CM11

Protein target name:

VHL

Mechanism of action:

DegraderPROTAC

Recommended Concentration for use in cells:

10-500 nM

Probe Availability

Tocris

MedChemExpress

Probe Information

Target and Probe Information

Target Details

Target class:

Other

Define other target class:

E3 ubiquitin ligase

Subclass:

E3 ubiquitin protein ligase

HUGO ID:

HGNC:12687

Entrez gene ID:

7428

UNIPROT ID:

P40337

Target alias:

HRCA1, RCA1, VHL1, pVHL

Probe Details

Chemical Probes Portal ID:

CPP1825

Probe alias:

PROTAC

PubChem CID:

134160242

SMILES string:

CC1=C(C2=CC=C(CNC([C@@H]3C[C@@]([H])(O)CN3C([C@H](C(C)(C)C)NC(COCCOCCOCCOCCOCCOCC(N[C@@H](C(C)(C)C)C(N4[C@H](C(NCC5=CC=C(C6=C(C)N=CS6)C=C5)=O)C[C@@]([H])(O)C4)=O)=O)=O)=O)=O)C=C2)SC=N1

InChi Key:

WGJCHHJGGFCCRS-DEYDLUNASA-N

Control compound:

CMP98 (cis-cis) - inactive epimer on each side CMP99 (cis-trans) - inactive epimer on one side, act as VHL inhibitor but not degrader

Physico-chemical properties

Solubility - preferred solvent:

DMSO

Solubility - concentration:

Up to 100 mM in DMSO. Up to 100 uM in aqueous buffer / cell media.

Potential reactivities:

unknown

NMR:

1H NMR (400 MHz, CDCl3): δ 8.61 (s, 2H), 7.41–7.38 (m, 2H), 7.29 (t, J = 7.6 Hz, 10H), 4.66–4.61 (m, 2H), 4.49–4.41 (m, 6H), 4.35–4.29
(m, 2H), 3.98–3.91 (m, 6H), 3.62–3.50 (m, 24H), 2.45 (s, 6H), 2.42–2.35 (m, 2H), 2.11–2.06 (m, 2H), 0.88 (s, 18H); 13C NMR (101 MHz, CDCl3): δ 171.2, 170.9, 170.4, 150.3, 148.5, 138.3, 131.6, 130.9, 129.5, 128.1, 71.2, 70.61, 70.59, 70.5, 70.4, 70.3, 58.6, 57.0, 43.2, 36.5, 35.6, 26.4, 16.1. HRMS (ESI) m/z: [M + H]+ calculated for: C58H82N8O14S2: 1178.54; observed: 1179.6015.

Storage Recommendations

Storage (dry powder):

-20o C freezer

Storage (solution):

4o C DMSO solution

Storage sensitivities:

not known

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

10 nM

Potency assay:

ITC

Off target activity

Probe Selectivity in Vitro:

Kinase off-target screening results. CM11 was screened at 1 μM concentration against a panel of 50 kinases (Dundee MRC-PPU Express Screen, http://www.kinase-screen.mrc.ac.uk/services/express- screen). The remaining kinase activity was recorded at the end of the assay. The data is reported as average % activity remaining of assay duplicates for each kinase tested (± standard deviation in brackets), ranked from highest to lowest. Plate Barcode CM11 D6769PM 1uM % activity (s.d.) RIPK2 130 (37) VEG-FR 126 (17) MKK1 126 (2) IGF-1R 118 (14) HER4 115 (11) CHK2 114 (3) MARK3 113 (3) SYK 113 (28) MLK3 112 (2) TAK1 112 (2) TBK1 112 (8) BTK 112 (5) MST2 111 (3) Lck 111 (2) HIPK2 111 (9) EF2K 110 (9) PDK1 109 (8) SmMLCK 109 (3) JAK3 108 (2) JNK1 108 (1) ROCK 2 108 (8) IRAK4 107 (5) CK1δ 107 (4) PIM1 107 (1) MSK1 106 (8) NEK6 106 (4) EPH-A2 105 (11) CAMK1 105 (5) PRK2 104 (7) LKB1 104 (5) PKD1 103 (10) p38a MAPK 102 (1) GSK3b 101 (2) DYRK1A 100 (4) AMPK (hum) 100 (11) CK2 100 (3) CAMKKb 99 (3) PKBa 97 (8) SRPK1 97 (12) PLK1 97 (4) S6K1 97 (7) RSK1 96 (6) Aurora B 96 (8) Src 95 (10) PKCa 95 (1) SGK1 95 (5) PKA 90 (5) PAK4 90 (10) TTK 89 (2) TrkA 89 (4)

In cell validation

On target activity in cells

Potency in cells:

DC50

10-100 nM

Potency assay (cells):

Western blot

Target engagement assay (cells):

Western Blot

Off target activity in cells

Potency assay, off target (cells):

To evaluate the specificity of homo-PROTAC-induced degradation, and identify potential off-targets, we performed isobaric tagging mass spectrometry proteomics to quantify degradation at the proteome level in an unbiased fashion. Amongst the 6,450 detected proteins that passed filtering criteria no proteins other than Cul2 was substantially depleted by homo-PROTACs CM09, CM10 or 6 compared to DMSO or VHL inhibitor treatment. Crucially, no effect on protein levels of other Cullins (Cul1, Cul3, Cul4A, Cul4B, Cul5 and Cul7) or CRL-associated subunits was observed. Together, the data demonstrate that CM11 mainly induce depletion of pVHL30 and Cul2 but not other proteins. The proteomics data further evidenced no increase in protein levels of HIF-1α with homo-PROTACs (but a small decrease with CM09) relative to DMSO (Supplementary Fig. 6). In contrast, treatment with 150 μM VH032 led to increased HIF-1α levels, as expected.

Primary Reference

Reference (doi):

10.1038/s41467-017-00954-1

Reference (PMID):

29018234

CM11

Probe Availability

Probe Information

Target Details

HRCA1, RCA1, VHL1, pVHL

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Primary Reference

Supporting Organizations

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CM11

Probe Availability

Probe Information

Target Details

HRCA1, RCA1, VHL1, pVHL

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?