Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design

Abstract

Stabilization of a G-quadruplex (G4) DNA structure in the proto-oncogene c-MYC using small molecule ligands has emerged as an attractive strategy for the development of anticancer therapeutics. To understand the subtle structural changes in the G4 structure upon ligand binding, molecular dynamics (MD) simulations of c-MYC G4 DNA were carried out in a complex with six different potent ligands: 3AQN, 6AQN, 3APN, 360A, Nap-Et, and Nap-Pr. The results show that the ligands 3AQN, 6AQN, 3APN, and 360A stabilize the G4 structure by making stacking interactions with the top quartet. On the other hand, Nap-Et and Nap-Pr bind at the groove of the G4 structure. These groove binding ligands make crucial H-bond contacts with the guanines and electrostatic interactions with the phosphate backbone. Two-dimensional dynamic correlation maps unraveled the ligand-induced correlated motions between the guanines in the quartet and a di-nucleotide present in the propeller loop-2 of the G4 structure. Cluster analysis and ONIOM calculations revealed the structural dynamics in the loop of the quadruplex upon ligand binding. Overall, the results from the present study suggest that engineering specific contacts with the propeller loop can be an efficient way to design c-MYC G4-specific ligands.

Superiority of an Asymmetric Perylene Diimide in Terms of Hydrosolubility, G-Quadruplex Binding, Cellular Uptake, and Telomerase Inhibition in Prostate Cancer Cells

“…The above results were obtained with the telomeric and the hTERT promoter sequences. However, G4 DNAs can be formed from DNA sequences found in the promoter region of several oncogenes, including c-Myc , VEGF , BCL-2 , c-KIT , c-MYB , HIF-1α , HRAS , KRAS , PDGF-A , PDGFR-β , RET , and SRC ; these sites are potential targets for anticancer therapy by G4 ligands. − The structural variations of G4 are diverse, and specific G4 ligands can explicitly bind one topology, among others. , To investigate whether our three PDIs could differentially interact with different G4 DNAs at these three pHs (pH 6–8), we employed a duplex–quadruplex competition assay with two more sequences, the c-Myc promoter and VEGF promoter sequences. The results are shown in Figure S4, Supporting Information.…”

“…33−35 The structural variations of G4 are diverse, and specific G4 ligands can explicitly bind one topology, among others. 34,36 To investigate whether our three PDIs could differentially interact with different G4 DNAs at these three pHs (pH 6−8), we employed a duplex−quadruplex competition assay with two more sequences, the c-Myc promoter and VEGF promoter sequences. The results are shown in Figure S4, Supporting Information.…”

Identification of G-Quadruplex-Binding Inhibitors of Myc Expression through Affinity Selection–Mass Spectrometry

“…Reasons for the differences between binding and function include the possibility that in vitro folded G4s differ structurally from those found in cells and lack accessory proteins that play a physiological role in G4 folding. 17,39,40 Moreover, our ALIS screen tested for binding to a prefolded G4 DNA sequence, and compounds that rely on the dynamic nature of these structures, or bind to other versions of the diversity of these structures were possibly missed. Different binding assays also may report different results, even for the same compound and folded G4, due to different assay conditions, such as solution-based versus immobilization-based screening; 41 this may be the case regarding the different G4-binding profiles that we observed for control A compared with published results using surface plasmon resonance (SPR).…”

Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking

“…In order to examine binding affinity of ligands to G-quadruplex, MM-PBSA analysis [49][50][51] was employed via g_mmpbsa tool [52]. For each complex, the binding free energy was calculated based on 100 snapshots extracted from the MD trajectory.…”