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J Med Chem. 2019 Sep 12;62(17):7669-7683. doi: 10.1021/acs.jmedchem.9b00112. Epub 2019 Sep 3.

Selective, Small-Molecule Co-Factor Binding Site Inhibition of a Su(var)3-9, Enhancer of Zeste, Trithorax Domain Containing Lysine Methyltransferase.

Author information

1
Pfizer Medicine Design, Medicinal Chemistry , Pfizer Worldwide Research and Development , Eastern Point Road , Groton , Connecticut 06340 , United States.
2
Pfizer Medicine Design, Medicinal Chemistry , Pfizer Worldwide Research and Development , San Diego , California 92121 , United States.
3
Pfizer Medicine Design, Medicinal Chemistry , Pfizer Worldwide Research and Development , 1 Portland Street , Cambridge , Massachusetts 02139 , United States.
4
Department of Pharmacology and Toxicology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.

Abstract

The first chemical probe to primarily occupy the co-factor binding site of a Su(var)3-9, enhancer of a zeste, trithorax (SET) domain containing protein lysine methyltransferase (PKMT) is reported. Protein methyltransferases require S-adenosylmethionine (SAM) as a co-factor (methyl donor) for enzymatic activity. However, SAM itself represents a poor medicinal chemistry starting point for a selective, cell-active inhibitor given its extreme physicochemical properties and its role in multiple cellular processes. A previously untested medicinal chemistry strategy of deliberate file enrichment around molecules bearing the hallmarks of SAM, but with improved lead-like properties from the outset, yielded viable hits against SET and MYND domain-containing protein 2 (SMYD2) that were shown to bind in the co-factor site. These leads were optimized to identify a highly biochemically potent, PKMT-selective, and cell-active chemical probe. While substrate-based inhibitors of PKMTs are known, this represents a novel, co-factor-derived strategy for the inhibition of SMYD2 which may also prove applicable to lysine methyltransferase family members previously thought of as intractable.

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