Binding thermodynamics of 1,3-bis(((E-1H-pyrrol-2-yl) methylene) amino) propan-2-ol palladium(II) with HSA and its intercalative behaviour in ctDNA

Abstract

The development of novel metallodrugs needs to be investigated against several criteria: (i) whether the metallodrug remains intact and what species are present at different pH levels, (ii) the stability of the drug in serum and its components, (iii) a proposed mode of action (MOA), such as its interaction with DNA, and (iv) monitoring its binding to human serum albumin (HSA), the most abundant blood protein responsible for transporting many exogenous compounds. Here, Ni(II), Pd(II) and Pt(II) chelates of a tetradentate 1,3-bis(((E-1H-pyrrol-2-yl) methylene) amino) propan-2-ol ligand, H2 L, were intended to be assessed for their stability at varying pH's and in human serum. . However, only PdL and PtL were sufficiently stable and resisted demetallation. Thereafter, we aimed to delineate how the identity of the stable d8 metal ion impacts the compound's affinity for calf thymus DNA (ctDNA). The data acquired indicates that only PdL bound to ctDNA with a $K_a$ 0.114 (± 0.02) × 104 M through intercalation confirmed by UV-LD spectroscopy and in silico molecular dynamic (MD) simulations. Finally, we found that PdL binds to HSA in a 2:1 ratio occupying both major drug binding sites on the protein with a $K_a$ ∼6.56 ×103 M–1 at 37 °C. The thermodynamics reflect enthalpically driven ligand uptake, hinging mainly on London dispersion forces (metal ion dependent), along with general multi-site binding (i.e., 2 PdL per HSA). Although far- and near-UV CD spectroscopy indicated that the optically inactive ligands negligibly perturb the secondary and tertiary structure of HSA, substantial induced CD (ICD) spectra were recorded for the protein-bound ligands and could be simulated by hybrid QM:MM TD-DFT methods. This study highlights a step-by-step guide in going about physical biochemistry and in silico methods to analyse novel drugs.