver disorders. Inhibition of A2A receptors is one of caffeine's principal effects and we now understand this interaction at the atomic level. The A2A receptor has become a prototypical example of utilizing high-resolution structures of GPCRs for the rational design of chemically diverse drug molecules. The previous focus on discovery of selective A2A receptor antagonists for neurodegenerative diseases has expanded to include immunotherapy for cancer, and clinical trials have ensued. LINKED ARTICLES: This article is part of a themed issue on Structure Guided Pharmacology of Membrane Proteins (BJP 75th Anniversary). To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v179.14/issuetoc.
Collapse
Affiliation(s)
- Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pierre Matricon
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew T. Eddy
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| |
Collapse
|
11
|
Wang X, Yuan S, Chan HCS. Translocation Mechanism of Allosteric Sodium Ions in β 2-Adrenoceptor. J Chem Inf Model 2022; 62:3090-3095. [PMID: 35695388 DOI: 10.1021/acs.jcim.2c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The allosteric modulation of G-protein-coupled receptors (GPCRs) by sodium ions has received significant attention as the crystal structures of several receptors show the binding of sodium ions (Na+) at the conserved D2.50. Theoretical studies have shown that extracellular Na+ would enter the allosteric D2.50 via the orthosteric site. However, it remains unclear how the bound allosteric Na+ would leave the GPCRs. In this study, we performed molecular dynamics (MD) simulations to illustrate the energy barriers of Na+ transfer through the transmembrane helix bundle of β2AR. In contrast to the postulations from other GPCRs, the translocation of this allosteric Na+ into the intracellular side is found to be significantly difficult. Hence, the translocation direction could be receptor-specific.
Collapse
Affiliation(s)
- Xueying Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Alpha Mol Science Ltd, Shenzhen 518055, China
| | - H C Stephen Chan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
12
|
Claff T, Klapschinski TA, Tiruttani Subhramanyam UK, Vaaßen VJ, Schlegel JG, Vielmuth C, Voß JH, Labahn J, Müller CE. Single Stabilizing Point Mutation Enables High-Resolution Co-Crystal Structures of the Adenosine A 2A Receptor with Preladenant Conjugates. Angew Chem Int Ed Engl 2022; 61:e202115545. [PMID: 35174942 PMCID: PMC9310709 DOI: 10.1002/anie.202115545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 01/08/2023]
Abstract
The G protein-coupled adenosine A2A receptor (A2A AR) is an important new (potential) drug target in immuno-oncology, and for neurodegenerative diseases. Preladenant and its derivatives belong to the most potent A2A AR antagonists displaying exceptional selectivity. While crystal structures of the human A2A AR have been solved, mostly using the A2A -StaR2 protein that bears 9 point mutations, co-crystallization with Preladenant derivatives has so far been elusive. We developed a new A2A AR construct harboring a single point mutation (S913.39 K) which renders it extremely thermostable. This allowed the co-crystallization of two novel Preladenant derivatives, the polyethylene glycol-conjugated (PEGylated) PSB-2113, and the fluorophore-labeled PSB-2115. The obtained crystal structures (2.25 Å and 2.6 Å resolution) provide explanations for the high potency and selectivity of Preladenant derivatives. They represent the first crystal structures of a GPCR in complex with PEG- and fluorophore-conjugated ligands. The applied strategy is predicted to be applicable to further class A GPCRs.
Collapse
Affiliation(s)
- Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Tim A Klapschinski
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Udaya K Tiruttani Subhramanyam
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany.,Research Centre Jülich, Institute of Complex Systems (IBI-7), Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Victoria J Vaaßen
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jonathan G Schlegel
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Christin Vielmuth
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jan H Voß
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany.,Research Centre Jülich, Institute of Complex Systems (IBI-7), Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| |
Collapse
|
13
|
Yeast-based directed-evolution for high-throughput structural stabilization of G protein-coupled receptors (GPCRs). Sci Rep 2022; 12:8657. [PMID: 35606532 PMCID: PMC9126886 DOI: 10.1038/s41598-022-12731-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/10/2022] [Indexed: 11/08/2022] Open
Abstract
The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery is not fully realized due to the enormous difficulties associated with structure elucidation of these profoundly unstable membrane proteins. The existing methods of GPCR stability-engineering are cumbersome and low-throughput; in addition, the scope of GPCRs that could benefit from these techniques is limited. Here, we present a yeast-based screening platform for a single-step isolation of GRCR variants stable in the presence of short-chain detergents, a feature essential for their successful crystallization using vapor diffusion method. The yeast detergent-resistant cell wall presents a unique opportunity for compartmentalization, to physically link the receptor's phenotype to its encoding DNA, and thus enable discovery of stable GPCR variants with unprecedent efficiency. The scope of mutations identified by the method reveals a surprising amenability of the GPCR scaffold to stabilization, and suggests an intriguing possibility of amending the stability properties of GPCR by varying the structural status of the C-terminus.
Collapse
|
14
|
Mahmood A, Iqbal J. Purinergic receptors modulators: An emerging pharmacological tool for disease management. Med Res Rev 2022; 42:1661-1703. [PMID: 35561109 DOI: 10.1002/med.21888] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/16/2022] [Accepted: 05/04/2022] [Indexed: 11/10/2022]
Abstract
Purinergic signaling is mediated through extracellular nucleotides (adenosine 5'-triphosphate, uridine-5'-triphosphate, adenosine diphosphate, uridine-5'-diphosphate, and adenosine) that serve as signaling molecules. In the early 1990s, purines and pyrimidine receptors were cloned and characterized drawing the attention of scientists toward this aspect of cellular signaling. This signaling pathway is comprised of four subtypes of adenosine receptors (P1), eight subtypes of G-coupled protein receptors (P2YRs), and seven subtypes of ligand-gated ionotropic receptors (P2XRs). In current studies, the pathophysiology and therapeutic potentials of these receptors have been focused on. Various ligands, modulating the functions of purinergic receptors, are in current clinical practices for the treatment of various neurodegenerative disorders and cardiovascular diseases. Moreover, several purinergic receptors ligands are in advanced phases of clinical trials as a remedy for depression, epilepsy, autism, osteoporosis, atherosclerosis, myocardial infarction, diabetes, irritable bowel syndrome, and cancers. In the present study, agonists and antagonists of purinergic receptors have been summarized that may serve as pharmacological tools for drug design and development.
Collapse
Affiliation(s)
- Abid Mahmood
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad, Pakistan
| |
Collapse
|
15
|
IJzerman AP, Jacobson KA, Müller CE, Cronstein BN, Cunha RA. International Union of Basic and Clinical Pharmacology. CXII: Adenosine Receptors: A Further Update. Pharmacol Rev 2022; 74:340-372. [PMID: 35302044 PMCID: PMC8973513 DOI: 10.1124/pharmrev.121.000445] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our previous International Union of Basic and Clinical Pharmacology report on the nomenclature and classification of adenosine receptors (2011) contained a number of emerging developments with respect to this G protein-coupled receptor subfamily, including protein structure, protein oligomerization, protein diversity, and allosteric modulation by small molecules. Since then, a wealth of new data and results has been added, allowing us to explore novel concepts such as target binding kinetics and biased signaling of adenosine receptors, to examine a multitude of receptor structures and novel ligands, to gauge new pharmacology, and to evaluate clinical trials with adenosine receptor ligands. This review should therefore be considered a further update of our previous reports from 2001 and 2011. SIGNIFICANCE STATEMENT: Adenosine receptors (ARs) are of continuing interest for future treatment of chronic and acute disease conditions, including inflammatory diseases, neurodegenerative afflictions, and cancer. The design of AR agonists ("biased" or not) and antagonists is largely structure based now, thanks to the tremendous progress in AR structural biology. The A2A- and A2BAR appear to modulate the immune response in tumor biology. Many clinical trials for this indication are ongoing, whereas an A2AAR antagonist (istradefylline) has been approved as an anti-Parkinson agent.
Collapse
Affiliation(s)
- Adriaan P IJzerman
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Kenneth A Jacobson
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Christa E Müller
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Bruce N Cronstein
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Rodrigo A Cunha
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| |
Collapse
|
16
|
Kepa MW, Tomizaki T, Sato Y, Ozerov D, Sekiguchi H, Yasuda N, Aoyama K, Skopintsev P, Standfuss J, Cheng R, Hennig M, Tsujino S. Acoustic levitation and rotation of thin films and their application for room temperature protein crystallography. Sci Rep 2022; 12:5349. [PMID: 35354848 PMCID: PMC8967846 DOI: 10.1038/s41598-022-09167-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 03/18/2022] [Indexed: 11/18/2022] Open
Abstract
Acoustic levitation has attracted attention in terms of chemical and biochemical analysis in combination with various analytical methods because of its unique container-less environment for samples that is not reliant on specific material characteristics. However, loading samples with very high viscosity is difficult. To expand the scope, we propose the use of polymer thin films as sample holders, whereby the sample is dispensed on a film that is subsequently loaded onto an acoustic levitator. When applied for protein crystallography experiments, rotation controllability and positional stability are important prerequisites. We therefore study the acoustic levitation and rotation of thin films with an aspect ratio (the diameter-to-thickness ratio) of 80-240, which is an order of magnitude larger than those reported previously. For films with empirically optimized shapes, we find that it is possible to control the rotation speed in the range of 1-4 rotations per second while maintaining a positional stability of 12 ± 5 µm. The acoustic radiation force acting on the films is found to be a factor of 26-30 higher than that for same-volume water droplets. We propose use cases of the developed films for protein crystallography experiments and demonstrate data collections for large single crystal samples at room temperature.
Collapse
Affiliation(s)
- Michal W Kepa
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - Takashi Tomizaki
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland.
| | - Yohei Sato
- Nuclear Energy and Safety Research Division, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - Dmitry Ozerov
- Photon Science Division, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Nobuhiro Yasuda
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Koki Aoyama
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Petr Skopintsev
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland
| | - Robert Cheng
- leadXpro AG, PARK InnovAARE, 5234, Villigen-PSI, Switzerland
| | - Michael Hennig
- leadXpro AG, PARK InnovAARE, 5234, Villigen-PSI, Switzerland
| | - Soichiro Tsujino
- Division of Biology and Chemistry, Paul Scherrer Institut, 5232, Villigen-PSI, Switzerland.
| |
Collapse
|
17
|
Zhang J, Luo Z, Duan W, Yang K, Ling L, Yan W, Liu R, Wüthrich K, Jiang H, Xie C, Cheng J. Dual-acting antitumor agents targeting the A 2A adenosine receptor and histone deacetylases: Design and synthesis of 4-(furan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-6-amine derivatives. Eur J Med Chem 2022; 236:114326. [PMID: 35390714 DOI: 10.1016/j.ejmech.2022.114326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/17/2022]
Abstract
Based on its inhibition by antagonists, the A2A adenosine receptor (A2AAR) has attracted attention as an anti-tumor drug target; however, in preclinical models and clinical trials, A2AAR antagonists have so far shown only limited efficacy as standalone therapies. The design of dual-acting compounds, targeting the A2AAR and histone deacetylases (HDACs), is used here as an approach to the discovery of novel and more potent antitumor agents. Based on the core structures of the A2AAR antagonists V-2006 and CPI-444, novel 4-(furan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-6-amine derivatives were designed as such dual-acting compounds. The binding affinities for A2AAR of all the new compounds were tested, and their HDAC inhibitory activity was evaluated. Compounds with balanced A2AAR antagonism and HDAC inhibition were tested for their in vitro anti-proliferative activity and pharmacokinetic properties. One of the compounds, 14c (4-(2-(6-Amino-4-(furan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)ethyl)-N-(2-amino-phenyl)benzamide) showed an overall favorable pharmacokinetic profile; in the mouse MC38 xenograft model, it showed potent anti-tumor effects with inhibition rates of 44% (90 mg/kg, po, bid) and 85% (60 mg/kg, ip, bid), respectively.
Collapse
Affiliation(s)
- Jinfeng Zhang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ziwei Luo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wenwen Duan
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Kexin Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Lijun Ling
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Wenzhong Yan
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Ruiquan Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China; Department of Integrated Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Chengying Xie
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
| |
Collapse
|
18
|
Claff T, Klapschinski TA, Tiruttani Subhramanyam UK, Vaaßen VJ, Schlegel JG, Vielmuth C, Voß JH, Labahn J, Müller CE. Eine einzige stabilisierende Punktmutation ermöglicht hochaufgelöste Co‐Kristallstrukturen des Adenosin‐A
2A
‐Rezeptors mit Preladenant‐Konjugaten. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tobias Claff
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Tim A. Klapschinski
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Udaya K. Tiruttani Subhramanyam
- Centre for Structural Systems Biology (CSSB) Notkestraße 85 22607 Hamburg Germany
- Research Centre Jülich Institute of Complex Systems (IBI-7) Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Victoria J. Vaaßen
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jonathan G. Schlegel
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Christin Vielmuth
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jan H. Voß
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB) Notkestraße 85 22607 Hamburg Germany
- Research Centre Jülich Institute of Complex Systems (IBI-7) Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Christa E. Müller
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| |
Collapse
|
19
|
Wang J, Bhattarai A, Do HN, Akhter S, Miao Y. Molecular Simulations and Drug Discovery of Adenosine Receptors. Molecules 2022; 27:2054. [PMID: 35408454 PMCID: PMC9000248 DOI: 10.3390/molecules27072054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 02/02/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A1AR, A2AAR, A2BAR and A3AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A1AR and A3AR preferentially couple to the Gi/o proteins, while the A2AAR and A2BAR prefer coupling to the Gs proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.
Collapse
Affiliation(s)
| | | | | | | | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA; (J.W.); (A.B.); (H.N.D.); (S.A.)
| |
Collapse
|
20
|
García-Nafría J, Tate CG. Structure determination of GPCRs: cryo-EM compared with X-ray crystallography. Biochem Soc Trans 2021; 49:2345-2355. [PMID: 34581758 PMCID: PMC8589417 DOI: 10.1042/bst20210431] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest single family of cell surface receptors encoded by the human genome and they play pivotal roles in co-ordinating cellular systems throughout the human body, making them ideal drug targets. Structural biology has played a key role in defining how receptors are activated and signal through G proteins and β-arrestins. The application of structure-based drug design (SBDD) is now yielding novel compounds targeting GPCRs. There is thus significant interest from both academia and the pharmaceutical industry in the structural biology of GPCRs as currently only about one quarter of human non-odorant receptors have had their structure determined. Initially, all the structures were determined by X-ray crystallography, but recent advances in electron cryo-microscopy (cryo-EM) now make GPCRs tractable targets for single-particle cryo-EM with comparable resolution to X-ray crystallography. So far this year, 78% of the 99 GPCR structures deposited in the PDB (Jan-Jul 2021) were determined by cryo-EM. Cryo-EM has also opened up new possibilities in GPCR structural biology, such as determining structures of GPCRs embedded in a lipid nanodisc and multiple GPCR conformations from a single preparation. However, X-ray crystallography still has a number of advantages, particularly in the speed of determining many structures of the same receptor bound to different ligands, an essential prerequisite for effective SBDD. We will discuss the relative merits of cryo-EM and X-ray crystallography for the structure determination of GPCRs and the future potential of both techniques.
Collapse
Affiliation(s)
- Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018 Zaragoza, Spain
| | | |
Collapse
|
21
|
Healey RD, Basu S, Humm AS, Leyrat C, Cong X, Golebiowski J, Dupeux F, Pica A, Granier S, Márquez JA. An automated platform for structural analysis of membrane proteins through serial crystallography. CELL REPORTS METHODS 2021; 1:None. [PMID: 34723237 PMCID: PMC8545655 DOI: 10.1016/j.crmeth.2021.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 09/22/2021] [Indexed: 11/01/2022]
Abstract
Membrane proteins are central to many pathophysiological processes, yet remain very difficult to analyze structurally. Moreover, high-throughput structure-based drug discovery has not yet been exploited for membrane proteins because of lack of automation. Here, we present a facile and versatile platform for in meso membrane protein crystallization, enabling rapid atomic structure determination at both cryogenic and room temperatures. We apply this approach to human integral membrane proteins, which allowed us to identify different conformational states of intramembrane enzyme-product complexes and analyze by molecular dynamics simulations the structural dynamics of the ADIPOR2 integral membrane protein. Finally, we demonstrate an automated pipeline combining high-throughput microcrystal soaking, automated laser-based harvesting, and serial crystallography, enabling screening of small-molecule libraries with membrane protein crystals grown in meso. This approach brings needed automation to this important class of drug targets and enables high-throughput structure-based ligand discovery with membrane proteins.
Collapse
Affiliation(s)
- Robert D. Healey
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Shibom Basu
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Anne-Sophie Humm
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Cedric Leyrat
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Xiaojing Cong
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Jérôme Golebiowski
- Institute of Chemistry of Nice UMR7272, Université Côte d’Azur, CNRS, 28 Avenue Valrose, 06108 Nice, France
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Technology, 711-873 Daegu, South Korea
| | - Florine Dupeux
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- Institut de Biologie Structurale, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Andrea Pica
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- ALPX S.A.S. 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Sébastien Granier
- IGF, University of Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - José Antonio Márquez
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38000 Grenoble, France
- ALPX S.A.S. 71 Avenue des Martyrs, 38000 Grenoble, France
| |
Collapse
|
22
|
Kampen S, Duy Vo D, Zhang X, Panel N, Yang Y, Jaiteh M, Matricon P, Svenningsson P, Brea J, Loza MI, Kihlberg J, Carlsson J. Structure‐Guided Design of G‐Protein‐Coupled Receptor Polypharmacology. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefanie Kampen
- Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| | - Duc Duy Vo
- Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| | - Xiaoqun Zhang
- Department of Clinical Neuroscience Karolinska Institute 17177 Stockholm Sweden
| | - Nicolas Panel
- Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| | - Yunting Yang
- Department of Clinical Neuroscience Karolinska Institute 17177 Stockholm Sweden
| | - Mariama Jaiteh
- Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| | - Pierre Matricon
- Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience Karolinska Institute 17177 Stockholm Sweden
| | - Jose Brea
- USEF Screening Platform-BioFarma Research Group Centre for Research in Molecular Medicine and Chronic Diseases University of Santiago de Compostela 15706 Santiago de Compostela Spain
| | - Maria Isabel Loza
- USEF Screening Platform-BioFarma Research Group Centre for Research in Molecular Medicine and Chronic Diseases University of Santiago de Compostela 15706 Santiago de Compostela Spain
| | - Jan Kihlberg
- Department of Chemistry-BMC Uppsala University 75123 Uppsala Sweden
| | - Jens Carlsson
- Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden
| |
Collapse
|
23
|
Zou R, Wang X, Li S, Chan HCS, Vogel H, Yuan S. The role of metal ions in G protein‐coupled receptor signalling and drug discovery. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rongfeng Zou
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
| | - Xueying Wang
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Shu Li
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - H. C. Stephen Chan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Horst Vogel
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
- Ecole Polytechnique Fédérale de Lausanne (EPFL) Lausanne Switzerland
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
- AlphaMol Science Ltd Shenzhen China
| |
Collapse
|
24
|
Kampen S, Duy Vo D, Zhang X, Panel N, Yang Y, Jaiteh M, Matricon P, Svenningsson P, Brea J, Loza MI, Kihlberg J, Carlsson J. Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology. Angew Chem Int Ed Engl 2021; 60:18022-18030. [PMID: 33904641 PMCID: PMC8456950 DOI: 10.1002/anie.202101478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 12/29/2022]
Abstract
Many diseases are polygenic and can only be treated efficiently with drugs that modulate multiple targets. However, rational design of compounds with multi-target profiles is rarely pursued because it is considered too difficult, in particular if the drug must enter the central nervous system. Here, a structure-based strategy to identify dual-target ligands of G-protein-coupled receptors is presented. We use this approach to design compounds that both antagonize the A2A adenosine receptor and activate the D2 dopamine receptor, which have excellent potential as antiparkinson drugs. Atomic resolution models of the receptors guided generation of a chemical library with compounds designed to occupy orthosteric and secondary binding pockets in both targets. Structure-based virtual screens identified ten compounds, of which three had affinity for both targets. One of these scaffolds was optimized to nanomolar dual-target activity and showed the predicted pharmacodynamic effect in a rat model of Parkinsonism.
Collapse
Affiliation(s)
- Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Duc Duy Vo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Xiaoqun Zhang
- Department of Clinical Neuroscience, Karolinska Institute, 17177, Stockholm, Sweden
| | - Nicolas Panel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Yunting Yang
- Department of Clinical Neuroscience, Karolinska Institute, 17177, Stockholm, Sweden
| | - Mariama Jaiteh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institute, 17177, Stockholm, Sweden
| | - Jose Brea
- USEF Screening Platform-BioFarma Research Group, Centre for Research in Molecular Medicine and Chronic Diseases, University of Santiago de Compostela, 15706, Santiago, de Compostela, Spain
| | - Maria Isabel Loza
- USEF Screening Platform-BioFarma Research Group, Centre for Research in Molecular Medicine and Chronic Diseases, University of Santiago de Compostela, 15706, Santiago, de Compostela, Spain
| | - Jan Kihlberg
- Department of Chemistry-BMC, Uppsala University, 75123, Uppsala, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| |
Collapse
|
25
|
Salmaso V, Jain S, Jacobson KA. Purinergic GPCR transmembrane residues involved in ligand recognition and dimerization. Methods Cell Biol 2021; 166:133-159. [PMID: 34752329 PMCID: PMC8620127 DOI: 10.1016/bs.mcb.2021.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2023]
Abstract
We compare the GPCR-ligand interactions and highlight important residues for recognition in purinergic receptors-from both X-ray crystallographic and cryo-EM structures. These include A1 and A2A adenosine receptors, and P2Y1 and P2Y12 receptors that respond to ADP and other nucleotides. These receptors are important drug discovery targets for immune, metabolic and nervous system disorders. In most cases, orthosteric ligands are represented, except for one allosteric P2Y1 antagonist. This review catalogs the residues and regions that engage in contacts with ligands or with other GPCR protomers in dimeric forms. Residues that are in proximity to bound ligands within purinergic GPCR families are correlated. There is extensive conservation of recognition motifs between adenosine receptors, but the P2Y1 and P2Y12 receptors are each structurally distinct in their ligand recognition. Identifying common interaction features for ligand recognition within a receptor class that has multiple structures available can aid in the drug discovery process.
Collapse
Affiliation(s)
- Veronica Salmaso
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Shanu Jain
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States.
| |
Collapse
|
26
|
Chatzigoulas A, Cournia Z. Rational design of allosteric modulators: Challenges and successes. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1529] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alexios Chatzigoulas
- Biomedical Research Foundation Academy of Athens Athens Greece
- Department of Informatics and Telecommunications National and Kapodistrian University of Athens Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation Academy of Athens Athens Greece
| |
Collapse
|
27
|
Do HN, Akhter S, Miao Y. Pathways and Mechanism of Caffeine Binding to Human Adenosine A 2A Receptor. Front Mol Biosci 2021; 8:673170. [PMID: 33987207 PMCID: PMC8111288 DOI: 10.3389/fmolb.2021.673170] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/24/2021] [Indexed: 11/13/2022] Open
Abstract
Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the pathways and mechanism of CFF binding to the target receptors remain unclear. In this study, we have performed all-atom-enhanced sampling simulations using a robust Gaussian-accelerated molecular dynamics (GaMD) method to elucidate the binding mechanism of CFF to human adenosine A2A receptor (A2AAR). Multiple 500–1,000 ns GaMD simulations captured both binding and dissociation of CFF in the A2AAR. The GaMD-predicted binding poses of CFF were highly consistent with the x-ray crystal conformations with a characteristic hydrogen bond formed between CFF and residue N6.55 in the receptor. In addition, a low-energy intermediate binding conformation was revealed for CFF at the receptor extracellular mouth between ECL2 and TM1. While the ligand-binding pathways of the A2AAR were found similar to those of other class A GPCRs identified from previous studies, the ECL2 with high sequence divergence serves as an attractive target site for designing allosteric modulators as selective drugs of the A2AAR.
Collapse
Affiliation(s)
- Hung N Do
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Sana Akhter
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| |
Collapse
|
28
|
Amelia T, van Veldhoven JPD, Falsini M, Liu R, Heitman LH, van Westen GJP, Segala E, Verdon G, Cheng RKY, Cooke RM, van der Es D, IJzerman AP. Crystal Structure and Subsequent Ligand Design of a Nonriboside Partial Agonist Bound to the Adenosine A 2A Receptor. J Med Chem 2021; 64:3827-3842. [PMID: 33764785 PMCID: PMC8154574 DOI: 10.1021/acs.jmedchem.0c01856] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
In this study, we
determined the crystal structure of an engineered
human adenosine A2A receptor bound to a partial agonist
and compared it to structures cocrystallized with either a full agonist
or an antagonist/inverse agonist. The interaction between the partial
agonist, belonging to a class of dicyanopyridines, and amino acids
in the ligand binding pocket inspired us to develop a small library
of derivatives and assess their affinity in radioligand binding studies
and potency and intrinsic activity in a functional, label-free, intact
cell assay. It appeared that some of the derivatives retained the
partial agonist profile, whereas other ligands turned into inverse
agonists. We rationalized this remarkable behavior with additional
computational docking studies.
Collapse
Affiliation(s)
- Tasia Amelia
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands.,School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, 40132 Bandung, Indonesia
| | - Jacobus P D van Veldhoven
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Matteo Falsini
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Rongfang Liu
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and 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 and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Elena Segala
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, United Kingdom
| | - Grégory Verdon
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, United Kingdom
| | - Robert K Y Cheng
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, United Kingdom
| | - Robert M Cooke
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, United Kingdom
| | - Daan van der Es
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
29
|
Waltenspühl Y, Ehrenmann J, Klenk C, Plückthun A. Engineering of Challenging G Protein-Coupled Receptors for Structure Determination and Biophysical Studies. Molecules 2021; 26:molecules26051465. [PMID: 33800379 PMCID: PMC7962830 DOI: 10.3390/molecules26051465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 01/14/2023] Open
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) exert fundamental biological functions and are involved in a multitude of physiological responses, making these receptors ideal drug targets. Drug discovery programs targeting GPCRs have been greatly facilitated by the emergence of high-resolution structures and the resulting opportunities to identify new chemical entities through structure-based drug design. To enable the determination of high-resolution structures of GPCRs, most receptors have to be engineered to overcome intrinsic hurdles such as their poor stability and low expression levels. In recent years, multiple engineering approaches have been developed to specifically address the technical difficulties of working with GPCRs, which are now beginning to make more challenging receptors accessible to detailed studies. Importantly, successfully engineered GPCRs are not only valuable in X-ray crystallography, but further enable biophysical studies with nuclear magnetic resonance spectroscopy, surface plasmon resonance, native mass spectrometry, and fluorescence anisotropy measurements, all of which are important for the detailed mechanistic understanding, which is the prerequisite for successful drug design. Here, we summarize engineering strategies based on directed evolution to reduce workload and enable biophysical experiments of particularly challenging GPCRs.
Collapse
|
30
|
Marlow B, Kuenze G, Li B, Sanders CR, Meiler J. Structural determinants of cholesterol recognition in helical integral membrane proteins. Biophys J 2021; 120:1592-1604. [PMID: 33640379 DOI: 10.1016/j.bpj.2021.02.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 01/12/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Cholesterol is an integral component of mammalian membranes. It has been shown to modulate membrane fluidity and dynamics and alter integral membrane protein function. However, understanding the molecular mechanisms of how cholesterol impacts protein function is complicated by limited and conflicting structural data. Because of the nature of the crystallization and cryo-EM structure determination, it is difficult to distinguish between specific and biologically relevant interactions and a nonspecific association. The only widely recognized search algorithm for cholesterol-integral-membrane-protein interaction sites is sequence based, i.e., searching for the so-called "Cholesterol Recognition/interaction Amino acid Consensus" motif. Although these motifs are present in numerous integral membrane proteins, there is inconclusive evidence to support their necessity or sufficiency for cholesterol binding. Here, we leverage the increasing number of experimental cholesterol-integral-membrane-protein structures to systematically analyze putative interaction sites based on their spatial arrangement and evolutionary conservation. This analysis creates three-dimensional representations of general cholesterol interaction sites that form clusters across multiple integral membrane protein classes. We also classify cholesterol-integral-membrane-protein interaction sites as either likely-specific or nonspecific. Information gleaned from our characterization will eventually enable a structure-based approach to predict and design cholesterol-integral-membrane-protein interaction sites.
Collapse
Affiliation(s)
- Brennica Marlow
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Bian Li
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee; Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany.
| |
Collapse
|
31
|
The Specificity of Downstream Signaling for A 1 and A 2AR Does Not Depend on the C-Terminus, Despite the Importance of This Domain in Downstream Signaling Strength. Biomedicines 2020; 8:biomedicines8120603. [PMID: 33322210 PMCID: PMC7764039 DOI: 10.3390/biomedicines8120603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 11/17/2022] Open
Abstract
Recent efforts to determine the high-resolution crystal structures for the adenosine receptors (A1R and A2AR) have utilized modifications to the native receptors in order to facilitate receptor crystallization and structure determination. One common modification is a truncation of the unstructured C-terminus, which has been utilized for all the adenosine receptor crystal structures obtained to date. Ligand binding for this truncated receptor has been shown to be similar to full-length receptor for A2AR. However, the C-terminus has been identified as a location for protein-protein interactions that may be critical for the physiological function of these important drug targets. We show that variants with A2AR C-terminal truncations lacked cAMP-linked signaling compared to the full-length receptor constructs transfected into mammalian cells (HEK-293). In addition, we show that in a humanized yeast system, the absence of the full-length C-terminus affected downstream signaling using a yeast MAPK response-based fluorescence assay, though full-length receptors showed native-like G-protein coupling. To further study the G protein coupling, we used this humanized yeast platform to explore coupling to human-yeast G-protein chimeras in a cellular context. Although the C-terminus was essential for Gα protein-associated signaling, chimeras of A1R with a C-terminus of A2AR coupled to the A1R-specific Gα (i.e., Gαi1 versus Gαs). This surprising result suggests that the C-terminus is important in the signaling strength, but not specificity, of the Gα protein interaction. This result has further implications in drug discovery, both in enabling the experimental use of chimeras for ligand design, and in the cautious interpretation of structure-based drug design using truncated receptors.
Collapse
|
32
|
A comprehensive approach to X-ray crystallography for drug discovery at a synchrotron facility - The example of Diamond Light Source. DRUG DISCOVERY TODAY. TECHNOLOGIES 2020; 37:83-92. [PMID: 34895658 DOI: 10.1016/j.ddtec.2020.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 11/21/2022]
Abstract
A detailed understanding of the interactions between drugs and their targets is crucial to develop the best possible therapeutic agents. Structure-based drug design relies on the availability of high-resolution structures obtained primarily through X-ray crystallography. Collecting and analysing quickly a large quantity of structural data is crucial to accelerate drug discovery pipelines. Researchers from academia and industry can access the highly automated macromolecular crystallography (MX) beamlines of Diamond Light Source, the UK national synchrotron, to rapidly collect diffraction data from large numbers of crystals. With seven beamlines dedicated to MX, Diamond offers bespoke solutions for a wide variety of user requirements. Working in synergy with state-of-the-art laboratories and other life science instruments to provide an integrated offering, the MX beamlines provide innovative and multidisciplinary approaches to the determination of structures of new pharmacological targets as well as the efficient study of protein-ligand complexes.
Collapse
|
33
|
Reis RI, Moraes I. Probing Membrane Protein Assembly into Nanodiscs by In Situ Dynamic Light Scattering: A 2A Receptor as a Case Study. BIOLOGY 2020; 9:biology9110400. [PMID: 33202740 PMCID: PMC7696381 DOI: 10.3390/biology9110400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/02/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
Simple Summary Located within the biological cell membranes, integral membrane proteins are responsible for a large variety of vital cellular processes. In humans, nearly a quarter of the genome codes integral membrane proteins, therefore malfunction of these proteins is associated with a variety of symptoms and diseases such as obesity, cancer and Parkinson’s disease. Clearly, knowledge of membrane proteins behaviour, in both structural and functional terms, is important not only in medicine but also in the design of better drugs with improved pharmaceutical properties. Nevertheless, much still remains unknown about these proteins, mainly because of the technical challenges associated with their production and stability in vitro once removed from their native lipidic environment. Recently, several membrane mimetic systems have been developed including nanodisc lipid particles. Nanodiscs are self-assembled lipidic structures that “trap” membrane proteins into a disc shaped phospholipid bilayer that is stabilised by a belt made of a protein know as membrane scaffold protein (MSP). Membrane proteins assembled into lipidic nanodiscs can maintain their structural and functional integrity and are compatible with most biophysical methods. Here we demonstrate the use of in situ dynamic light scattering as a high-throughput screening tool to assess the best conditions for nanodisc assembly and protein incorporation. Abstract Membrane proteins play a crucial role in cell physiology by participating in a variety of essential processes such as transport, signal transduction and cell communication. Hence, understanding their structure–function relationship is vital for the improvement of therapeutic treatments. Over the last decade, based on the development of detergents, amphipoles and styrene maleic-acid lipid particles (SMALPs), remarkable accomplishments have been made in the field of membrane protein structural biology. Nevertheless, there are still many drawbacks associated with protein–detergent complexes, depending on the protein in study or experimental application. Recently, newly developed membrane mimetic systems have become very popular for allowing a structural and functional characterisation of membrane proteins in vitro. The nanodisc technology is one such valuable tool, which provides a more native-like membrane environment than detergent micelles or liposomes. In addition, it is also compatible with many biophysical and biochemical methods. Here we describe the use of in situ dynamic light scattering to accurately and rapidly probe membrane proteins’ reconstitution into nanodiscs. The adenosine type 2A receptor (A2AR) was used as a case study.
Collapse
Affiliation(s)
- Rosana I. Reis
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK;
- Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot OX11 0FA, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK;
- Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot OX11 0FA, UK
- Correspondence:
| |
Collapse
|
34
|
Isoprenoid-chained lipid EROCOC 17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography. Sci Rep 2020; 10:19305. [PMID: 33168855 PMCID: PMC7652841 DOI: 10.1038/s41598-020-76277-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/26/2020] [Indexed: 11/08/2022] Open
Abstract
In meso crystallization of membrane proteins relies on the use of lipids capable of forming a lipidic cubic phase (LCP). However, almost all previous crystallization trials have used monoacylglycerols, with 1-(cis-9-octadecanoyl)-rac-glycerol (MO) being the most widely used lipid. We now report that EROCOC17+4 mixed with 10% (w/w) cholesterol (Fig. 1) serves as a new matrix for crystallization and a crystal delivery medium in the serial femtosecond crystallography of Adenosine A2A receptor (A2AR). The structures of EROCOC17+4-matrix grown A2AR crystals were determined at 2.0 Å resolution by serial synchrotron rotation crystallography at a cryogenic temperature, and at 1.8 Å by LCP-serial femtosecond crystallography, using an X-ray free-electron laser at 4 and 20 °C sample temperatures, and are comparable to the structure of the MO-matrix grown A2AR crystal (PDB ID: 4EIY). Moreover, X-ray scattering measurements indicated that the EROCOC17+4/water system did not form the crystalline LC phase at least down to - 20 °C, in marked contrast to the equilibrium MO/water system, which transforms into the crystalline LC phase below about 17 °C. As the LC phase formation within the LCP-matrix causes difficulties in protein crystallography experiments in meso, this feature of EROCOC17+4 will expand the utility of the in meso method.
Collapse
|
35
|
Lee MY, Geiger J, Ishchenko A, Han GW, Barty A, White TA, Gati C, Batyuk A, Hunter MS, Aquila A, Boutet S, Weierstall U, Cherezov V, Liu W. Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase. IUCRJ 2020; 7:976-984. [PMID: 33209312 PMCID: PMC7642783 DOI: 10.1107/s2052252520012701] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 05/31/2023]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A2A receptor (A2AAR) at 2.0 Å resolution is determined and compared with previous A2AAR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.
Collapse
Affiliation(s)
- Ming-Yue Lee
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - James Geiger
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Andrii Ishchenko
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Alexander Batyuk
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Vadim Cherezov
- Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, 1002 W. Childs Way, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Wei Liu
- Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-1604, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| |
Collapse
|
36
|
Jespers W, Verdon G, Azuaje J, Majellaro M, Keränen H, García‐Mera X, Congreve M, Deflorian F, de Graaf C, Zhukov A, Doré AS, Mason JS, Åqvist J, Cooke RM, Sotelo E, Gutiérrez‐de‐Terán H. X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A 2A Adenosine Receptor Antagonists. Angew Chem Int Ed Engl 2020; 59:16536-16543. [PMID: 32542862 PMCID: PMC7540567 DOI: 10.1002/anie.202003788] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/18/2020] [Indexed: 01/04/2023]
Abstract
We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A2A adenosine receptor (AR). Eight A2A AR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A2A AR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A2A AR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A2A AR, an emerging target in immuno-oncology.
Collapse
Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
| | - Grégory Verdon
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Jhonny Azuaje
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de CompostelaSpain
| | - Maria Majellaro
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de CompostelaSpain
| | - Henrik Keränen
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
- Present address: H. Lundbeck A/SOttiliavej 92500ValbyDenmark
| | - Xerardo García‐Mera
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
| | - Miles Congreve
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | | | - Chris de Graaf
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Andrei Zhukov
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Andrew S. Doré
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Jonathan S. Mason
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Johan Åqvist
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
| | - Robert M. Cooke
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Eddy Sotelo
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de CompostelaSpain
| | - Hugo Gutiérrez‐de‐Terán
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
| |
Collapse
|
37
|
Zhang J, Yan W, Duan W, Wüthrich K, Cheng J. Tumor Immunotherapy Using A 2A Adenosine Receptor Antagonists. Pharmaceuticals (Basel) 2020; 13:ph13090237. [PMID: 32911819 PMCID: PMC7558881 DOI: 10.3390/ph13090237] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022] Open
Abstract
The A2A adenosine receptor (A2AAR) plays critical roles in human physiology and pathophysiology, which makes it an important drug target. Previous drug-discovery efforts targeting the A2AAR have been focused on the use of A2AAR antagonists for the treatment of Parkinson's disease. More recently, the A2AAR has attracted additional attention for its roles in immuno-oncology, and a number of A2AAR antagonists are currently used as lead compounds for antitumor drugs in both preclinical models and clinical trials. This review surveys recent advances in the development of A2AAR antagonists for cancer immunotherapy. The therapeutic potential of representative A2AAR antagonists is discussed based on both animal efficacy studies and clinical data.
Collapse
Affiliation(s)
- Jinfeng Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (J.Z.); (W.Y.); (W.D.); (K.W.)
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenzhong Yan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (J.Z.); (W.Y.); (W.D.); (K.W.)
| | - Wenwen Duan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (J.Z.); (W.Y.); (W.D.); (K.W.)
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (J.Z.); (W.Y.); (W.D.); (K.W.)
- Department of Integrated Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; (J.Z.); (W.Y.); (W.D.); (K.W.)
- Correspondence: ; Tel.: +86-21-20685237
| |
Collapse
|
38
|
Yu F, Zhu C, Xie Q, Wang Y. Adenosine A 2A Receptor Antagonists for Cancer Immunotherapy. J Med Chem 2020; 63:12196-12212. [PMID: 32667814 DOI: 10.1021/acs.jmedchem.0c00237] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Currently, the most promising therapeutic modality for cancer treatment is the blockade of immune checkpoint pathways, which has revolutionized cancer therapy in the past 15 years. Strategies targeting and modulating adenosine A2A receptor (A2AR), an emerging alternative immune checkpoint, have shown the potential to produce significant therapeutic effects. In this review, we describe the immunosuppressive activities of A2AR and A2BR in the tumor microenvironment (TME), followed by a summary and discussion of the structure-activity relationship (SAR) of the A2AR (and dual A2AR/A2BR) antagonists that have been experimentally confirmed to exert oncoimmunological effects. This review also provides an update on the compounds under clinical evaluation and insights into the ligand binding modes of the receptor.
Collapse
Affiliation(s)
- Fazhi Yu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Chenyu Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Qiong Xie
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Yonghui Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| |
Collapse
|
39
|
Jespers W, Verdon G, Azuaje J, Majellaro M, Keränen H, García‐Mera X, Congreve M, Deflorian F, Graaf C, Zhukov A, Doré AS, Mason JS, Åqvist J, Cooke RM, Sotelo E, Gutiérrez‐de‐Terán H. X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A
2A
Adenosine Receptor Antagonists. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
| | - Grégory Verdon
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Jhonny Azuaje
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de Compostela Spain
| | - Maria Majellaro
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de Compostela Spain
| | - Henrik Keränen
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
- Present address: H. Lundbeck A/S Ottiliavej 9 2500 Valby Denmark
| | - Xerardo García‐Mera
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
| | - Miles Congreve
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | | | - Chris Graaf
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Andrei Zhukov
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Andrew S. Doré
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Jonathan S. Mason
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Johan Åqvist
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
| | - Robert M. Cooke
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Eddy Sotelo
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de Compostela Spain
| | - Hugo Gutiérrez‐de‐Terán
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
| |
Collapse
|
40
|
Deflorian F, Perez-Benito L, Lenselink EB, Congreve M, van Vlijmen HWT, Mason JS, Graaf CD, Tresadern G. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. J Chem Inf Model 2020; 60:5563-5579. [PMID: 32539374 DOI: 10.1021/acs.jcim.0c00449] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The computational prediction of relative binding free energies is a crucial goal for drug discovery, and G protein-coupled receptors (GPCRs) are arguably the most important drug target class. However, they present increased complexity to model compared to soluble globular proteins. Despite breakthroughs, experimental X-ray crystal and cryo-EM structures are challenging to attain, meaning computational models of the receptor and ligand binding mode are sometimes necessary. This leads to uncertainty in understanding ligand-protein binding induced changes such as, water positioning and displacement, side chain positioning, hydrogen bond networks, and the overall structure of the hydration shell around the ligand and protein. In other words, the very elements that define structure activity relationships (SARs) and are crucial for accurate binding free energy calculations are typically more uncertain for GPCRs. In this work we use free energy perturbation (FEP) to predict the relative binding free energies for ligands of two different GPCRs. We pinpoint the key aspects for success such as the important role of key water molecules, amino acid ionization states, and the benefit of equilibration with specific ligands. Initial calculations following typical FEP setup and execution protocols delivered no correlation with experiment, but we show how results are improved in a logical and systematic way. This approach gave, in the best cases, a coefficient of determination (R2) compared with experiment in the range of 0.6-0.9 and mean unsigned errors compared to experiment of 0.6-0.7 kcal/mol. We anticipate that our findings will be applicable to other difficult-to-model protein ligand data sets and be of wide interest for the community to continue improving FE binding energy predictions.
Collapse
Affiliation(s)
- Francesca Deflorian
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2300, RA, The Netherlands
| | - Miles Congreve
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Herman W T van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Jonathan S Mason
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG United Kingdom
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| |
Collapse
|
41
|
Huang CY, Meier N, Caffrey M, Wang M, Olieric V. 3D-printed holders for in meso in situ fixed-target serial X-ray crystallography. J Appl Crystallogr 2020; 53:854-859. [PMID: 32684901 PMCID: PMC7312129 DOI: 10.1107/s1600576720002897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/01/2020] [Indexed: 11/10/2022] Open
Abstract
The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information.
Collapse
Affiliation(s)
- Chia-Ying Huang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Nathalie Meier
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, Trinity Biomedical Sciences Institute, Trinity College, Dublin 2, D02 R590, Ireland
| | - Meitian Wang
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| | - Vincent Olieric
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen-PSI, 5232, Switzerland
| |
Collapse
|
42
|
Salmaso V, Jacobson KA. In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors. Biomolecules 2020; 10:E812. [PMID: 32466404 PMCID: PMC7356333 DOI: 10.3390/biom10060812] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022] Open
Abstract
Molecular modeling has contributed to drug discovery for purinergic GPCRs, including adenosine receptors (ARs) and P2Y receptors (P2YRs). Experimental structures and homology modeling have proven to be useful in understanding and predicting structure activity relationships (SAR) of agonists and antagonists. This review provides an excursus on molecular dynamics (MD) simulations applied to ARs and P2YRs. The binding modes of newly synthesized A1AR- and A3AR-selective nucleoside derivatives, potentially of use against depression and inflammation, respectively, have been predicted to recapitulate their SAR and the species dependence of A3AR affinity. P2Y12R and P2Y1R crystallographic structures, respectively, have provided a detailed understanding of the recognition of anti-inflammatory P2Y14R antagonists and a large group of allosteric and orthosteric antagonists of P2Y1R, an antithrombotic and neuroprotective target. MD of A2AAR (an anticancer and neuroprotective target), A3AR, and P2Y1R has identified microswitches that are putatively involved in receptor activation. The approach pathways of different ligands toward A2AAR and P2Y1R binding sites have also been explored. A1AR, A2AAR, and A3AR were utilizes to study allosteric phenomena, but locating the binding site of structurally diverse allosteric modulators, such as an A3AR enhancer LUF6000, is challenging. Ligand residence time, a predictor of in vivo efficacy, and the structural role of water were investigated through A2AAR MD simulations. Thus, new MD and other modeling algorithms have contributed to purinergic GPCR drug discovery.
Collapse
Affiliation(s)
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| |
Collapse
|
43
|
Burggraaff L, van Vlijmen HWT, IJzerman AP, van Westen GJP. Quantitative prediction of selectivity between the A 1 and A 2A adenosine receptors. J Cheminform 2020; 12:33. [PMID: 33431012 PMCID: PMC7222572 DOI: 10.1186/s13321-020-00438-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/04/2020] [Indexed: 11/10/2022] Open
Abstract
The development of drugs is often hampered due to off-target interactions leading to adverse effects. Therefore, computational methods to assess the selectivity of ligands are of high interest. Currently, selectivity is often deduced from bioactivity predictions of a ligand for multiple targets (individual machine learning models). Here we show that modeling selectivity directly, by using the affinity difference between two drug targets as output value, leads to more accurate selectivity predictions. We test multiple approaches on a dataset consisting of ligands for the A1 and A2A adenosine receptors (among others classification, regression, and we define different selectivity classes). Finally, we present a regression model that predicts selectivity between these two drug targets by directly training on the difference in bioactivity, modeling the selectivity-window. The quality of this model was good as shown by the performances for fivefold cross-validation: ROC A1AR-selective 0.88 ± 0.04 and ROC A2AAR-selective 0.80 ± 0.07. To increase the accuracy of this selectivity model even further, inactive compounds were identified and removed prior to selectivity prediction by a combination of statistical models and structure-based docking. As a result, selectivity between the A1 and A2A adenosine receptors was predicted effectively using the selectivity-window model. The approach presented here can be readily applied to other selectivity cases.
Collapse
Affiliation(s)
- Lindsey Burggraaff
- 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, 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.
| |
Collapse
|
44
|
Errey JC, Fiez-Vandal C. Production of membrane proteins in industry: The example of GPCRs. Protein Expr Purif 2020; 169:105569. [DOI: 10.1016/j.pep.2020.105569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 01/08/2023]
|
45
|
Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions. PLoS Comput Biol 2020; 16:e1007818. [PMID: 32298258 PMCID: PMC7188303 DOI: 10.1371/journal.pcbi.1007818] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/28/2020] [Accepted: 03/23/2020] [Indexed: 12/18/2022] Open
Abstract
The activation process of G protein-coupled receptors (GPCRs) has been extensively studied, both experimentally and computationally. In particular, Molecular Dynamics (MD) simulations have proven useful in exploring GPCR conformational space. The typical behaviour of class A GPCRs, when subjected to unbiased MD simulations from their crystallized inactive state, is to fluctuate between inactive and intermediate(s) conformations, even with bound agonist. Fully active conformation(s) are rarely stabilized unless a G protein is also bound. Despite several crystal structures of the adenosine A2a receptor (A2aR) having been resolved in complex with co-crystallized agonists and Gs protein, its agonist-mediated activation process is still not completely understood. In order to thoroughly examine the conformational landscape of A2aR activation, we performed unbiased microsecond-length MD simulations in quadruplicate, starting from the inactive conformation either in apo or with bound agonists: endogenous adenosine or synthetic NECA, embedded in two homogeneous phospholipid membranes: 1,2-dioleoyl-sn-glycerol-3-phosphoglycerol (DOPG) or 1,2-dioleoyl-sn-glycerol-3-phosphocholine (DOPC). In DOPC with bound adenosine or NECA, we observe transition to an intermediate receptor conformation consistent with the known adenosine-bound crystal state. In apo state in DOPG, two different intermediate conformations are obtained. One is similar to that observed with bound adenosine in DOPC, while the other is closer to the active state but not yet fully active. Exclusively, in DOPG with bound adenosine or NECA, we reproducibly identify receptor conformations with fully active features, which are able to dock Gs protein. These different receptor conformations can be attributed to the action/absence of agonist and phospholipid-mediated allosteric effects on the intracellular side of the receptor.
Collapse
|
46
|
Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures on Drug Discovery. Cell 2020; 181:81-91. [DOI: 10.1016/j.cell.2020.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
|
47
|
Abstract
The advent of the X-ray free electron laser (XFEL) in the last decade created the discipline of serial crystallography but also the challenge of how crystal samples are delivered to X-ray. Early sample delivery methods demonstrated the proof-of-concept for serial crystallography and XFEL but were beset with challenges of high sample consumption, jet clogging and low data collection efficiency. The potential of XFEL and serial crystallography as the next frontier of structural solution by X-ray for small and weakly diffracting crystals and provision of ultra-fast time-resolved structural data spawned a huge amount of scientific interest and innovation. To utilize the full potential of XFEL and broaden its applicability to a larger variety of biological samples, researchers are challenged to develop better sample delivery methods. Thus, sample delivery is one of the key areas of research and development in the serial crystallography scientific community. Sample delivery currently falls into three main systems: jet-based methods, fixed-target chips, and drop-on-demand. Huge strides have since been made in reducing sample consumption and improving data collection efficiency, thus enabling the use of XFEL for many biological systems to provide high-resolution, radiation damage-free structural data as well as time-resolved dynamics studies. This review summarizes the current main strategies in sample delivery and their respective pros and cons, as well as some future direction.
Collapse
|
48
|
Ishchenko A, Stauch B, Han GW, Batyuk A, Shiriaeva A, Li C, Zatsepin N, Weierstall U, Liu W, Nango E, Nakane T, Tanaka R, Tono K, Joti Y, Iwata S, Moraes I, Gati C, Cherezov V. Toward G protein-coupled receptor structure-based drug design using X-ray lasers. IUCRJ 2019; 6:1106-1119. [PMID: 31709066 PMCID: PMC6830214 DOI: 10.1107/s2052252519013137] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Rational structure-based drug design (SBDD) relies on the availability of a large number of co-crystal structures to map the ligand-binding pocket of the target protein and use this information for lead-compound optimization via an iterative process. While SBDD has proven successful for many drug-discovery projects, its application to G protein-coupled receptors (GPCRs) has been limited owing to extreme difficulties with their crystallization. Here, a method is presented for the rapid determination of multiple co-crystal structures for a target GPCR in complex with various ligands, taking advantage of the serial femtosecond crystallography approach, which obviates the need for large crystals and requires only submilligram quantities of purified protein. The method was applied to the human β2-adrenergic receptor, resulting in eight room-temperature co-crystal structures with six different ligands, including previously unreported structures with carvedilol and propranolol. The generality of the proposed method was tested with three other receptors. This approach has the potential to enable SBDD for GPCRs and other difficult-to-crystallize membrane proteins.
Collapse
Affiliation(s)
- Andrii Ishchenko
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Anna Shiriaeva
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Cornelius Gati
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vadim Cherezov
- Bridge Institute, Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
49
|
Al-Attraqchi OH, Attimarad M, Venugopala KN, Nair A, Al-Attraqchi NH. Adenosine A2A Receptor as a Potential Drug Target - Current Status and Future Perspectives. Curr Pharm Des 2019; 25:2716-2740. [DOI: 10.2174/1381612825666190716113444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022]
Abstract
Adenosine receptors (ARs) are a class of G-protein coupled receptors (GPCRs) that are activated by
the endogenous substance adenosine. ARs are classified into 4 subtype receptors, namely, the A1, A2A, A2B and A3
receptors. The wide distribution and expression of the ARs in various body tissues as well as the roles they have
in controlling different functions in the body make them potential drug targets for the treatment of various pathological
conditions, such as cardiac diseases, cancer, Parkinson’s disease, inflammation and glaucoma. Therefore,
in the past decades, there have been extensive investigations of ARs with a high number of agonists and antagonists
identified that can interact with these receptors. This review shall discuss the A2A receptor (A2AAR) subtype
of the ARs. The structure, properties and the recent advances in the therapeutic potential of the receptor are discussed
with an overview of the recent advances in the methods of studying the receptor. Also, molecular modeling
approaches utilized in the design of A2AAR ligands are highlighted with various recent examples.
Collapse
Affiliation(s)
- Omar H.A. Al-Attraqchi
- Faculty of Pharmacy, Philadelphia University-Jordan, P.O BOX (1), Philadelphia University-19392, Amman, Jordan
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Katharigatta N. Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Anroop Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | | |
Collapse
|
50
|
García-Nafría J, Tate CG. Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development. Annu Rev Pharmacol Toxicol 2019; 60:51-71. [PMID: 31348870 DOI: 10.1146/annurev-pharmtox-010919-023545] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein-coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR-G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR-G protein selectivity, how accessory membrane proteins alter receptor-ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.
Collapse
Affiliation(s)
- Javier García-Nafría
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; .,Current affiliation: Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopias Avanzadas, University of Zaragoza, 50018 Zaragoza, Spain;
| | | |
Collapse
|