Abstract

CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases2 including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer3. These disease associations have motivated numerous preclinical studies and clinical trials4 (see http://www.clinicaltrials.gov) in search of therapies that target the CCR2–chemokine axis. To aid drug discovery efforts5, here we solve a structure of CCR2 in a ternary complex with an orthosteric (BMS-681 (ref. 6)) and allosteric (CCR2-RA-[R]7) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in class A G-protein-coupled receptors so far; this site spatially overlaps the G-protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G-protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive G-protein-coupled receptor structures solved so far. Like other protein–protein interactions, receptor–chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome obstacles in drug design.

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Acknowledgements

We thank A. Ishchenko and H. Zhang for help with X-ray data collection, C. Wang and H. X. Wu for suggestions on construct design, F. Li for help with data processing, and M. Galella for assistance with BMS compound data and statistics. We thank C. Ogata, R. Sanishvili, N. Venugopalan, M. Becker, and S. Corcoran at beamline 23ID at GM/CA CAT Advanced Photon Source. Funding for this research was provided by National Institutes of Health grants R01 GM071872, U54 GM094618, R01 AI118985, R21 AI121918, and R21 AI122211. GM/CA@APS has been funded in whole or in part with federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source, a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract number DE-AC02-06CH11357.

Author information

Affiliations

  1. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA

    • Yi Zheng
    • , Ling Qin
    • , Martin Gustavsson
    • , Chunxia Zhao
    • , Ruben Abagyan
    • , Irina Kufareva
    •  & Tracy M. Handel
  2. Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden 2333 CC, The Netherlands

    • Natalia V. Ortiz Zacarías
    • , Henk de Vries
    • , Adriaan P. IJzerman
    •  & Laura H. Heitman
  3. Bridge Institute, Departments of Chemistry and Physics & Astronomy, University of Southern California, Los Angeles, California 90089, USA

    • Gye Won Han
    •  & Vadim Cherezov
  4. Bristol-Myers Squibb Company, Princeton, New Jersey 08543, USA

    • Marta Dabros
    • , Robert J. Cherney
    • , Percy Carter
    •  & Andrew Tebben
  5. Vertex Pharmaceuticals Inc., 11010 Torreyana Road, San Diego, California 92121, USA

    • Dean Stamos
  6. The Bridge Institute, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California 90089, USA

    • Raymond C. Stevens

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Contributions

I.K. and T.M.H. designed the study and coordinated all experiments. Y.Z. designed and engineered protein constructs, performed crystallization experiments, collected the diffraction data, and determined the structure. L.Q., M.G., and C.Z. assisted with protein engineering and crystallization. G.W.H. assisted with structure determination and refinement. A.P.I. and L.H.H. designed, and N.V.O.Z. and H.d.V. performed, equilibrium and kinetics binding experiments. I.K. performed computational and bioinformatics analyses. R.J.C., P.C., and A.T. synthesized, characterized, and crystallized the BMS compound analogues. M.D. assisted with compound crystallization. D.S. assisted with the allosteric compound characterization. R.A. assisted with structure analysis. V.C. and R.C.S. assisted with crystallization. Y.Z., N.V.O.Z., A.P.I., L.H.H., I.K., and T.M.H. wrote the paper.

Competing interests

R.A. has an equity interest in Molsoft, LLC. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. R.C., P.C., and A.T. are employees of Bristol-Myers Squibb Company. D.S. is an employee of Vertex Pharmaceuticals, Inc.

Corresponding authors

Correspondence to Laura H. Heitman or Irina Kufareva or Tracy M. Handel.

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https://doi.org/10.1038/nature20605

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