• A Corrigendum to this article was published on 01 March 2010
  • A Corrigendum to this article was published on 01 April 2010

This article has been updated

Abstract

Deregulation of the phosphoinositide-3-OH kinase (PI(3)K) pathway has been implicated in numerous pathologies including cancer, diabetes, thrombosis, rheumatoid arthritis and asthma. Recently, small-molecule and ATP-competitive PI(3)K inhibitors with a wide range of selectivities have entered clinical development. In order to understand the mechanisms underlying the isoform selectivity of these inhibitors, we developed a new expression strategy that enabled us to determine to our knowledge the first crystal structure of the catalytic subunit of the class IA PI(3)K p110δ. Structures of this enzyme in complex with a broad panel of isoform- and pan-selective class I PI(3)K inhibitors reveal that selectivity toward p110δ can be achieved by exploiting its conformational flexibility and the sequence diversity of active site residues that do not contact ATP. We have used these observations to rationalize and synthesize highly selective inhibitors for p110δ with greatly improved potencies.

  • Compound C22H19N7O

    2-((6-Amino-9H-purin-9-yl)methyl)-5-methyl-3-o-tolylquinazolin-4(3H)-one

  • Compound C21H15ClN6O2S

    2-((9H-Purin-6-ylthio)methyl)-5-chloro-3-(2-methoxyphenyl)quinazolin-4(3H)-one

  • Compound C28H22FN7O2

    2-((4-Amino-3-(3-fluoro-5-hydroxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)methyl)-5-methyl-3-o-tolylquinazolin-4(3H)-one

  • Compound C28H22FN7O2

    2-((4-Amino-3-(3-fluoro-4-hydroxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)methyl)-5-methyl-3-o-tolylquinazolin-4(3H)-one

  • Compound C25H21N7O2

    2-((4-Amino-3-(3-hydroxyprop-1-ynyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl)methyl)-5-methyl-3-o-tolylquinazolin-4(3H)-one

  • Compound C29H28N10OS

    N-(6-(4-Amino-1-((2-(4-methylpiperazin-1-yl)quinolin-3-yl)methyl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl)benzo[d]thiazol-2-yl)acetamide

  • Compound C27H26N10S

    6-(4-Amino-1-((2-(4-methylpiperazin-1-yl)quinolin-3-yl)methyl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl)benzo[d]thiazol-2-amine

  • Compound C19H21F2N7O2

    4,4'-(6-(2-(Difluoromethyl)-1H-benzo[d]imidazol-1-yl)-1,3,5-triazine-2,4-diyl)dimorpholine

  • Compound C15H14N6

    1-Isopropyl-3-(pyridin-3-ylethynyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine

  • Compound C16H15N5O

    3-((4-Amino-1-isopropyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl)ethynyl)phenol

  • Compound C22H19FN4O4S

    N-(3-(3,5-Dimethoxyphenylamino)quinoxalin-2-yl)-4-fluorobenzenesulfonamide

  • Compound C23H27N7O3S2

    4-(2-(1H-Indazol-4-yl)-6-((4-(methylsulfonyl)piperazin-1-yl)methyl)thieno[3,2-d]pyrimidin-4-yl)morpholine

  • Compound C25H23N5O3S

    2-(3-(2-Methoxyphenyl)-4-oxo-3,4,5,6,7,8-hexahydroquinazolin-2-ylthio)-N-quinozalin-6-yl)acetamide

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Change history

  • 12 February 2010

    In the version of this article initially published, Pingda Ren was inadvertently left off the author list. The error has been corrected in the author list, author contributions and conflict of financial interest declaration of the HTML and PDF versions of the article.

  • 02 March 2010

    In the version of this article initially published, the structure of p110δ in complex with the inhibitor IC87114 was refined with an incorrect inhibitor structure (original Protein Data Bank accession code 2WXE). The structure has now been refined with the correct inhibitor structure and redeposited in the PDB with accession code 2X38. The structural image in Fig. 2a and the PDB accession code in the Methods section of the paper have been corrected in the HTML and PDF versions of the article.

Accessions

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Acknowledgements

We thank the beamline scientists and members of staff at the European Synchrotron Radiation Facility beamlines ID14-1, ID14-2, ID14-4, ID23-1, ID29 and BM30A (Grenoble, France), the Swiss Light Source beamline X06SA (Villigen, Switzerland) and the Diamond beamline I02 (Oxfordshire, UK). We are grateful to M. Allen for collecting the p110δ-ZSTK474 dataset and to O. Perisic for her help with the manuscript and for numerous contributions to this study. Part of this material is based on work supported under a US National Science Foundation Graduate Research Fellowship to O.W. and was supported by the Graduate Research and Education in Adaptive bio-Technology Training Program of the University of California Systemwide Biotechnology Research and Education Program, grant number 2008-005 to O.W. A.B. is supported by Merck-Serono, Geneva.

Author information

Affiliations

  1. Medical Research Council-Laboratory of Molecular Biology, Cambridge, UK.

    • Alex Berndt
    • , Simon Miller
    • , Joseph I Pacold
    • , Fabrice Gorrec
    • , Wai-Ching Hon
    •  & Roger L Williams
  2. Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA.

    • Olusegun Williams
    • , Daniel D Le
    • , Benjamin T Houseman
    •  & Kevan M Shokat
  3. Intellikine Inc., La Jolla, California, USA.

    • Pingda Ren
    • , Yi Liu
    •  & Christian Rommel
  4. Merck-Serono Research Center, Geneva, Switzerland.

    • Pascale Gaillard
    • , Thomas Rückle
    • , Matthias K Schwarz
    •  & Jeffrey P Shaw

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Contributions

A.B. expressed and purified the ΔABDp110δ construct, crystallized the first ΔABDp110δ-inhibitor complexes, collected datasets, determined and refined their structures and performed the kinase activity assay. S.M. helped in the purification, crystallization and structure determination and refinement of several ΔABDp110δ-inhibitor complexes. O.W., D.D.L. and B.T.H. synthesized and characterized the inhibitors SW13, SW14, SW30, DL06 and DL07 with input from K.M.S. and determined their IC50 values. J.I.P. performed the molecular dynamics and free energy perturbation experiments. F.G. devised and provided access to the Morpheus Screen and helped with the implementation of a microseeding protocol. W.-C.H. helped with the insect cell culture and crystal data collection. P.R., Y.L. and C.R. designed and characterized the inhibitors INK654 and INK666. P.G., T.R., M.K.S. and J.P.S. synthesized and characterized the inhibitors AS5 and AS15 and helped with large-scale insect cell expression. J.P.S. also provided valuable advice and support throughout the project. R.L.W. helped with the crystal data collection, the structure determination and refinement and the preparation of the movies. The manuscript was written by R.L.W. and A.B.

Competing interests

P.R., Y.L. and C.R. are employees of Intellikine Inc., which is involved in the discovery and development of therapeutics for the prevention and treatment of human diseases.

O.W. and K.M.S. are inventors on a University of California, San Francisco–owned patent application covering the SW series of compounds. This patent application is licensed to Intellikine Inc. K.M.S. is a consultant and stockholder of Intellikine Inc.

Corresponding author

Correspondence to Roger L Williams.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8, Supplementary Tables 1–3 and Supplementary Methods

Videos

  1. 1.

    Supplementary Movie 1

    Movie showing conformational changes that occur upon binding of PIK-39 to the apo- or ATP-bound form of p110γ (PDB entries 1e8y and 1e8x, respectively).

  2. 2.

    Supplementary Movie 2

    Movie morphing between the apo- and PIK-39-bound structures of p110δ.

  3. 3.

    Supplementary Movie 3

    The movie illustrates frames from a 20ns molecular dynamics simulation for the isolated p110γ catalytic domain, which is rendered as a cartoon with residues Met804 (right), Trp812 (middle) and Glu814 (left) shown in a stick representation.

  4. 4.

    Supplementary Movie 4

    Movie illustrating frames from a 20ns molecular dynamics simulation for the isolated p110δ catalytic domain, which is rendered as a cartoon with residues Met752 (right), Trp760 (middle) and Met762 (left) shown in a stick representation.

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DOI

https://doi.org/10.1038/nchembio.293

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