Selectivity of an indolyl berberine derivative for tetrameric G‐quadruplex DNA

Abstract

Negative ion electrospray ionization mass spectrometry (ESI-MS) was used to compare the binding affinities and stoichiometries of the alkaloid berberine, a 13-substituted indolyl berberine derivative, SS14, and the chemotherapeutic agent, daunomycin, for 16-mer double-stranded (ds) DNA (D1 and D2) and for an 8-mer tetrameric quadruplex, Q1 (d(TTGGGGGT)(4)). Under the experimental conditions presented here, ESI mass spectra of Q1 showed that the major ions were from Q1 with three ammonium ions bound in the structure. Ions from Q1 with four ammonium ions were of lower abundance. In agreement with other work, there were multiple binding sites on the dsDNA and the quadruplex for daunomycin and berberine. The binding of SS14 to both dsDNA and Q1 was less extensive. Although the binding affinity of SS14 for Q1 was modest, this compound showed a clear preference for Q1 DNA over D1 or D2 DNA. Berberine and daunomycin bound with greater affinity to both types of DNA secondary structure, with the former showing a slight preference for Q1 over D1 while the latter showed a slight preference for D1 over Q1. While at least five berberine molecules bound to Q1, this quadruplex could accommodate only two SS14 molecules. These investigations show that SS14 is a promising lead compound for drugs that may selectively bind quadruplex over duplex DNA.

A mass spectrometric investigation of novel quadruplex DNA-selective berberine derivatives

“…2(A) and (B) show that the 5À ions of Q4 ([Q4 + 4NH 4 + À 9H] 5À ) were the most abundant under the conditions. Berb (1) bound extensively to Q4 as previously observed, 7 and to every sequence tested with the exception of Q2. Fig.…”

“…This extensive binding to Q4 and lack of selectivity for DNA structure was observed in our earlier experiments and may suggest multiple binding modes. 7 The binding stoichiometry of the duplex intercalator, Dn, was similar. In mixtures containing the ligands with a preference for Q4 (2-4, 5 and 7) no clear preference for a particular binding stoichiometry was observed (Fig.…”

“…6 Recently we showed using electrospray ionisation mass spectrometry (ESI-MS) that a berberine derivative substituted at its 13-position with a 5-nitro-2-phenylindolylmethyl group (2) had modest binding affinity for a tetrameric qDNA, and significant selectivity over duplex DNA. 7 Compound 2 and its meta and para isomers, 3 and 4 ( Fig. 1), were originally designed and synthesised as dual action hybrid antibacterials.…”

“…[9][10][11] Analogues bearing a methylene ether linkage at the berberine 13-position, 5, and a 2-naphthalenyl congener, 6, were similarly synthesised and studied as dual action antibacterials. 12 As berberine is known to interact with DNA 7 and to have effects on telomerase activity, 13 it was of interest to characterise and compare the qDNA binding properties of these 13-substituted berberines. In the current work, compounds 2-6 were investigated using ESI-MS alongside berberine and daunomycin (Dn, a DNA-intercalating anticancer anthracycline) for their abilities to bind three different qDNA (Q4, Q1, Q2) and duplex DNA (D1, D2, F10) sequences.z A 2-naphthalenyl analogue 7 was also studied to explore how changing the heteroaryl substituent affects DNA binding.…”

“…No NH 4 + was associated with Q1 as has been observed in other work, 16 but ions corresponding to adduction of Q1 with adventitious Na + and K + were present.y Each DNA sequence was treated with each ligand in 1 : 1, 1 : 3, 1 : 6 and 1 : 9 (DNA : ligand) molar ratios and ESI mass spectra of each mixture acquired as previously described. 7 Fig . 2 shows representative examples of the mass spectra obtained.…”