Pyridopyrimidinone Derivatives as ΙDNAG-Quadruplex-Stabilizing Agents: Design, Synthesis and Biophysical Studies

Published in: Journal, Volume : 2, Issue : 18, Pages : 5206-5213

DOI : 10.1002/slct.201700677

Author : Malhotra, Rajesh; Rarhi, Chhanda; Diveshkumar, K. V.; Bommisetti, P.; Pany, Sushree Prangya P.; Roy, Subho; Pradeepkumar, P. I.; Kundu, Mrinalkanti

Abstract : With an aim to engineer drug-like properties, pyridopyrimidinone based selective G4 DNA stabilizing agents, e.g., I were designed, synthesized and further they were evaluated for G4 DNA recognition properties. CD melting studies revealed the preferential stabilization of parallel topol. of promoter c-MYC and c-KIT G4 DNAs by the ligands, especially compound I and 4-[7-chloro-3-methyl-8-(4-methyl-piperazin-1-yl)-4-oxo-4H-pyrido[1,2-a]pyrimidin-2-yloxymethyl]-N-(2-dimethylamino-ethyl)-benzamide, over the different topologies of telomeric G4 DNA. UV melting experiments suggested that no significant stabilization was observed for duplex DNA. Further, the results from ITC experiments substantiated the preferential stabilization of parallel topol. of c-MYC G4 DNA over telomeric and duplex DNA by the ligands I. These data showed that ligand I has moderate binding affinity to the c-MYC G4 DNA and is ~49-fold and ~25-fold selective over the telomeric G4 DNA and the duplex DNA resp. The mol. modeling and dynamics studies of the ligand I in complex with c-MYC and c-KIT1 G4 DNAs showed that this ligand stacks on the 5′-quartet of c-MYC and 3′-quartet of c-KIT1 G4 DNA structures.