G4-QuadScreen: A Computational Tool for Identifying Multi-Target-Directed Anticancer Leads against G-Quadruplex DNA.

The study presents 'G4-QuadScreen', a user-friendly computational tool for identifying MTDLs against G4s. Also, it offers a few hit MTDLs based on in silico and in vitro approaches. Multi-tasking QSAR models were developed using linear discriminant analysis and random forest machine learning techniques for predicting the responses of interest (G4 interaction, G4 stabilization, G4 selectivity, and cytotoxicity) considering the variations in the experimental conditions (e.g., G4 sequences, endpoints, cell lines, buffers, and assays). A virtual screening with G4-QuadScreen and molecular docking using YASARA (AutoDock-Vina) was performed. G4 activities were confirmed via FRET melting, FID, and cell viability assays. Validation metrics demonstrated the high discriminatory power and robustness of the models (the accuracy of all models is ~>90% for the training sets and ~>80% for the external sets). The experimental evaluations showed that ten screened MTDLs have the capacity to selectively stabilize multiple G4s. Three screened MTDLs induced a strong inhibitory effect on various human cancer cell lines. This pioneering computational study serves a tool to accelerate the search for new leads against G4s, reducing false positive outcomes in the early stages of drug discovery. The G4-QuadScreen tool is accessible on the ChemoPredictionSuite website.

Development and application of metallo-phthalocyanines as potent G-quadruplex DNA binders and photosensitizers.

Metallo-phthalocyanines (MPc) are common photosensitizers with ideal photophysical and photochemical properties. Also, these molecules have shown to interact with non-canonical nucleic acid structures, such as G-quadruplexes, and modulate oncogenic expression in cancer cells. Herein, we report the synthesis and characterisation of two metallo-phthalocyanines containing either zinc (ZnPc) or nickel (NiPc) in the central aromatic core and four alkyl ammonium lateral chains. The interaction of both molecules with G-quadruplex DNA was assessed by UV-Vis, fluorescence and FRET melting experiments. Both molecules bind strongly to G-quadruplexes and stabilise these structures, being NiPc the most notable G-quadruplex stabiliser. In addition, the photosensitizing ability of both metal complexes was explored by the evaluation of the singlet oxygen generation and their photoactivation in cells. Only ZnPc showed a high singlet oxygen generation either by direct observation or by indirect evaluation using a DPBF dye. The cellular evaluation showed mainly cytoplasmic localization of ZnPc and a decrease of the IC50 values of the cell viability of ZnPc upon light activation of two orders of magnitude. Two metallo-phthalocyanines containing zinc and nickel within the aromatic core have been investigated as G-quadruplex stabilizers and photosensitizers. NiPc shows a high G4 binding but negligible photosensitizing ability while ZnPc exhibits a moderate binding to G-quadruplex together with a high potency to generate singlet oxygen and photocytotoxicity. The interaction with G4s and capacity to be photosensitized is associated with the geometry adopted by the central metal core of the phthalocyanine scaffold.

Modulating the G-Quadruplex and Duplex DNA Binding by Controlling the Charge of Fluorescent Molecules.

Two fluorescent and non-toxic spirobifluorene molecules bearing either positive (Spiro-NMe3) or negative (Spiro-SO3) charged moieties attached to the same aromatic structure have been investigated as binders for DNA. The novel Spiro-NMe3 containing four alkylammonium substituents interacts with G-quadruplex (G4) DNA structures and shows preference for G4s over duplex by means of FRET melting and fluorescence experiments. The interaction is governed by the charged substituents of the ligands as deduced from the lower binding of the sulfonate analogue (Spiro-SO3). On the contrary, Spiro-SO3 exhibits higher binding affinity to duplex DNA structure than to G4. Both molecules show a moderate quenching of the fluorescence upon DNA binding. The confocal microscopy evaluation shows the internalization of both molecules in HeLa cells and their lysosomal accumulation.

Alkaloids as Photosensitisers for the Inactivation of Bacteria.

Antimicrobial photodynamic therapy has emerged as a powerful approach to tackle microbial infections. Photodynamic therapy utilises a photosensitiser, light, and oxygen to generate singlet oxygen and/or reactive oxygen species in an irradiated tissue spot, which subsequently react with nearby biomolecules and destroy the cellular environment. Due to the possibility to irradiate in a very precise location, it can be used to eradicate bacteria, fungus, and parasites upon light activation of the photosensitiser. In this regard, natural products are low-cost molecules capable of being obtained in large quantities, and some of them can be used as photosensitisers. Alkaloids are the largest family among natural products and include molecules with a basic nature and aromatic rings. For this study, we collected the naturally occurring alkaloids used to treat microorganism infections using a photodynamic inactivation approach. We gathered their main photophysical properties (excitation/emission wavelengths, quantum yields, and oxygen quantum yield) which characterise the ability to efficiently photosensitise. In addition, we described the antibacterial activity of alkaloids upon irradiation and the mechanisms involved in the microorganism killing. This review will serve as a reference source to obtain the main information on alkaloids used in antimicrobial photodynamic therapy.

Influence of the chain length and metal : ligand ratio on the self-organization processes of Cu2+ complexes of [1 + 1] 1H-pyrazole azamacrocycles.

Three new [1 + 1] macrocycles formed by the reaction of 1H-3,5-bis(chloromethyl)pyrazole with the tosylated amines 1,4,7,10-tetraazadecane (L1), 1,4,8,11-tetraazaundecane (L2) and 1,5,10,14-tetraazatetradecane (L3) are described. Potentiometric studies and HR-ESI-Mass spectrometry show the formation of dimeric binuclear Cu2+ complexes whose organization depends on the type of hydrocarbon chains connecting the amine groups. Furthermore, trinuclear or/and tetranuclear complexes are formed depending also on the length of the polyaminic bridge and on the sequence of the hydrocarbon chains. The crystal structures of the [2 + 2] [Cu2(H(H-1L2))2](ClO4)4·4H2O (1) and [Cu2(H-1L2)2](ClO4)2 (2) complexes show in both of them two macrocycles self-assembled by the metal ions which interconnect their pyrazolate fragments that behave as bis(monodentate) ligands. While in 1 one central amine of each macrocycle binds to the axial position of a distorted square-pyramid and the other ones remain protonated, in 2 all the amine groups are involved in the coordination giving rise to a strongly distorted octahedral geometry. Paramagnetic 1H NMR measurements support that these structures also form in solution. Interestingly, tetranuclear complexes [Cu4(H-1L4)2(OH)2.08](ClO4)2.92Br0.54Cl0.46 (3) and [Pd2.39Cu1.61(H-1L4)2(OH)2](ClO4)2Cl1.33Br0.67·2.87H2O (4) have been isolated for the macrocycle containing the 1,5,9,13-tetraamine chain (L4). 3 has two binucleating units, one of them formed by the pyrazolate moieties and their neighbouring secondary amines and the other by the two central amines of both macrocycles. This latter Cu2+ coordination site is completed by two hydroxide anions as bridging ligands. 4 was obtained from a solution prepared to achieve full formation of the dimeric cage [Cu2(H-1(HL4))2]4+ by addition of K2PdCl4. The Pd2+ ion due to its softer acidic characteristics displaces the Cu2+ ions from the pyrazolate site. UV-vis spectroscopy suggests that the exchange is completed at room temperature after one hour.