The Interaction of Small Molecules with Biomolecules

Abstract

The binding of small molecules with biological targets is associated to interesting chemical and biological properties of the resulting supramolecular systems. We have recently reported on the synthesis and characterization of cationic first row transition metal complexes and the study of their DNA binding properties, in aqueous solutions at neutral pH, essentially investigated by viscosimetry and spectroscopic techniques such as circular dichroism, absorption and fluorescence in the UV-visible wavelength range. Of course, such procedure cannot furnish atomic level details of the molecule-DNA interaction. Computational Chemistry may provide support for the interpretation of experimental data on an atomistic level (Fig.1). For example, we have recently shown that Molecular Dynamics (MD) simulations, followed by quantum mechanics/molecular mechanics (QM/MM) calculation, provided detailed structural informations and binding energies of the complexes between nickel(II), copper(II), zinc(II) metallointercalators with nucleic acids in the canonical B conformation [1]. We are presently applying such complementary experimental and computational approach to the interaction of small molecules with G-quadruplex (G4) DNA. The latter is a non-canonical conformation recently observed in human cells [2], and it has been proposed as a target for a novel class of anticancer drugs. Recently we have performed MD simulation to have an insight into the molecular recognition process of small organic ligands and other biological targets, such as mRNA and proteins [3].