Novel Semisynthetic Derivatives of Bile Acids as Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibitors

Abstract

An Important task in the treatment of oncological and neurodegenerative diseases is the search for new inhibitors of DNA repair system enzymes. Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is one of the DNA repair system enzymes involved in the removal of DNA damages caused by topoisomerase I inhibitors. Thus, reducing the activity of Tdp1 can increase the effectiveness of currently used anticancer drugs. We describe here a new class of semisynthetic small molecule Tdp1 inhibitors based on the bile acid scaffold that were originally identified by virtual screening. The influence of functional groups of bile acids (hydroxy and acetoxy groups in the steroid framework and amide fragment in the side chain) on inhibitory activity was investigated. In vitro studies demonstrate the ability of the semisynthetic derivatives to effectively inhibit Tdp1 with IC₅₀ up to 0.29 µM. Furthermore, an excellent fit is realized for the ligands when docked into the active site of the Tdp1 enzyme.

Keywords: Tdp1 inhibitor; amide; cancer; chenodeoxycholic acid; deoxycholic acid; molecular modelling; tumor; ursodeoxycholic acid; virtual screening.

Figure 1

Structures of reported Tdp1 inhibitors.

Scheme 1

Synthesis of compound 1a,b, 2a,b and 3a,b that combine the residues of bile acids and tryptamine: reagent and conditions: (a) Ac₂O, DMAP, CH₂Cl₂ (RT); (b) (COCl)₂, DMF, CH₂Cl₂ (0 °C); (c) tryptamine, NEt₃, CH₂Cl₂ (0 °C, RT); (d) KOH, MeOH (reflux); (e) KOH, MeOH (RT); (f) Ac₂O, AcOH.

Scheme 2

Synthesis of deoxycholic acid amides 4a,b–8a,b and 9a–11a: (a) (COCl)₂, DMF, CH₂Cl₂ (0 °C); (b) tryptamine, NEt₃, CH₂Cl₂ (0 °C, RT); (c) KOH, MeOH (reflux).

Figure 2

The docked configuration of 9a to the binding site of Tdp1 using the ChemPLP scoring function. (A) Hydrogen bond is depicted as a green line between the ligand and the amino acid TYR204. (B) The protein surface is rendered. The steroid group is inserted in a lipophilic pocket and the acyl groups are exposed to the water environment. Red depicts a positive partial charge on the surface, blue depicts a negative partial charge and grey shows the neutral/lipophilic areas.