Discovery of Mono- and Disubstituted 1H-Pyrazolo[3,4]pyrimidines and 9H-Purines as Catalytic Inhibitors of Human DNA Topoisomerase IIα

• Published in: ChemMedChem Vol. 10; no. 2; pp. 345 - 359
• Main Authors: Pogorelčnik, Barbara, Brvar, Matjaž, Žegura, Bojana, Filipič, Metka, Solmajer, Tom, Perdih, Andrej
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 01.02.2015; WILEY‐VCH Verlag; Wiley
• Subjects: anticancer agents; Antigens, Neoplasm - metabolism; Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacology; Binding Sites; catalytic inhibitors; Cell Survival - drug effects; Chemistry, Medicinal; DNA Gyrase - chemistry; DNA Gyrase - metabolism; DNA Topoisomerases, Type II - metabolism; DNA-Binding Proteins - antagonists & inhibitors; DNA-Binding Proteins - metabolism; Drug Design; Drug Evaluation, Preclinical; Hep G2 Cells; human DNA topoisomerase IIα; Human Umbilical Vein Endothelial Cells; Humans; Life Sciences & Biomedicine; MCF-7 Cells; Molecular Docking Simulation; MTT assay; Pharmacology & Pharmacy; Protein Binding; Protein Structure, Tertiary; Purines - chemistry; Purines - pharmacology; Pyrazoles - chemistry; Pyrazoles - pharmacology; Pyrimidines - chemistry; Pyrimidines - pharmacology; Science & Technology; Structure-Activity Relationship; Surface Plasmon Resonance; Topoisomerase II Inhibitors - chemistry; Topoisomerase II Inhibitors - pharmacology; virtual screening; MOLECULAR-DYNAMICS; virtual screening; IN-SILICO DISCOVERY; MECHANISM; human DNA topoisomerase II alpha; SUBSTITUTED PURINE ANALOGS; FORCE-FIELDS; MTT assay; ANTITUMOR DRUGS; anticancer agents; GYRASE B; ATPASE DOMAIN; catalytic inhibitors; BINDING; human DNA topoisomerase IIα
• ISSN: 1860-7179; 1860-7187
• DOI: 10.1002/cmdc.201402459

Human DNA topoisomerase IIα (htIIα) is a validated target for the development of anticancer agents. Based on structural data regarding the binding mode of AMP‐PNP (5′‐adenylyl‐β,γ‐imidodiphosphate) to htIIα, we designed a two‐stage virtual screening campaign that combines structure‐based pharmacophores and molecular docking. In the first stage, we identified several monosubstituted 9H‐purine compounds and a novel class of 1H‐pyrazolo[3,4]pyrimidines as inhibitors of htIIα. In the second stage, disubstituted analogues with improved cellular activities were discovered. Compounds from both classes were shown to inhibit htIIα‐mediated DNA decatenation, and surface plasmon resonance (SPR) experiments confirmed binding of these two compounds on the htIIα ATPase domain. Proposed complexes and interaction patterns between both compounds and htIIα were further analyzed in molecular dynamics simulations. Two compounds identified in the second stage showed promising anticancer activities in hepatocellular carcinoma (HepG2) and breast cancer (MCF‐7) cell lines. The discovered compounds are suitable starting points for further hit‐to‐lead development in anticancer drug discovery. Anticancer target revisited: In a two‐stage virtual screening campaign, we discovered novel catalytic inhibitors that target the human DNA topoisomerase IIα ATP binding site. The binding of a new class of pyrazolopyrimidines was fully characterized by surface plasmon resonance experiments. In subsequent optimization, compounds with promising cytotoxicity against HepG2 and MCF‐7 cancer cell lines were identified.