The Benzothiazine Core as a Novel Motif for DNA-Binding Small Molecules

Abstract

A new series of 4H-1,3-benzothiazine dyes were prepared and fully characterized in an aqueous medium. Benzothiazine salts were synthesized either through the classical synthetic pathway using Buchwald-Hartwig amination or through economical and environmentally friendly electrochemical synthesis. The latest synthetic approach employs successful electrochemical intramolecular dehydrogenative cyclization of N-benzylbenzenecarbothioamides to form 4H-1,3-benzothiazines. 4H-1,3-Benzothiazines were evaluated as novel DNA/RNA probes. Through the use of several methods such as UV/vis spectrophotometric titrations, circular dichroism and thermal melting experiments, the binding of four benzothiazine-based molecules to polynucleotides was examined. Compounds 1 and 2 acted as DNA/RNA groove binders, thus suggesting the potential of these compounds as novel DNA/RNA probes. This is a proof-of-concept study and will be expanded to include SAR/QSAR studies.

Keywords: 4H-1,3-benzothiazines; DNA/RNA binding; UV/vis spectroscopy; circular dichroism; electrochemical dehydrogenative cyclization.

Scheme 1

Reaction pathway for the synthesis of benzothiazines 1 and 2.

Scheme 2

Reaction pathway for the synthesis of benzothiazines 3, 4 and 8.

Scheme 3

Structure of compounds 1′ and 2′.

Scheme 4

Structure of compounds 3′ and 4′.

Scheme 5

Structure of compounds 1 and 2.

Scheme 6

Structure of compounds 3 and 4.

Scheme 7

Structure of compounds 8′ and 8.

Figure 1

Aromatic parts of the ¹H NMR spectra (CDCl₃) of benzothiazines 1 (a) and 2 (b).

Figure 2

Molecular structure of compound 8′. Displacement ellipsoids are drawn for the probability of 20% and hydrogen atoms are shown as spheres of arbitrary radii.

Figure 3

Crystal packing of 8′ is characterized by hydrogen bonds and stacking interactions.

Figure 4

UV/vis spectra of studied compounds (c = 1 × 10⁻⁵ M) in water.

Figure 5

(a) Changes in the UV/vis spectra of 2 (c = 2 × 10⁻⁵ M) upon titration with ct-DNA, inset: absorbance changes at λ_max = 403 nm, fitted to Scatchard eq. (red line) [21]; (b) normalized absorbance changes at the respective λ_max for all studied compounds upon titration with ct-DNA, fitted to Scatchard eq. (red line) [21]; (c) normalized absorbance changes at the respective λ_max for all studied compounds upon titration with pApU, fitted to Scatchard eq. (red line) [21].

Figure 6

CD titration of pApU (c = 2 × 10⁻⁵ M) with 1 and 2 at molar ratios r = [compound]/[polynucleotide] (pH 7.0, buffer sodium cacodylate, I = 0.05 M). (a) pApU with 1, inset: ICD at 440 nm, (b) pApU with 2, inset: ICD at 410 nm.