azacitidine   Click here for help

GtoPdb Ligand ID: 6796

Synonyms: 5-AZAC | 5-azacytidine | ladakamycin | Onureg® | Onureg® (CC-486; oral azacitidine) | U-18496 | Vidaza®
Approved drug PDB Ligand Immunopharmacology Ligand
azacitidine is an approved drug (FDA (2004), EMA (2009))
Compound class: Synthetic organic
Comment: DNA methyltransferase and RNA inhibitor. Azacitidine inhibits DNA methylation in vitro [3], but not by directly interacting with the methyltransferase enzyme DNMT1.

azacitidine is commercially available from our sponsors

2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 8
Hydrogen bond donors 4
Rotatable bonds 2
Topological polar surface area 143.72
Molecular weight 244.08
XLogP -1.81
No. Lipinski's rules broken 0

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES OCC1OC(C(C1O)O)n1cnc(nc1=O)N
Isomeric SMILES OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1cnc(nc1=O)N
InChI InChI=1S/C8H12N4O5/c9-7-10-2-12(8(16)11-7)6-5(15)4(14)3(1-13)17-6/h2-6,13-15H,1H2,(H2,9,11,16)/t3-,4-,5-,6-/m1/s1
InChI Key NMUSYJAQQFHJEW-KVTDHHQDSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
No information available.
Summary of Clinical Use Click here for help
Antineoplastic agent used in the treatment of myelodysplastic syndrome.
entinostat (an HDAC inhibitor, which has an epigenetic priming effect [2]) is being evaluated in a Phase 2 clinical trial alongside azacitidine prior to check-point immunotherapy with nivolumab in patients with recurrent metastatic non-small cell lung cancer- see NCT01928576. Onureg® was approved by the EMA in 2021, for the treatment of AML.
Mechanism Of Action and Pharmacodynamic Effects Click here for help
A pyrimidine nucleoside analogue that inhibits DNA methyltransferase, impairing DNA methylation. Azacitidine does not directly interact with DNMT1 to cause inhibition. The metabolic product 5-aza-2'-deoxycytidine-triphosphate is a substrate for DNA replication and becomes incorporated into the DNA substituting for cytosine, which is then recognised by the DMT enzyme. But, the presence of the azacitidine blocks resolution of the covalent bond formed between the nucleotide and the enzyme, and compromises the DNA methylation function of DNMT1. This also triggers DNA damage signalling, promoting degradation of the trapped enzyme, thereby further reducing methylation capacity. This process results in a drastic reduction of epigenetic methylation marks during DNA replication [4]. Other data suggests that decitabine (and, presumably azacitidine also) causes the formation of double strand breaks in the DNA of human cancer cell lines and that DNMT1 might play a role in mediating the cellular damage response to the drug. The induction of direct DNA damage by these drugs, combined with the role of DNMT1 in DNA repair indicates that drug-induced demethylation patterns might be influenced by DNA repair mechanisms [1].