Abstract
The chemokine receptor CCR5 is an important anti-HIV (human immunodeficiency virus) drug target owning to its pivotal role in HIV-1 viral entry as a co-receptor. Here, we present a 2.9 Å resolution crystal structure of CCR5 bound to PF-232798, a second-generation oral CCR5 antagonist currently in phase II clinical trials. PF-232798 and the marketed HIV drug maraviroc share a similar tropane scaffold with different amino (N)- and carboxyl (C)- substituents. Comparison of the CCR5–PF-232798 structure with the previously determined structure of CCR5 in complex with maraviroc reveals different binding modes of the two allosteric antagonists and subsequent conformational changes of the receptor. Our results not only offer insights into the phenomenon that PF-232798 has higher affinity and alternative resistance profile to maraviroc, but also will facilitate the design of new anti-HIV drugs.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Centers for Disease Control. Update on acquired immune deficiency syndrome (AIDS)–United States. MMWR Morb Mortal Wkly Rep. 1982;31:507–8, 513-4.
Acquired immunodeficiency syndrome (AIDS). HIV infections, 1989. Wkly Epidemiol Rec. 1990;65:302–3.
Berger EA, Murphy PM, Farber JM. Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol. 1999;17:657–700.
Simmons G, Clapham PR, Picard L, Offord RE, Rosenkilde MM, Schwartz TW, et al. Potent inhibition of HIV-1 infectivity in macrophages and lymphocytes by a novel CCR5 antagonist. Science. 1997;276:276–9.
Murakami T, Nakajima T, Koyanagi Y, Tachibana K, Fujii N, Tamamura H, et al. A small molecule CXCR4 inhibitor that blocks T cell line-tropic HIV-1 infection. J Exp Med. 1997;186:1389–93.
Howard OM, Korte T, Tarasova I, Grimm M, Turpin JA, Rice WG, et al. Small molecule inhibitor of HIV-1 cell fusion blocks chemokine receptor-mediated function. J Leukoc Biol. 1998;64:6–13.
Temesgen Z, Warnke D, Kasten MJ. Current status of antiretroviral therapy. Expert Opin Pharmacother. 2006;7:1541–54.
Gottardo R, Bailer RT, Korber BT, Gnanakaran S, Phillips J, Shen XY, et al. Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial. PLoS ONE. 2013;8:e75665.
Palani A, Tagat JR. Discovery and development of small-molecule chemokine coreceptor CCR5 antagonists. J Med Chem. 2006;49:2851–7.
FDA notifications. Maraviroc approved as a CCR5 co-receptor antagonist. AIDS Alert. 2007;22:103.
Watson C, Jenkinson S, Kazmierski W, Kenakin T. The CCR5 receptor-based mechanism of action of 873140, a potent allosteric noncompetitive HIV entry inhibitor. Mol Pharmacol. 2005;67:1268–82.
Muniz-Medina VM, Jones S, Maglich JM, Galardi C, Hollingsworth RE, Kazmierski WM, et al. The relative activity of “function sparing” HIV-1 entry inhibitors on viral entry and CCR5 internalization: is allosteric functional selectivity a valuable therapeutic property? Mol Pharmacol. 2009;75:490–501.
Garcia-Perez J, Rueda P, Alcami J, Rognan D, Arenzana-Seisdedos F, Lagane B, et al. Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5). J Biol Chem. 2011;286:33409–21.
Stupple PA, Batchelor DV, Corless M, Dorr PK, Ellis D, Fenwick DR, et al. An imidazopiperidine series of CCR5 antagonists for the treatment of HIV: the discovery of N-{(1S)-1-(3-fluorophenyl)-3-[(3-endo)-3-(5-isobutyryl-2-methyl-4,5,6,7-tetrahydr o-1H-imidazo[4,5-c]pyridin-1-yl)-8-azabicyclo[3.2.1]oct-8-yl]propyl}acetamide (PF-232798). J Med Chem. 2011;54:67–77.
Tan QX, Zhu Y, Li J, Chen ZX, Han GW, Kufareva I, et al. Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science. 2013;341:1387–90.
Chun E, Thompson AA, Liu W, Roth CB, Griffith MT, Katritch V, et al. Fusion partner toolchest for the stabilization and crystallization of G protein-coupled receptors. Structure. 2012;20:967–76.
Juan A. Ballesteros HW. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. In: Sealfon SC, editor. Methods in Neurosciences; v 25. Receptor Molecular Biology. Amsterdam: Elsevier; 1995;366–428.
Caffrey M, Cherezov V. Crystallizing membrane proteins using lipidic mesophases. Nat Protoc. 2009;4:706–31.
Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–26.
Dauter Z, Wilson KS, Sieker LC, Moulis JM, Meyer J. Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein. Proc Natl Acad Sci USA. 1996;93:8836–40.
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr. 2007;40:658–74.
Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997;53:240–55.
Smart OS, Womack TO, Flensburg C, Keller P, Paciorek W, Sharff A, et al. Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER. Acta Crystallogr D Biol Crystallogr. 2012;68:368–80.
Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of coot. Acta Crystallogr D Biol Crystallogr. 2010;66:486–501.
Abrol R, Trzaskowski B, Goddard WA, Nesterov A, Olave I, Irons C. Ligand- and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor. Proc Natl Acad Sci USA. 2014;111:13040–5.
Hollenstein K, Kean J, Bortolato A, Cheng RK, Dore AS, Jazayeri A, et al. Structure of class B GPCR corticotropin-releasing factor receptor 1. Nature. 2013;499:438–43.
Kruse AC, Ring AM, Manglik A, Hu JX, Hu K, Eitel K, et al. Activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature. 2013;504:101–6.
Zheng Y, Qin L, Zacarias NV, de Vries H, Han GW, Gustavsson M, et al. Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists. Nature. 2016;540:458–61.
Oswald C, Rappas M, Kean J, Doré AS, Errey JC, Bennett K, et al. Intracellular allosteric antagonism of the CCR9 receptor. Nature. 2016;540:462–5.
Liu XY, Ahn SG, Kahsai AW, Meng KC, Latorraca NR, Pani B, et al. Mechanism of intracellular allosteric β2AR antagonist revealed by X-ray crystal structure. Nature. 2017;548:480–4.
Zhang HN, Qiao AN, Yang DH, Yang LL, Dai AT, de Graaf C, et al. Structure of the full-length glucagon class B G-protein-coupled receptor. Nature. 2017;546:259–64.
Jazayeri A, Dore AS, Lamb D, Krishnamurthy H, Southall SM, Baig AH, et al. Extra-helical binding site of a glucagon receptor antagonist. Nature. 2016;533:274–7.
Zhang DD, Gao ZG, Zhang KH, Kiselev E, Crane S, Wang J, et al. Two disparate ligand-binding sites in the human P2Y1 receptor. Nature. 2015;520:317–21.
Cheng RKY, Fiez-Vandal C, Schlenker O, Edman K, Aggeler B, Brown DG, et al. Structural insight into allosteric modulation of protease-activated receptor 2. Nature. 2017;545:112–5.
Acknowledgements
This research was supported by the National Natural Science Foundation of China (No. 31730027). We are grateful to the staff of 23ID-D beamline (GM/CA CAT) of the Advanced Photon Source for support during data collection.
Author contributions
YZ performed the CPM assay, protein purification and crystallization. YZ and Y-LZ analyzed the data and wrote the manuscript. JL synthesized the compounds. HL oversaw compound synthesis. QZ collected the diffraction data and solved the structure. B-LW and Z-LY designed the research and revised the manuscript.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Additional information
Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Zhu, Y., Zhao, Yl., Li, J. et al. Molecular binding mode of PF-232798, a clinical anti-HIV candidate, at chemokine receptor CCR5. Acta Pharmacol Sin 40, 563–568 (2019). https://doi.org/10.1038/s41401-018-0054-2
Received:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41401-018-0054-2
