Application of Oxime Diversification to Develop Multidentate Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Inhibitors by Optimizing Interactions with the Catalytic Pocket and the DNA and Protein Substrate Binding Sites

Authors

• G Cheng
• F Pratto
• K Brick
• M Huang
• G Lam
• RD Camerini-Otero

Abstract

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a phospholipase D (PLD) family member that can downregulate the anticancer effects of inhibitors of the type I topoisomerase (TOP1) by hydrolyzing the 3'-phosphodiester bond between DNA and the TOP1 catalytic residue Y723. This ester bond results in a stalled covalent intermediate, which is central to the mechanism of action of TOP1 inhibitors. Thus, TDP1 antagonists are being pursued by several laboratories as potency-enhancers of TOP1 inhibitors. However, the open and extended nature of the substrate-binding regions of TDP1 have made the development of inhibitors extremely challenging. In our current work, we have applied an oxime-based click protocol to the imidazopyridine platforms of our recently identified small molecule microarray (SMM)-derived TDP1 in order to extend them into the DNA and TOP1 peptide substrate-binding channels. By reacting the aminooxy-containing precursors with approximately 250 aldehydes in microtiter format, we screened a library of 500 oximes for their in vitro TDP1 inhibitory potencies in a florescence-based catalytic assay. Select hits identified by this process were further converted to their triazole- and ether-based isosteres. We obtained crystal structures of two of the resulting inhibitors bound to the TDP1 catalytic domain. In this way, we identified TDP1 inhibitors that bind in a tridentate fashion, with a central component situated within the catalytic pocket and extensions that project into both the DNA and TOP1 peptide substrate-binding regions. The trivalent nature of these interactions could serve as a basis for further development of multivalent inhibitors.

Scientific Focus Area: Chemical Biology

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