Photoactivatable V-Shaped Bifunctional Quinone Methide Precursors as a New Class of Selective G-quadruplex Alkylating Agents.

Combining the selectivity of G-quadruplex (G4) ligands with the spatial and temporal control of photochemistry is an emerging strategy to elucidate the biological relevance of these structures. In this work, we developed six novel V-shaped G4 ligands that can, upon irradiation, form stable covalent adducts with G4 structures via the reactive intermediate, quinone methide (QM). We thoroughly investigated the photochemical properties of the ligands and their ability to generate QMs. Subsequently, we analyzed their specificity for various topologies of G4 and discovered a preferential binding towards the human telomeric sequence. Finally, we tested the ligand ability to act as photochemical alkylating agents, identifying the covalent adducts with G4 structures. This work introduces a novel molecular tool in the chemical biology toolkit for G4s.

A Fragment-Based Approach for the Development of G-Quadruplex Ligands: Role of the Amidoxime Moiety.

G-quadruplex (G4) nucleic acid structures have been reported to be involved in several human pathologies, including cancer, neurodegenerative disorders and infectious diseases; however, G4 targeting compounds still need implementation in terms of drug-like properties and selectivity in order to reach the clinical use. So far, G4 ligands have been mainly identified through high-throughput screening methods or design of molecules with pre-set features. Here, we describe the development of new heterocyclic ligands through a fragment-based drug discovery (FBDD) approach. The ligands were designed against the major G4 present in the long terminal repeat (LTR) promoter region of the human immunodeficiency virus-1 (HIV-1), the stabilization of which has been shown to suppress viral gene expression and replication. Our method is based on the generation of molecular fragment small libraries, screened against the target to further elaborate them into lead compounds. We screened 150 small molecules, composed by structurally and chemically different fragments, selected from commercially available and in-house compounds; synthetic elaboration yielded several G4 ligands and two final G4 binders, both embedding an amidoxime moiety; one of these two compounds showed preferential binding for the HIV-1 LTR G4. This work presents the discovery of a novel potential pharmacophore and highlights the possibility to apply a fragment-based approach to develop G4 ligands with unexpected chemical features.

Conjugation, Substituent, and Solvent Effects on the Photogeneration of Quinone Methides.

4- and 5-arylethynyl water-soluble Mannich bases and related quaternary ammonium salts were synthesized and investigated as a model of conjugated quinone methide precursors (QMPs) by UV-vis light activation. Preparative photohydration and trapping reactions by thiols were studied, together with the detection of both transient QMs and competing QMP lowest triplet excited states (T1), by laser flash photolysis. The efficiency of the arylethynyl derivatives as QMPs was remarkably affected by structural features (i.e., conjugating arylethynyl moieties, substituents, and leaving groups) and protic vs aprotic solvation. Our collective data clarify the dichotomy in the photoreactivity of conjugated Mannich bases and related quaternary ammonium salts as alkylating agents and singlet oxygen sensitizers.