3‐substituted‐1H‐indazoles as Catalytic Inhibitors of the Human DNA Topoisomerase IIα

Abstract

Catalytic inhibitors represent an attractive possibility of revisiting the established anticancer target human DNA topoisomerase IIa, taking advantage of the many different inhibition steps in its catalytic cycle. In this study we present our efforts to expand the chemical space of inhibitors of the human DNA topoisomerase IIa with a combination of in silico and in vitro methods. Using our previously reported compounds as a base, we constructed a ligand-based pharmacophore and conducted a virtual screening campaign. This led to the discovery of 1Hindazole inhibitors for which the SAR data was subsequently expanded. Additionally, several in vitro methods; cleavage assay, competitive cleavage assay, ATPase assay and microscale thermophoresis (MST) binding studies were employed to study the inhibitory mechanism, and it was confirmed that our compounds are catalytic inhibitors that bind to the ATPase domain. IC 50 values were in the lower micromolar range with multiple compounds showing stronger inhibitory activity than the established topoisomerase poison etoposide. Using in silico methods we proposed a binding mode and evaluated it using molecular dynamics simulation. 1H-indazoles represent a new versatile scaffold that could be utilized for further development of catalytic inhibitors of the human DNA topoisomerase IIa targetting the ATPase domain where ATP binding site is located.

Substituted 4,5′-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα

“…The single monomer was preprocessed for MD as described previously. 34 , 36 − 38 The hydrated protein–compound complex was generated with the CHARMM-GUI tool. 81 Parameter and topology files for the monomer were generated with CHARMM—version 36, 82 , 83 while compound 1 was parameterized with the CHARMM general force field (CGenFF).…”

“…So far, we have characterized several classes of catalytic inhibitors targeting the ATP binding site, including triazin-2(1 H )-ones, 34 , 35 1,3,5-triazines, 36 1 H -pyrazolo[3,4]pyrimidines, 37 9 H -purines, 37 and 1 H -indazoles. 38 In addition, we also investigated inhibitors of bacterial DNA gyrase. Starting from the binding mode of the natural product clorobiocin, we identified a series of 4′-methyl- N 2-phenyl-[4,5′-bithiazole]-2,2′-diamines as inhibitors of DNA gyrase and determined for the representative compound 13 its binding mode in the ATP binding site using protein crystallography.…”

An Overview of Recent Advances in the Applications of Click Chemistry in the Synthesis of Bioconjugates with Anticancer Activities

“…Topoisomerase IIα has significant roles in maintaining chromosomes in appropriate topological state and cellular life. Due to these roles, TOPO IIα considered to be as an excellent anti‐cancer target …”

Dynophore-Based Approach in Virtual Screening: A Case of Human DNA Topoisomerase IIα

“…In our previous studies, we have developed drug-like small catalytic inhibitors that target the ATP binding site of topo IIα and mimic the ATP adenine moiety with a variety of scaffolds, all of synthetic origin [37][38][39][40]. This time we explored another region of chemical space-compounds isolated from nature.…”

“…Thus, we fully validated both our whole filtering protocol and our initial molecular recognition models. of scaffolds, all of synthetic origin [37][38][39][40]. This time we explored another region of chemical space-compounds isolated from nature.…”