ИСТИНА

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a DNA repair enzyme and a promising target for anticancer treatment. It cleaves chemotherapy-induced stalled topoisomerase-DNA complexes, where a catalytic tyrosine is linked to the 3'-terminal phosphate, thus maintaining the DNA structure in cancer cells. There are several compounds known to suppress TDP1 activity, but their inhibitory mechanisms and specific interactions are still to be uncovered. We identified two binding cavities in the active site of the constructed molecular model of human TDP1: one for the phosphotyrosine and the second for the oligonucleotide moiety of the substrate. The binding site of the first (from the 3’-terminus) phosphate group of the substrate is located in the phosphotyrosine cavity and comprises residues Lys265, Asn283, Lys495, Asn516, as well as a conserved water molecule. The second phosphate group binds in the oligonucleotide cavity forming interaction with Ser400, Ser518, and two conserved water molecules. Virtual screening was performed to identify bifunctional inhibitors targeted toward both phosphate binding sites and able to form specific hydrogen bonds with the above-mentioned residues and water molecules. Since sulfo group is a structural analogue and isostere of the phosphate group, we retrieved sulfonates from the ZINC database (2227 compounds) and docked them into the TDP1 active site using the Lead Finder software. Docking poses were then filtered using an in-house script to identify compounds capable of forming specified interactions. Several potential TDP1 inhibitors containing two sulfo groups joined together via a linker (e.g. dimesna) were selected for experimental evaluation. The flexible linker allowed functional substituents to occupy both the phosphotyrosine and oligonucleotide cavities and form hydrogen-bonding networks with the phosphate binding sites.