G-quadruplexes (G4 s), as non-canonical DNA structures, attract a great deal of research interest in the molecular biology as well as in the material science fields. The use of small molecules as ligands for G-quadruplexes has emerged as a tool to regulate gene expression and telomeres maintenance. Meso-tetrakis-(N-methyl-4-pyridyl) porphyrin (TMPyP4) was shown as one of the first ligands for G-quadruplexes and it is still widely used. We report an investigation comprising molecular docking and dynamics, synthesis and multiple spectroscopic and spectrometric determinations on simple cationic porphyrins and their interaction with different DNA sequences. This study enabled the synthesis of tetracationic porphyrin derivatives that exhibited binding and stabilizing capacity against G-quadruplex structures; the detailed characterization has shown that the presence of amide groups at the periphery improves selectivity for parallel G4 s binding over other structures. Taking into account the ease of synthesis, 5,10,15,20-tetrakis-(1-acetamido-4-pyridyl) porphyrin bromide could be considered a better alternative to TMPyP4 in studies involving G4 binding.

Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G+Na]⁺ ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G+Na]⁺ interaction in the gas phase was determined from E_com50 - the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G+Na]⁺ interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.

In drug discovery, ligand-mediated stabilization of G-quadruplexes is pursued for regulating gene expression and key cellular processes. Electrospray ionization mass spectrometry (ESI-MS) has been optimized for screening putative DNA-binding small molecules of natural and synthetic origin. Several flavonoids were reported to interact with G-quadruplex, and quercetin is among them. In this contribution, the interaction with G-quadruplex DNA of rutin, a glycoside of quercetin extracted from flower buds of Styphnolobium japonicum (L.) Schott, was investigated by means of ESI-MS and molecular docking. While rutin and quercetin showed similar G-quadruplex binding affinity values, rutin was characterized by enhanced selectivity for G-quadruplex over double stranded DNA. Moreover, collision-induced dissociation (CID) assays demonstrated that rutin stabilizes the G-quadruplex arrangement more efficiently, and molecular docking predicted stacking as the preferential interaction pattern.

G-quadruplex DNA stabilization mediated by small molecules is an attractive approach to modulate the transcription of guanine-rich sequences and contrast unregulated cell proliferation. Natural alkaloids have been reported to target this macromolecular arrangement, and such mechanism may be among these underlying the antiproliferative effect of some flavonoids. The binding affinity for G-quadruplex and double stranded DNA of 4 isoflavones from Maclura pomifera, namely osajin, pomiferin, scandenone and auriculasin, was evaluated using electrospray mass spectrometry (ESI-MS). The experiments pointed out that osajin and scandenone preferentially bind G-quadruplex. Moreover, since G-quadruplex stabilization is a crucial aim for triggering biological effects such as gene expression, collision-induced dissociation (CID) assays were performed to study the relative gas-phase kinetic stability of the DNA/ligand complexes. Osajin was identified as the best G-quadruplex stabilizer of the set, and in silico docking studies indicate that stacking is the preferred interaction motif of this natural compound.

Aminomethylation reactions between chiral amino compounds (S)-(-)-1-phenylethylamine and l-proline with tetranonylresorcinarene and tetra-(4-hydroxyphenyl)resorcinarene in presence of formaldehyde were studied. The reaction between l-proline and resorcinarenes generated regioselectively chiral tetra-Mannich bases, due to the molecular incorporation of the fragment of the chiral amino acid. On the other hand, tetranonylresorcinarene and (S)-(-)-1-phenylethylamine formed regio- and diasteroselectively chiral tetrabenzoxazines, both by chiral auxiliary functionalization and by the transformation of the molecular structure that confers inherent chirality. The products obtained were characterized using IR, 1H-NMR, 13C-NMR, COSY, HMQC, and HMBC techniques. The reaction of (S)-(-)-1-phenylethylamine with tetra-(4-hydroxyphenyl)resorcinarene did not proceed under the experimental conditions. Once the chiral aminomethylated tetra-(4-hydroxyphenyl)resorcinarene was obtained, the chemical modification of poly(GMA-co-EDMA) was studied, and the results showed an efficient incorporation of the aminomethylated compound. For the physical modification, chiral aminomethylated tetranonylresorcinarenes were employed, finding that the incorporation of modified resorcinarenes occurs, but with less efficiency than that observed using chemical modification. The modified polymers were characterized via FT-IR, scanning electron microscopy imaging, and elemental analysis. Finally, polymers modified with chiral resorcinarenes were used as sorbents in norepinephrine microextraction; for practical purposes, artificial urine was prepared and used. To perform the microextraction, the decision was made to use the modern rotating-disk sorptive extraction technique (RDSE), because of its analytical attributes as a green, or eco-friendly, technique. According to the results, the method preliminarily validated for the determination of norepinephrine in artificial urine shows that the modified polymer with chiral derivative of tetra-(4-hydroxyphenyl)resorcinarene worked effectively as a new sorbent phase for the quantitative microextraction of norepinephrine, exhibiting high stability and homogeneity of composition and structure within the working range.

This paper describes non-covalent complexes between zwitterionic 3-(1-alkyl-3N-imidazolio)- propane-1-sulfonates and different amines. Electrospray ionization (ESI) mass spectrometry and collision- induced dissociation were used to measure the stability of such complexes in solution and in the gas phase. Generally, zwitterionic sulfonates formed more abundant complexes with protonated 5-methylcytosine (5-MCH) than with aliphatic amines. The results show that the association constants and half-dissociation threshold energies of these complexes nonlinearly depend on the alkyl chain length of the zwitterion. It is shown that the complexes with the lowest stability exist in acetonitrile solution or in the gas phase. The factors responsible for this complicated behavior are discussed. The structure of the complexes was investigated by quantum chemical calculations using molecular mechanics and density functional theory. Hydrogen bonding is proposed as the main type of interaction responsible for the stability of ion-zwitterion complexes. In summary, the information obtained in this study could be used for the development of the new derivatization reagents for some compounds containing amidinium groups, like 5-MCH, to increase selectivity of ESI-based methods.