HyTdb

Nutlin-3a-HT

HyT-058 | Adamantane | Published 2019.11.05

Basic Information

Nutlin-3a
Linker
Adamantane
POIMDM2 — E3 ubiquitin-protein ligase Mdm2(MDM2)
Degradation Pathway
Published2019.11.05

Remarks

Chemical Identifiers

SMILESO=C1N(CCCCCC(NCCCCCCOCCOCCNC(CC23C[C@H](C[C@@H]4C3)C[C@H](C4)C2)=O)=O)CCN(C(N5[C@H](C6=CC=C(Cl)C=C6)[C@H](C7=CC=C(Cl)C=C7)N=C5C8=CC=C(OC)C=C8OC(C)C)=O)C1
Molecular FormulaC58H78Cl2N6O8
InChIInChI=1S/C58H78Cl2N6O8/c1-40(2)74-50-34-48(71-3)20-21-49(50)56-63-54(44-12-16-46(59)17-13-44)55(45-14-18-47(60)19-15-45)66(56)57(70)65-26-25-64(53(69)39-65)24-9-6-7-11-51(67)61-22-8-4-5-10-27-72-29-30-73-28-23-62-52(68)38-58-35-41-31-42(36-58)33-43(32-41)37-58/h12-21,34,40-43,54-55H,4-11,22-33,35-39H2,1-3H3,(H,61,67)(H,62,68)/t41-,42+,43-,54-,55+,58?/m0/s1
InChI KeyLGZFPZYADHMYEZ-TWWRNFNOSA-N
IUPAC Name/
PubChem CID/

Basic Properties

TPSAComputing…
RingsComputing…
FSP3Computing…
Heavy Atom CountComputing…

Lipinski RO5

RO5 ViolationComputing…
MWComputing…
ClogPComputing…
HBDComputing…
HBAComputing…
RBComputing…

Hydrophobic Tag Properties

Tag Structure
Tag TypeAdamantane
Tag SMILESC1(CC2C3)CC(C2)CC3C1
Tag ClogP5.022
HydrophobicityHigh(ClopP>5)

Mechanism of Action

POI (Protein of Interest)

POI NameE3 ubiquitin-protein ligase Mdm2(MDM2)
GeneMDM2
UniProt IDQ00987

Amino Acid Sequence

MCNTNMSVPTDGAVTTSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSENRCHLEGGSDQKDLVQELQEEKPSSSHLVSRPSTSSRRRAISETEENSDELSGERQRKRHKSDSISLSFDESLALCVIREICCERSSSSESTGTPSNPDLDAGVSEHSGDWLDQDSVSDQFSVEFEVESLDSEDYSLSEEGQELSDEDDEVYQVTVYQAGESDTDSFEEDPEISLADYWKCTSCNEMNPPLPSHCNRCWALRENWLPEDKGKDKGEISEKAKLENSTQAEEGFDVPDCKKTIVNDSRESCVEENDDKITQASQSQESEDYSQPSTSSSIIYSSQEDVKEFEREETQDKEESVESSLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP

3D Structure (/structures/AF-Q00987-F1-model_v6.cif)

Loading /structures/AF-Q00987-F1-model_v6.cif …

Function

E3 ubiquitin-protein ligase that mediates ubiquitination of p53/TP53, leading to its degradation by the proteasome. Inhibits p53/TP53- and p73/TP73-mediated cell cycle arrest and apoptosis by binding its transcriptional activation domain. Also acts as a ubiquitin ligase E3 toward itself and ARRB1. Permits the nuclear export of p53/TP53. Promotes proteasome-dependent ubiquitin-independent degradation of retinoblastoma RB1 protein. Inhibits DAXX-mediated apoptosis by inducing its ubiquitination and degradation. Component of the TRIM28/KAP1-MDM2-p53/TP53 complex involved in stabilizing p53/TP53. Also a component of the TRIM28/KAP1-ERBB4-MDM2 complex which links growth factor and DNA damage response pathways. Mediates ubiquitination and subsequent proteasome degradation of DYRK2 in nucleus. Ubiquitinates IGF1R and SNAI1 and promotes them to proteasomal degradation. Ubiquitinates DCX, leading to DCX degradation and reduction of the dendritic spine density of olfactory bulb granule cells. Ubiquitinates DLG4, leading to proteasomal degradation of DLG4 which is required for AMPA receptor endocytosis. Negatively regulates NDUFS1, leading to decreased mitochondrial respiration, marked oxidative stress, and commitment to the mitochondrial pathway of apoptosis. Binds NDUFS1 leading to its cytosolic retention rather than mitochondrial localization resulting in decreased supercomplex assembly (interactions between complex I and complex III), decreased complex I activity, ROS production, and apoptosis.

Degradation Pathway

Activity Data

TypeIC50
Value2.83 ± 0.40μM
POI NameMDM2
Cell Line/
Cell Line ID/
Assay Methodfluorescence polarization based assay (FP)
Reference10.1039/c9cc07795b

Description

In a fluorescence polarization (FP)-based assay, Nutlin-3a-HT(2) displaced a fluorophore-labeled, p53-derived peptide from MDM2 with low micromolar activity (IC50 = 2.83 0.40 μM, Ki = 1.24 0.18 μM)19 (Fig. 3) .

TypeIC50
Value10.5±2.5 μM(48h),0.83±0.17 μM (120 h)
POI NameMDM2
Cell LineHCT-116
Cell Line IDCVCL_0291
Assay MethodWST-1 solution
Reference10.1039/c9cc07795b

Description

After 48 h ofexposure, 2 had an IC50 value of10.5±2.5 μM, whereas 1 only exhibited a 41% reduction of cell viability at 30 mM (Fig. S6, ESI†). After 120 h, 2 exhibited an IC50 value of 0.83±0.17 μM, which is 2.4-fold lower compared to 1 (IC50 =2.00±0.09 μM, Fig. 5C). (B and C) Cell viability assays of HCT-116 cells after (B) 24 h, and (C) 120 h exposure to 1, 2,and 7 (n = 3). Cell viability in the presence of DMSO control was defined as 100%. Mean values and standard deviations are shown. *p o 0.05, **p o 0.01, ***p o 0.001 (t-test, two-tailed, paired).

TypeKi
Value1.24±0.18 μM
POI NameMDM2
Cell Line/
Cell Line ID/
Assay Methodfluorescence polarization assay(FP)
Reference10.1039/c9cc07795b

Description

In a fluorescence polarization (FP)-based assay, Nutlin-3a-HT (2) displaced a fluorophore-labeled, p53-derived peptide from MDM2 with low micromolar activity (IC50 = 2.83 ± 0.40 μM, Ki = 1.24 ± 0.18 μM)

Disease Information

DiseaseICD-11Source
Colon carcinoma2B90.YCell Line Origin
Li-Fraumeni Syndrome2B51.YGene-Disease Association
Dedifferentiated LiposarcomaXH1C03Gene-Disease Association
Sarcoma2B5F.3Gene-Disease Association
Well-Differentiated LiposarcomaXH7Y61Gene-Disease Association
Glioma Susceptibility2A00.0ZGene-Disease Association
Neuroblastoma2D11.2Gene-Disease Association
Breast Cancer2C6ZGene-Disease Association