Home LiteratureArticle Details
PMID: 23517028 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Biophysical fragment screening of the β1-adrenergic receptor: identification of high affinity arylpiperazine leads using structure-based drug design.

Journal of medicinal chemistry ·Vol. 56 ·No. 9 ·2013-05-09 ·Pages 3446-55

Christopher JA, Brown J, Doré AS, Errey JC, Koglin M, Marshall FH, Myszka DG, Rich RL, Tate CG, Tehan B, Warne T, Congreve M

Abstract

Biophysical fragment screening of a thermostabilized β1-adrenergic receptor (β1AR) using surface plasmon resonance (SPR) enabled the identification of moderate affinity, high ligand efficiency (LE) arylpiperazine hits 7 and 8. Subsequent hit to lead follow-up confirmed the activity of the chemotype, and a structure-based design approach using protein-ligand crystal structures of the β1AR resulted in the identification of several fragments that bound with higher affinity, including indole 19 and quinoline 20. In the first example of GPCR crystallography with ligands derived from fragment screening, structures of the stabilized β1AR complexed with 19 and 20 were determined at resolutions of 2.8 and 2.7 Å, respectively.

MeSH Terms
Biophysical Phenomena Drug Design Drug Evaluation, Preclinical HEK293 Cells Humans Molecular Docking Simulation Piperazine Piperazines/chemistry,metabolism Protein Binding Protein Conformation Receptors, Adrenergic, beta-1/chemistry,metabolism Surface Plasmon Resonance
Chemicals
Piperazines Receptors, Adrenergic, beta-1 Piperazine
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Christopher John A
Heptares Therapeutics Ltd. , BioPark, Welwyn Garden City, Hertfordshire, AL7 3AX, U.K. john.christopher@heptares.com
Brown Jason
Doré Andrew S
Errey James C
Koglin Markus
Marshall Fiona H
Myszka David G
Rich Rebecca L
Tate Christopher G
Tehan Benjamin
Warne Tony
Congreve Miles
References (70)
70 references, click to expand
  1. Biacore analysis with stabilized G-protein-coupled receptors.
    Anal Biochem. 2011 Feb 15;409(2):267-72 PMID: 20969829
  2. Structure-based discovery of A2A adenosine receptor ligands.
    J Med Chem. 2010 May 13;53(9):3748-55 PMID: 20405927
  3. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist.
    Science. 2008 Nov 21;322(5905):1211-7 PMID: 18832607
  4. Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity.
    Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3041-6 PMID: 18287029
  5. Development and crystallization of a minimal thermostabilised G protein-coupled receptor.
    Protein Expr Purif. 2009 Jun;65(2):204-13 PMID: 19297694
  6. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance.
    J Chem Inf Comput Sci. 2004 Sep-Oct;44(5):1708-18 PMID: 15446830
  7. Thermostabilization of the neurotensin receptor NTS1.
    J Mol Biol. 2009 Jul 10;390(2):262-77 PMID: 19422831
  8. Lurasidone (SM-13496), a novel atypical antipsychotic drug, reverses MK-801-induced impairment of learning and memory in the rat passive-avoidance test.
    Eur J Pharmacol. 2007 Oct 31;572(2-3):160-70 PMID: 17662268
  9. The importance of interactions with helix 5 in determining the efficacy of β-adrenoceptor ligands.
    Biochem Soc Trans. 2013 Feb 1;41(1):159-65 PMID: 23356277
  10. Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor.
    J Med Chem. 2011 Dec 8;54(23):8195-206 PMID: 22007643
  11. Structure of the human histamine H1 receptor complex with doxepin.
    Nature. 2011 Jun 22;475(7354):65-70 PMID: 21697825
  12. Structure of the human κ-opioid receptor in complex with JDTic.
    Nature. 2012 Mar 21;485(7398):327-32 PMID: 22437504
  13. Conserved binding mode of human beta2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography.
    J Am Chem Soc. 2010 Aug 25;132(33):11443-5 PMID: 20669948
  14. Structure-based discovery of beta2-adrenergic receptor ligands.
    Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6843-8 PMID: 19342484
  15. Crystal structures of a stabilized β1-adrenoceptor bound to the biased agonists bucindolol and carvedilol.
    Structure. 2012 May 9;20(5):841-9 PMID: 22579251
  16. REFMAC5 for the refinement of macromolecular crystal structures.
    Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67 PMID: 21460454
  17. Scaling and assessment of data quality.
    Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82 PMID: 16369096
  18. Structure of an agonist-bound human A2A adenosine receptor.
    Science. 2011 Apr 15;332(6027):322-7 PMID: 21393508
  19. Ligand discovery from a dopamine D3 receptor homology model and crystal structure.
    Nat Chem Biol. 2011 Sep 18;7(11):769-78 PMID: 21926995
  20. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.
    Science. 2010 Nov 19;330(6007):1066-71 PMID: 20929726
  21. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.
    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83 PMID: 17452350
  22. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor.
    Nature. 2007 Nov 15;450(7168):383-7 PMID: 17952055
  23. Emerging concepts and therapeutic implications of beta-adrenergic receptor subtype signaling.
    Pharmacol Ther. 2005 Dec;108(3):257-68 PMID: 15979723
  24. Crystal structure of the µ-opioid receptor bound to a morphinan antagonist.
    Nature. 2012 Mar 21;485(7398):321-6 PMID: 22437502
  25. Expression and purification of truncated, non-glycosylated turkey beta-adrenergic receptors for crystallization.
    Biochim Biophys Acta. 2003 Feb 17;1610(1):133-40 PMID: 12586387
  26. Recent progress in fragment-based lead discovery.
    Curr Opin Pharmacol. 2009 Oct;9(5):615-21 PMID: 19477685
  27. Structure of the δ-opioid receptor bound to naltrindole.
    Nature. 2012 May 16;485(7398):400-4 PMID: 22596164
  28. Interactions of the novel antipsychotic aripiprazole (OPC-14597) with dopamine and serotonin receptor subtypes.
    Neuropsychopharmacology. 1999 Jun;20(6):612-27 PMID: 10327430
  29. Engineering G protein-coupled receptors to facilitate their structure determination.
    Curr Opin Struct Biol. 2009 Aug;19(4):386-95 PMID: 19682887
  30. Two distinct conformations of helix 6 observed in antagonist-bound structures of a beta1-adrenergic receptor.
    Proc Natl Acad Sci U S A. 2011 May 17;108(20):8228-32 PMID: 21540331
  31. Crystal structure of rhodopsin: A G protein-coupled receptor.
    Science. 2000 Aug 4;289(5480):739-45 PMID: 10926528
  32. Structure and dynamics of the M3 muscarinic acetylcholine receptor.
    Nature. 2012 Feb 22;482(7386):552-6 PMID: 22358844
  33. From fragment to clinical candidate--a historical perspective.
    Drug Discov Today. 2009 Jul;14(13-14):668-75 PMID: 19427404
  34. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor.
    Science. 2007 Nov 23;318(5854):1258-65 PMID: 17962520
  35. The structural basis for agonist and partial agonist action on a β(1)-adrenergic receptor.
    Nature. 2011 Jan 13;469(7329):241-4 PMID: 21228877
  36. The selectivity of beta-adrenoceptor antagonists at the human beta1, beta2 and beta3 adrenoceptors.
    Br J Pharmacol. 2005 Feb;144(3):317-22 PMID: 15655528
  37. Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist.
    Science. 2010 Nov 19;330(6007):1091-5 PMID: 21097933
  38. Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic.
    Nature. 2012 May 16;485(7398):395-9 PMID: 22596163
  39. Conformational thermostabilization of the beta1-adrenergic receptor in a detergent-resistant form.
    Proc Natl Acad Sci U S A. 2008 Jan 22;105(3):877-82 PMID: 18192400
  40. Fragment screening of stabilized G-protein-coupled receptors using biophysical methods.
    Methods Enzymol. 2011;493:115-36 PMID: 21371589
  41. Structure of a nanobody-stabilized active state of the β(2) adrenoceptor.
    Nature. 2011 Jan 13;469(7329):175-80 PMID: 21228869
  42. An integrated approach to fragment-based lead generation: philosophy, strategy and case studies from AstraZeneca's drug discovery programmes.
    Curr Top Med Chem. 2007;7(16):1600-29 PMID: 17979771
  43. Crystal structure of a lipid G protein-coupled receptor.
    Science. 2012 Feb 17;335(6070):851-5 PMID: 22344443
  44. Structure of the agonist-bound neurotensin receptor.
    Nature. 2012 Oct 25;490(7421):508-13 PMID: 23051748
  45. The properties of thermostabilised G protein-coupled receptors (StaRs) and their use in drug discovery.
    Neuropharmacology. 2011 Jan;60(1):36-44 PMID: 20624408
  46. Progress in structure based drug design for G protein-coupled receptors.
    J Med Chem. 2011 Jul 14;54(13):4283-311 PMID: 21615150
  47. New β₂-adrenoceptor agonists for the treatment of chronic obstructive pulmonary disease.
    Drugs Today (Barc). 2010 Dec;46(12):911-8 PMID: 21589948
  48. Features and development of Coot.
    Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501 PMID: 20383002
  49. High-throughput virtual screening of proteins using GRID molecular interaction fields.
    J Chem Inf Model. 2010 Jan;50(1):155-69 PMID: 19919042
  50. Vemurafenib: the first drug approved for BRAF-mutant cancer.
    Nat Rev Drug Discov. 2012 Nov;11(11):873-86 PMID: 23060265
  51. Discovery of new GPCR biology: one receptor structure at a time.
    Structure. 2009 Jan 14;17(1):8-14 PMID: 19141277
  52. The integration of macromolecular diffraction data.
    Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):48-57 PMID: 16369093
  53. Structure-based drug screening for G-protein-coupled receptors.
    Trends Pharmacol Sci. 2012 May;33(5):268-72 PMID: 22503476
  54. A crystal clear solution for determining G-protein-coupled receptor structures.
    Trends Biochem Sci. 2012 Sep;37(9):343-52 PMID: 22784935
  55. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules.
    J Med Chem. 1985 Jul;28(7):849-57 PMID: 3892003
  56. New insights from structural biology into the druggability of G protein-coupled receptors.
    Trends Pharmacol Sci. 2012 May;33(5):249-60 PMID: 22465153
  57. Structure of a beta1-adrenergic G-protein-coupled receptor.
    Nature. 2008 Jul 24;454(7203):486-91 PMID: 18594507
  58. Ligand efficiency: a useful metric for lead selection.
    Drug Discov Today. 2004 May 15;9(10):430-1 PMID: 15109945
  59. Recent developments in fragment-based drug discovery.
    J Med Chem. 2008 Jul 10;51(13):3661-80 PMID: 18457385
  60. Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction.
    Biochem Pharmacol. 1973 Dec 1;22(23):3099-108 PMID: 4202581
  61. The significance of G protein-coupled receptor crystallography for drug discovery.
    Pharmacol Rev. 2011 Dec;63(4):901-37 PMID: 21969326
  62. Long-acting beta(2)-agonists in the management of asthma exacerbations.
    Curr Opin Pulm Med. 2005 Jan;11(1):69-73 PMID: 15591891
  63. High-resolution crystal structure of human protease-activated receptor 1.
    Nature. 2012 Dec 20;492(7429):387-92 PMID: 23222541
  64. Introduction to fragment-based drug discovery.
    Top Curr Chem. 2012;317:1-32 PMID: 21695633
  65. Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist.
    Nature. 2012 Jan 25;482(7386):547-51 PMID: 22278061
  66. Phaser crystallographic software.
    J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674 PMID: 19461840
  67. Co-evolving stability and conformational homogeneity of the human adenosine A2a receptor.
    Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10744-9 PMID: 18664584
  68. Ligand-directed signalling at beta-adrenoceptors.
    Br J Pharmacol. 2010 Mar;159(5):1022-38 PMID: 20132209
  69. Structural diversity of G protein-coupled receptors and significance for drug discovery.
    Nat Rev Drug Discov. 2008 Apr;7(4):339-57 PMID: 18382464
  70. The influence of drug-like concepts on decision-making in medicinal chemistry.
    Nat Rev Drug Discov. 2007 Nov;6(11):881-90 PMID: 17971784
Article Info
Journal
Journal of medicinal chemistry
Abbr.
J Med Chem
ISSN
1520-4804
Published
2013-05-09
Epub
2013-00-09
Pages
3446-55
Language
English
Region
United States
NLM ID
9716531
PMCID
PMC3654563
Subset
IM
Grants
Medical Research Council · MC_U105197215 · United Kingdom
Biotechnology and Biological Sciences Research Council · BB/G003653/1 · United Kingdom
Medical Research Council · U105197215 · United Kingdom
Databases
PDB
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com