Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites

Journal Article · Thu Jan 28 00:00:00 EST 2021 · Chemical Science

DOI:https://doi.org/10.1039/d0sc05411a· OSTI ID:1781727

Zhao, Xue Zhi ^[1]; Kiselev, Evgeny ^[2]; Lountos, George T. ^[3]; Wang, Wenjie ^[2]; Tropea, Joseph E. ^[1]; Needle, Danielle ^[1]; Hilimire, Thomas A. ^[1]; Schneekloth, John S. ^[1]; Waugh, David S. ^[1]; Pommier, Yves ^[2]; Burke, Terrence R. ^[1]

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1. National Cancer Institute, Frederick, MD (United States)
2. National Cancer Institute, Bethesda, MD (United States)
3. Frederick National Lab. for Cancer Research, Frederick, MD (United States)

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3'- and 5'-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3'-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors.

• Research Organization: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
• Sponsoring Organization: Frederick National Laboratory for Cancer Research; National Cancer Institute (NCI); National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)
• Grant/Contract Number: W-31109-ENG-38
• OSTI ID: 1781727
• Journal Information: Chemical Science, Journal Name: Chemical Science Journal Issue: 11 Vol. 12; ISSN 2041-6520
• Publisher: Royal Society of Chemistry
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY