Organic Letters
Letter
certain probes since these enzymes synthesize heterotypic Ub
chains containing a mixture of linkages.53−55 Instead, we
wanted to measure the efficiency of labeling for future
structural studies aiming to identify cryptic Ub binding sites
that are important for chain assembly. With both UBE3C and
ARE1L, we detected the formation of a covalent adduct
between probes 11a, 11b, and 11d*, and the catalytic domains
of UBE3C and AREL1 only when the catalytic Cys is present
(Figures 4A,B and S8). In general, the labeling efficiency is
higher with UBE3C compared to AREL1 (Figure S9).
Interestingly, there does appear to be some selectivity. Probe
11c containing the warhead at position-6 and an isopeptide
bond at position-63 does not react with either UBE3C or
ARE1L even though it does label nonselective DUBs, e.g.,
USP7, to some extent (Figure S10). This observation may
reflect the linkage preferences of UBE3C and ARE1L
considering Lys6 and Lys63 are not produced by these
enzymes to a significant degree.53−55 These results demon-
strate that, in addition to DUBs, the branched probes can be
used to generate complexes with HECT ligases.
In conclusion, we report on the synthesis and reactivity of a
new set of Ub ABPs based on branched trimers. To generate
these probes, we devised an alternative synthetic approach to
the Michael acceptor linking one arm of the branched trimer to
the proximal subunit. The advances made include a facile
cross-metathesis reaction and photodeprotection of a ketal. We
found that like other Ub ABPs the branched probes readily
react with E3 ligases and DUBs containing active-site Cys
residues. These probes will be valuable tools for uncovering
cryptic Ub binding sites on E3s and DUBs that lead to linkage
selectivity in both chain assembly and disassembly.
REFERENCES
■
(1) Hershko, A.; Ciechanover, A. Annu. Rev. Biochem. 1998, 67,
425−479.
(2) Oh, E.; Akopian, D.; Rape, M. Annu. Rev. Cell Dev. Biol. 2018,
34, 137−162.
(3) Komander, D.; Rape, M. Annu. Rev. Biochem. 2012, 81 (1), 203−
229.
(4) Swatek, K. N.; Komander, D. Cell Res. 2016, 26 (4), 399−422.
(5) Yau, R.; Rape, M. Nat. Cell Biol. 2016, 18 (6), 579−586.
(6) Mevissen, T. E. T.; Komander, D. Annu. Rev. Biochem. 2017, 86
(1), 159−192.
(7) Clague, M. J.; Urbe, S.; Komander, D. Nat. Rev. Mol. Cell Biol.
2019, 20, 338−352.
́
(8) Clague, M. J.; Barsukov, I.; Coulson, J. M.; Liu, H.; Rigden, D. J.;
Urbe, S. Physiol. Rev. 2013, 93 (3), 1289−1315.
(9) Husnjak, K.; Dikic, I. Annu. Rev. Biochem. 2012, 81, 291−322.
(10) Hewings, D. S.; Flygare, J. A.; Bogyo, M.; Wertz, I. E. FEBS J.
2017, 284 (10), 1555−1576.
(11) Witting, K. F.; Mulder, M. P. C.; Ovaa, H. J. Mol. Biol. 2017,
429 (22), 3388−3394.
(12) Cravatt, B. F.; Wright, A. T.; Kozarich, J. W. Annu. Rev.
Biochem. 2008, 77 (1), 383−414.
(13) Sanman, L. E.; Bogyo, M. Annu. Rev. Biochem. 2014, 83 (1),
249−273.
(14) Hershko, A.; Rose, I. A. Proc. Natl. Acad. Sci. U. S. A. 1987, 84
(7), 1829−1833.
(15) Pickart, C. M.; Rose, I. A. J. Biol. Chem. 1986, 261 (22),
10210−10217.
(16) Borodovsky, A.; Kessler, B. M.; Casagrande, R.; Overkleeft, H.
S.; Wilkinson, K. D.; Ploegh, H. L. EMBO J. 2001, 20, 5187.
(17) Borodovsky, A.; Ovaa, H.; Kolli, N.; Gan-Erdene, T.;
Wilkinson, K. D.; Ploegh, H. L.; Kessler, B. M. Chem. Biol. 2002, 9
(10), 1149−1159.
(18) Mulder, M. P. C.; Witting, K.; Berlin, I.; Pruneda, J. N.; Wu, K.
P.; Chang, J. G.; Merkx, R.; Bialas, J.; Groettrup, M.; Vertegaal, A. C.
O.; et al. Nat. Chem. Biol. 2016, 12 (7), 523−530.
(19) Whedon, S. D.; Markandeya, N.; Rana, A. S. J. B.; Senger, N.
A.; Weller, C. E.; Turecek, F.; Strieter, E. R.; Chatterjee, C. J. Am.
Chem. Soc. 2016, 138 (42), 13774.
(20) Ekkebus, R.; Van Kasteren, S. I.; Kulathu, Y.; Scholten, A.;
Berlin, I.; Geurink, P. P.; De Jong, A.; Goerdayal, S.; Neefjes, J.; Heck,
A. J. R.; et al. J. Am. Chem. Soc. 2013, 135 (8), 2867−2870.
(21) Sommer, S.; Weikart, N. D.; Linne, U.; Mootz, H. D. Bioorg.
Med. Chem. 2013, 21 (9), 2511−2517.
(22) Love, K. R.; Catic, A.; Schlieker, C.; Ploegh, H. L. Nature
Chemical Biology; Nature Publishing Group, 2007; pp 697−705.
(23) Keusekotten, K.; Elliott, P. R.; Glockner, L.; Fiil, B. K.;
Damgaard, R. B.; Kulathu, Y.; Wauer, T.; Hospenthal, M. K.; Gyrd-
Hansen, M.; Krappmann, D.; et al. Cell 2013, 153, 1312−1326.
(24) Kwasna, D.; Rehman, S. A. A.; Natarajan, J.; Matthews, S.;
Madden, R.; De Cesare, V.; Weidlich, S.; Virdee, S.; Ahel, I.; Gibbs
Seymour, I.; et al. Mol. Cell 2018, 70, 150−164.
(25) Haahr, P.; Borgermann, N.; Guo, X.; Typas, D.; Achuthankutty,
D.; Hoffman, S.; Shearer, R.; Sixma, T.; Mailand, N. Mol. Cell 2018,
70, 165−174.
(26) Hewings, D. S.; Heideker, J.; Ma, T. P.; AhYoung, A. P.; El
Oualid, F.; Amore, A.; Costakes, G. T.; Kirchhofer, D.; Brasher, B.;
Pillow, T.; et al. Nat. Commun. 2018, 9 (1), 1162.
(27) Hermanns, T.; Pichlo, C.; Woiwode, I.; Klopffleisch, K.;
Witting, K. F.; Ovaa, H.; Baumann, U.; Hofmann, K. Nat. Commun.
2018, 9 (1), 799.
(28) Johnston, S. C.; Riddle, S. M.; Cohen, R. E.; Hill, C. P. EMBO
J. 1999, 18 (14), 3877−3887.
(29) Hu, M.; Li, P.; Li, M.; Li, W.; Yao, T.; Wu, J.-W.; Gu, W.;
Cohen, R. E.; Shi, Y. Cell 2002, 111, 1041.
(30) Misaghi, S.; Galardy, P. J.; Meester, W. J. N.; Ovaa, H.; Ploegh,
H. L.; Gaudet, R. J. Biol. Chem. 2005, 280 (2), 1512−1520.
(31) Boudreaux, D. A.; Maiti, T. K.; Davies, C. W.; Das, C. Proc.
Natl. Acad. Sci. U. S. A. 2010, 107 (20), 9117−9122.
ASSOCIATED CONTENT
■
S
* Supporting Information
̌
The Supporting Information is available free of charge on the
Synthetic protocols, protein expression information,
enzyme assays, and characterization of crucial inter-
AUTHOR INFORMATION
■
Corresponding Author
ORCID
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
This work was supported by a research grant from the National
Institutes of Health (RO1GM110543) and an NSF graduate
research fellowship to K.K.D. (GRFP1451512). Mass spectral
data were acquired at the University of Massachusetts Mass
Spectrometry core facility. The Orbitrap Fusion was funded by
NIH SIG S10OD010645. We thank Dr. Steve Eyles (UMass
Amherst) for assistance with mass spectrometry.
D
Org. Lett. XXXX, XXX, XXX−XXX