Ligand binding mode to duplex and triplex dna assessed by combining electrospray tandem mass spectrometry and molecular modeling

Abstract

In this paper, we report the analysis of seven benzopyridoindole and benzopyridoquinoxaline drugs binding to different duplex DNA and triple helical DNA, using an approach combining electrospray ionization mass spectrometry (ESI-MS), tandem mass spectrometry (MS/MS), and molecular modeling. The ligands were ranked according to the collision energy (CE(50)) necessary to dissociate 50% of the complex with the duplex or the triplex in tandem MS. To determine the probable ligand binding site and binding mode, molecular modeling was used to calculate relative ligand binding energies in different binding sites and binding modes. For duplex DNA binding, the ligand-DNA interaction energies are roughly correlated with the experimental CE(50), with the two benzopyridoindole ligands more tightly bound than the benzopyridoquinoxaline ligands. There is, however, no marked AT versus GC base preference in binding, as supported both by the ESI-MS and the calculated ligand binding energies. Product ion spectra of the complexes with triplex DNA show only loss of neutral ligand for the benzopyridoquinoxalines, and loss of the third strand for the benzopyridoindoles, the ligand remaining on the duplex part. This indicates a higher binding energy of the benzopyridoindoles, and also shows that the ligands interact with the triplex via the duplex. The ranking of the ligand interaction energies compared with the CE(50) values obtained by MS/MS on the complexes with the triplex clearly indicates that the ligands intercalate via the minor groove of the Watson-Crick duplex. Regarding triplex versus duplex selectivity, our experiments have demonstrated that the most selective drugs for triplex share the same heteroaromatic core.

A study of the non-covalent interaction between flavonoids and DNA triplexes by electrospray ionization mass spectrometry

“…Electrospray ionization mass spectrometry (ESI-MS) has proved to be a powerful tool for drug discovery and examining drug/DNA complexes with advantages such as determination of precise stoichiometry, low sample consumption and short analysis time [24,25]. Many drug/DNA complexes have been extensively studied by ESI-MS, and the results have agreed well with those obtained using solution phase techniques [26][27][28][29][30][31][32][33][34][35][36][37]. The flavonoid/duplex DNA complexes were first investigated using ESI-MS in our laboratory [26].…”

“…For unknown duplex DNA binding-mode, it can be deduced by comparing drug-DNA complex dissociation pattern with those of known binding-modes of traditional major-groove binders or intercalators or drugs using ESI-MS [30,[35][36][37]. However, because few MS/MS studies of drug/triplex complexes have been performed [28], no dissociation pattern of drug/triplex complex is available as comparison. Furthermore, the dissociation pathways for drug-DNA complexes can vary with charge states and instruments [29,32], making justification of the binding mode based on the dissociation pattern only problematic.…”

“…As triplex DNA has base triplets not base pairs, the curved or unfused aromatic ring seems to stack better with the bases of triplex than the duplex [7,8]. The departure of ring B might change the binding of the saccharide as well and consequently lead to a different dissociation pathway, as the binding of the side chain influences the dissociation pattern [28].…”

Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry

“…Overall, the DNA-binding affinities of the APs obtained by ESI-MS screening correlated with their inhibitory activities. ESI-MS has also been used to evaluate the complexation of other types of novel ligands (28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40), including acridines (31), cationic porphyrins (36), cryptolepine alkaloids (37), protoberbine alkaloids (38), benzopyridoindole and benzopyridoquinoxaline compounds (32), and acridine-and naphthalene-derived macrocyclic bis-intercalators (33), with DNA duplexes.…”

Electrospray‐Ionization Mass Spectrometry for Screening the Specificity and Stability of Single‐Stranded‐DNA Templated Self‐Assemblies

“…We monitored the dissociative pathway and the degree of dissociation of the isolated ion as a function of the voltage in the collision cell. [29,62] Quantitative values for guestbinding energies cannot be obtained with these CID experiments, because the threshold energy of dissociation cannot be determined with our setup. The breakdown curve of a single complex is measured by selecting a narrow m/z range around the m/z value of the complex with the quadrupole and by increasing the V acc value in the collision cell.…”