Abstract
Ubiquitination controls the stability of most cellular proteins, and its deregulation contributes to human diseases including cancer. Deubiquitinases remove ubiquitin from proteins, and their inhibition can induce the degradation of selected proteins, potentially including otherwise ‘undruggable’ targets. For example, the inhibition of ubiquitin-specific protease 7 (USP7) results in the degradation of the oncogenic E3 ligase MDM2, and leads to re-activation of the tumour suppressor p53 in various cancers. Here we report that two compounds, FT671 and FT827, inhibit USP7 with high affinity and specificity in vitro and within human cells. Co-crystal structures reveal that both compounds target a dynamic pocket near the catalytic centre of the auto-inhibited apo form of USP7, which differs from other USP deubiquitinases. Consistent with USP7 target engagement in cells, FT671 destabilizes USP7 substrates including MDM2, increases levels of p53, and results in the transcription of p53 target genes, induction of the tumour suppressor p21, and inhibition of tumour growth in mice.
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Acknowledgements
We thank the Diamond Light Source for access to beamlines I03 and I04. We thank S. M. Boyd for providing Extended Data Fig. 4, and S. Suhrawardy, V. Smith and Z. Yu for help with experiments. Work in the D.K. laboratory is supported by the Medical Research Council (U105192732), the European Research Council (309756), and the Lister Institute for Preventive Medicine. Work in the B.M.K. laboratory was supported by a John Fell Fund 133/075, the Wellcome Trust (097813/Z/11/Z) and the Engineering and Physical Sciences Research Council (EP/N034295/1). L.S. received a stipend from North West Cancer Research.
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This study was directed by T.R.H., S.K., S.I., C.J.D., K.W.B., J.A.E., S.B.M., T.M.R., M.S., S.U., M.J.C., B.M.K. and D.K. S.I. led the chemistry, supported by C.J.D. and K.W.B. Synthetic routes and approaches were devised and carried out by B.C.F., A.C.T. and A.J.B., with computational chemistry support by D.R.L., J.A.C., M.W., C.L.M. and A.V.T. USP7 biochemical assays were developed and performed by C.L.M., A.C.L.M., L.M.T., C.A and F.S. USP10 and USP47 assays were performed by C.L.M. A.P.-F. carried out compound specificity studies and quantitative mass spectrometry using methods established by T.M.C., H.C. and J.F.M. under the guidance of B.M.K. Biophysical studies were performed as follows; surface plasmon resonance: A.C.L.M. and L.M.T.; circular dichroism: L.M.T.; kinact/Ki: A.C.L.M. using methods established by F.S. A.P.T. and W.W.K. performed the structural studies and analysis with input from D.R.L., A.V.T., N.J.E., M.G. and D.K. M.S.P. and L.M.T. produced protein for all experiments with input from L.M.D.S. Biological studies were designed and performed by C.H. with the help of L.S. under the guidance of S.U. and M.J.C., or performed independently by C.G.M., E.C.T., S.M.B., J.L., E.W. and M.S. under the guidance of S.I. and S.K. V.V.Z. carried out antiproliferative assay in MM.1S cells. J.L. and E.W. designed and supervised in vivo animal studies performed at Pharmaron, China. D.K., B.M.K., A.P.T. and S.I. wrote the manuscript, and all authors commented on the text. Authors S.I., C.J.D., T.R.H., S.K., S.U., M.J.C., B.M.K. and D.K. are current steering committee members of the DUB Alliance.
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A.P.T., W.W.K., A.C.L.M., L.M.T., N.J.E., C.A., F.S., M.S.P., T.M.R., L.M.D.S., S.B.M. and T.R.H. are employees of CRUK Therapeutic Discovery Laboratories. S.I., E.C.T., S.M.B., D.R.L., J.A.C., A.V.T., J.L., E.W., B.C.F., V.V.Z., A.C.T., A.J.B., M.W., C.L.M., C.G.M., M.S., J.A.E., K.W.B., C.J.D. and S.K. are employees of FORMA Therapeutics. This work was performed by the DUB Alliance and funded by FORMA Therapeutics.
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Extended data figures and tables
Extended Data Figure 1 Compound characterization.
a, Schematic diagram of the USP7 constructs used in this study. b, Representative SPR sensorgrams of USP7CD and Akt Pleckstrin homology (PH) domain (negative control) to measure affinity parameters (Kd values) of FT671 and FT827. Compounds were tested in twofold dilutions from 50 μM FT827) or 1.56 μM (FT671). Sensorgrams are plotted showing two technical replicates. Data are representative of three biological replicates. Values in parentheses represent s.e.m. range. c, IC50 curves for FT671 against USP7C-term (open triangles) and USP7CD (filled squares) in the ubiquitin-rhodamine assay. The graph displays three biological replicates, each point representing the mean of three technical replicates. d, Time course of the inhibition of USP7C-term by the covalent inhibitor FT827 used to derive kobs values at each concentration (left). kobs plot for covalent inhibitor FT827 used to derive the kinetic parameters (right). 18 biological replicates were run individually, a representative biological replicate is shown.
Extended Data Figure 2 USP7 target engagement and specificity in MCF7 cells.
a, Schematic representation of DUB activity-based profiling of small-molecule inhibitors. Compounds were incubated with either intact MCF7 cells (in situ) or crude cell extracts, followed by labelling with the active site DUB probe HA–UbC2Br. DUBs, either targeted by compounds or labelled by the DUB probe, were visualized by western blotting or subjected to immunoprecipitation for enrichment and analysis by quantitative mass spectrometry7,23. b–e, FT671 and FT827 selectively target USP7 and disallow HA–UbC2Br binding, but do not notably interact with other DUBs as assessed by anti-HA immunoblotting. One out of two independent biological replicates is shown. b, MCF7 cell extracts incubated with FT671. c, Intact MCF7 cells incubated with FT671. d, MCF7 cell extracts incubated with FT827. e, Intact MCF7 cells incubated with FT827. f, Immunoprecipitation of cellular DUBs captured by HA–UbC2Br labelling for 10 min after incubation of MCF7 cell extracts with DMSO, 1 μM or 10 μM of FT671 or FT827, or 50 μM P22077 for 60 min. Immunoprecipitated material was separated by SDS–PAGE and analysed by western blotting using the indicated antibodies. g, FT671, FT827 and P22077 were incubated with MCF7 cell extracts at the indicated concentrations for 60 min, followed by labelling with HA–UbC2Br for either 5 min (left) or 60 min (right). Samples were separated by SDS–PAGE and analysed by western blotting using the indicated antibodies. Uncropped images for gels are shown in Supplementary Fig. 1.
Extended Data Figure 3 Electron density for FT827 and FT671.
a–c, Stereo representation of 2|Fo| − |Fc| electron density maps, contoured at 1σ, covering all atoms of the inhibitors in each of the two independent USP7 molecules of the asymmetric unit. Protein is shown as in Fig. 2a, and compound carbon atoms are in yellow. a, FT671; b, FT827; c, FT827, in an orientation to show the covalent linkage between inhibitor and Cys223.
Extended Data Figure 4 Schematic of FT671 and FT827 interactions with USP7.
a, b, Compound interactions and surrounding residues are labelled, hydrogen bonds indicated, and residues shown according to their chemical properties (see key). The images were generated with Molecular Operating Environment (MOE) (v.2013.08, Montreal, Canada). a, FT671; b, FT827.
Extended Data Figure 5 Molecular basis for USP7 compound specificity.
a, Superposition of the USP7–FT671 complex with indicated DUBs. Shown are the isolated cartoon structures that are shown superimposed in Fig. 3a, b. USP7 apo and USP7–FT671 (top left) show an identical switching loop position, whereas the corresponding region in other apo USP structures is in a distinct conformation that resembles the USP7~Ub complex (see Fig. 3a–c). Structures displayed: USP7 apo (purple, PDB code 1NB824); USP4 apo (PDB code 2Y6E40); yUBP6 apo (PDB code 1VJV); USP8 apo (PDB code 2GFO46); USP12 apo (PDB code 5K1647); USP14 apo (PDB code 2AYN48). b, Binding site detail, showing the interactions between palm subdomain Tyr residues (Tyr465 and Tyr514 in USP7) and the thumb subdomain and switching loop backbone present in all USP apo structures. The USP7 apo switching loop conformation disallows the Tyr465 interaction, which rotates away from the thumb subdomain, and allows Tyr514 to adopt a buried conformation (Tyr514 ‘down’ position). This generates space for compound binding. In other USP apo structures, the equivalent Tyr residues form hydrogen bonds with the thumb subdomain and occupy the compound binding site.
Extended Data Figure 6 Characterization of compound resistant USP7 mutants.
a–c, SPR-based binding of FT671 (a), FT827 (b) and ubiquitin (c) to indicated USP7 mutants. For compound binding to wild-type USP7CD and Akt-PH controls, see Extended Data Fig. 1b. Sensorgrams are plotted showing two technical replicates. Data are representative of three biological replicates. Values in parentheses represent s.e.m. range. d, Summary table of binding constants observed for experiments in a–c and Extended Data Fig. 1b. Biological repeats are indicated (n = 9 for USP7CD wild type, n = 3 for USP7CD mutants), and values in parentheses indicate s.e.m. e, Circular dichroism profiles of wild-type USP7CD (red), USP7CD(F291N) (orange), USP7CD(Q297A) (green), and USP7CD(Y465N) (blue); each experiment was performed in triplicate. f, Tabulated values for experiments shown in Fig. 3f. g, Structure of activated USP7. The switching loop in USP7 is a point of intrinsic allosteric regulation, provided by a C-terminal module of five ubiquitin-like domains (termed HUBL1 to HUBL5) followed by an activation peptide (amino acids 1084–1102)26 (see Extended Data Fig. 1a). In full-length USP7, the activation peptide stabilizes the active conformation of the switching loop in the ubiquitin-bound state26,27,28, and this can be modulated by USP7-activating proteins, such as GMPS26,29. Shown is the structure of activated USP7 bound to its C-terminal activation peptide. The model was generated from PDB code 5JTV27, and shown are the catalytic domain with ubiquitin in the S1 site (coloured as in Fig. 2a) of molecule 1 in the asymmetric unit and the HUBL5 domain and activation peptide (orange) of molecule 2 in the asymmetric unit, which in the crystal binds to molecule 1 in trans.
Extended Data Figure 7 USP7 knockdown or inhibitors affect USP7 substrates in cell lines.
a, HCT116 cells were transfected with non-targeting control (NT1) or three different USP7-targeting siRNAs for 72 h, harvested and probed with indicated antibodies. A representative experiment from two biological replicates is shown. b, U2OS cells were transfected with a pool of four independent siRNAs targeting USP7 or a non-targeting control siRNA and processed as in a. A representative experiment from two biological replicates is shown. c, HCT116 cells were treated with 10 μM FT671 for 24 h and RNA was extracted for qPCR measurements with primer sets against indicated transcripts (see Methods). Data were analysed with the ΔCt method. Experiments were performed in triplicate. d, HCT116 cells were treated with FT671 (10 μM) for longer periods, harvested and probed with indicated antibodies. A representative experiment from two biological replicates is shown. e, Experiment as in Fig. 4d, with higher FT671 concentration. p53 levels are upregulated upon FT671 treatment in cells expressing GFP or GFP-tagged wild-type USP7, but not in cells expressing compound resistant mutants. USP7 expression was induced for 7 h by 1 μg ml−1 doxycycline, and cells were treated with 3 μM FT671 for the last 4 h before lysis. f, IMR-32 neuroblastoma cells33 were treated with indicated concentrations of FT671, and effects on p53 and N-Myc levels were tested by western blotting. A representative experiment from two biological replicates is shown. g, h, HCT116 (g) or MM.1S (h) cells were treated for indicated times with FT671, and western blotted for UHRF1 and DNMT1. Vinculin and β-actin serve as loading controls. A representative experiment from two biological replicates is shown. Uncropped images for gels are shown in Supplementary Fig. 1.
Extended Data Figure 8 Characterization of FT671 effects in vivo.
a, MM.1S cells were treated for the indicated times with 10 μM FT671, and proteins detected by western blotting with indicated antibodies (see Methods). A representative experiment from two biological replicates is shown. b, Meso Scale analysis (see Methods) measuring the ratio of ubiquitinated versus non-ubiquitinated MDM2 in MM.1S cells upon FT671 treatment and proteasome inhibition (25 μM MG132). c, MM.1S cells were treated with 10 μM FT671 for the indicated times and RNA was extracted for qPCR measurements with primer sets against indicated transcripts (see Methods). Data were analysed with the ΔCt method. Experiments were performed in duplicate. d, qPCR analysis as in c, using a single time point against MCL1 and MYC, which in this setting are not p53 target genes after 24 h of 10 μM FT671. Experiments were performed in triplicate. e, MM.1S tumour xenograft tissues were analysed for p53 expression by western blotting and normalized to the β-actin loading control. Uncropped images for gels are shown in Supplementary Fig. 1.
Supplementary information
Supplementary Information
This file contains chemical synthesis of USP7 compounds. (PDF 630 kb)
Supplementary Figure 1
This file contains annotated full gel blots for all figures in the main manuscript. (PDF 5083 kb)
Supplementary Table 1
This file contains DUBs identified by mass spectrometry after HA-UbC2Br labelling of MCF7 cell extracts. (XLSX 178 kb)
Supplementary Table 2
This file contains all proteins identified by mass spectrometry after HA-UbC2Br labelling of MCF7 cell extracts. (XLSX 3099 kb)
Supplementary Table 3
This file contains the sequences for any RNAi/small RNA constructs used in this study. (XLSX 10 kb)
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Turnbull, A., Ioannidis, S., Krajewski, W. et al. Molecular basis of USP7 inhibition by selective small-molecule inhibitors. Nature 550, 481–486 (2017). https://doi.org/10.1038/nature24451
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DOI: https://doi.org/10.1038/nature24451
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