Acid-base properties of functionalised tripodal polyamines and their interaction with nucleotides and nucleic acids

Novel Tripodal Polyamine Tris-Pyrene: DNA/RNA Binding and Photodynamic Antiproliferative Activity

A novel tri-pyrene polyamine (TAL3PYR) bearing net five positive charges at biorelevant conditions revealed strong intramolecular interactions in aqueous medium between pyrenes, characterised by pronounced excimer fluorescence. A novel compound revealed strong binding to ds-DNA and ds-RNA, along with pronounced thermal stabilisation of DNA/RNA and extensive changes in DNA/RNA structure, as evidenced by circular dichroism. New dye caused pronounced ds-DNA or ds-RNA condensation, which was attributed to a combination of electrostatic interactions between 5+ charge of dye and negatively charged polynucleotide backbone, accompanied by aromatic and hydrophobic interactions of pyrenes within polynucleotide grooves. New dye also showed intriguing antiproliferative activity, strongly enhanced upon photo-induced activation of pyrenes, and is thus a promising lead compound for theranostic applications on ds-RNA or ds-DNA targets, applicable as a new strategy in cancer and gene therapy.

Ditopic Aza-Scorpiand Ligands Interact Selectively with ds-RNA and Modulate the Interaction upon Formation of Zn2+ Complexes

Nucleic acids are essential biomolecules in living systems and represent one of the main targets of chemists, biophysics, biologists, and nanotechnologists. New small molecules are continuously developed to target the duplex (ds) structure of DNA and, most recently, RNA to be used as therapeutics and/or biological tools. Stimuli-triggered systems can promote and hamper the interaction to biomolecules through external stimuli such as light and metal coordination. In this work, we report on the interaction with ds-DNA and ds-RNA of two aza-macrocycles able to coordinate Zn²⁺ metal ions and form binuclear complexes. The interaction of the aza-macrocycles and the Zn²⁺ metal complexes with duplex DNA and RNA was studied using UV thermal and fluorescence indicator displacement assays in combination with theoretical studies. Both ligands show a high affinity for ds-DNA/RNA and selectivity for ds-RNA. The ability to interact with these duplexes is blocked upon Zn²⁺ coordination, which was confirmed by the low variation in the melting temperature and poor displacement of the fluorescent dye from the ds-DNA/RNA. Cell viability assays show a decrease in the cytotoxicity of the metal complexes in comparison with the free ligands, which can be associated with the observed binding to the nucleic acids.

Hybrid GMP-polyamine hydrogels as new biocompatible materials for drug encapsulation

Here we present the preparation and characterization of new biocompatible materials for drug encapsulation. These new gels are based on positively charged [1+1] 1H-pyrazole-based azamacrocycles which minimise the electrostatic repulsions between the negatively charged GMP molecules. Rheological measurements confirm the electroneutral hydrogel structure as the most stable for all the GMP-polyamine systems. Nuclear magnetic resonance (NMR) was employed to investigate the kinetics of the hydrogel formation and cryo-scanning electron microscopy (cryo-SEM) was used to obtain information about the hydrogel morphology, which exhibited a non-homogeneous structure with a high degree of cross-linking. It is possible to introduce isoniazid, which is the most employed antibiotic for tuberculosis treatment, into the hydrogels without disrupting the hydrogel structure at appropriate concentrations for oral administration.

Development of Polyamine-Substituted Triphenylamine Ligands with High Affinity and Selectivity for G-Quadruplex DNA

Currently, significant efforts are devoted to designing small molecules able to bind selectively to guanine quadruplexes (G4s). These noncanonical DNA structures are implicated in various important biological processes and have been identified as potential targets for drug development. Previously, a series of triphenylamine (TPA)-based compounds, including macrocyclic polyamines, that displayed high affinity towards G4 DNA were reported. Following this initial work, herein a series of second-generation compounds, in which the central TPA has been functionalised with flexible and adaptive linear polyamines, are presented with the aim of maximising the selectivity towards G4 DNA. The acid-base properties of the new derivatives have been studied by means of potentiometric titrations, UV/Vis and fluorescence emission spectroscopy. The interaction with G4s and duplex DNA has been explored by using FRET melting assays, fluorescence spectroscopy and circular dichroism. Compared with previous TPA derivatives with macrocyclic substituents, the new ligands reported herein retain the G4 affinity, but display two orders of magnitude higher selectivity for G4 versus duplex DNA; this is most likely due to the ability of the linear substituents to embrace the G4 structure.

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives

Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the ψ-type pattern in the CD spectra.

Aryl-bis-(scorpiand)-aza receptors differentiate between nucleotide monophosphates by a combination of aromatic, hydrogen bond and electrostatic interactions

Bis-polyaza pyridinophane scorpiands bind nucleotides in aqueous medium with 10-100 micromolar affinity, predominantly by electrostatic interactions between nucleotide phosphates and protonated aliphatic amines and assisted by aromatic stacking interactions. The pyridine-scorpiand receptor showed rare selectivity toward CMP with respect to other nucleotides, whereby two orders of magnitude affinity difference between CMP and UMP was the most appealing. The phenanthroline-scorpiand receptor revealed at pH 5 strong selectivity toward AMP with respect to other NMPs, based on the protonation of adenine heterocyclic N1. The results stress that the efficient recognition of small biomolecules within scorpiand-like receptors relies mostly on the electrostatic and H-bonding interactions despite the competitive interactions in the bulk solvent, thus supporting further optimisation of this versatile artificial moiety.

Molecular recognition of nucleotides in water by scorpiand-type receptors based on nucleobase discrimination

The detection of nucleotides is of crucial importance because they are the basic building blocks of nucleic acids. Scorpiand-based polyamine receptors functionalized with pyridine or anthracene units are able to form stable complexes with nucleotides in water, based on coulombic, π-π stacking, and hydrogen-bonding interactions. This behavior has been rationalized by means of an exploration with NMR spectroscopy and DFT calculations. Binding constants were determined by potentiometry. Fluorescence spectroscopy studies have revealed the potential of these receptors as sensors to effectively and selectively distinguish guanosine-5'-triphosphate (GTP) from adenosine-5'-triphosphate (ATP).

The size of the aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs. ds-DNA

Aryl-linked (pyridine- vs. phenanthroline-) bis-polyaza pyridinophane scorpiands PYPOD and PHENPOD strongly bind to the double stranded DNA and RNA, whereby very intriguing RNA over DNA selectivity is finely tuned by aryl-linker length and aromatic surface. Moreover, PYPOD and PHENPOD dimer formation at high compound/polynucleotide ratios is highly sensitive to the fine interplay between the steric and binding properties of compound-dimers and the DNA minor groove/RNA major groove. That is demonstrated by significantly different induced CD spectra, which allow spectroscopic differentiation between various DNA/RNA secondary structures. A significantly higher (micromolar) antiproliferative effect of PYPOD and PHENPOD on human cell lines with respect to previously reported pyridine-based tripodal aliphatic polyamines is attributed to masked positive charges and increased hydrophobicity of novel compounds, resulting in more efficient membrane permeation and cellular uptake.

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly A, poly G, poly C, poly U), double-stranded DNA polynucleotides (poly dAdT-poly dAdT, poly dGdC-poly dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly dAdT-poly dAdT, at variance to preferred binding of Im and Py to only major groove of poly dGdC-poly dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.