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

• The Pd II chelate is stable across pH levels in buffer and, despite serum hydrolysis, has twice the half-life of paclitaxel. • The Pd II ion enables DNA binding, unlike Pt II , highlighting the crucial role of metal ions within the right organic ligand. • The Pd II chelate binds uniquely to HSA at both Sudlow’s sites, near Trp-214, enabling static quenching mechanism. • We extend our novel Gibbs-Helmholtz approach (Fig. 8b), showing T∆S/∆G and ∆H/∆G remain linear across metal ions and ligands. • ICD spectra of achiral metal chelates bound to HSA are rich in data, confirming stability, site binding, and interaction strength. 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.