Characterizing activation mechanisms and binding preferences of ruthenium metallo-prodrugs by a competitive binding assay.

The activation mechanisms and reactivity of ruthenium metallo-prodrug lead structures were investigated in detail using capillary zone electrophoresis mass spectrometry (CZE-MS) in a time-dependent manner and by exposing to a protein/oligonucleotide mixture. The competitive assays were performed with sodium trans-[RuCl(HInd)] where Hind=indazole (NKP-1339), [(η-p-cymene)RuCl(pta)], where pta=1,3,5-triaza-7-phosphaadamantane (RAPTA-C) and [(η-biphenyl)RuCl(1,2-ethylenediamine)]PF (RM175). Molecular and quantitative information on binding preferences was obtained by coupling CZE to electrospray ionization MS (ESI-MS) and inductively coupled plasma MS (ICP-MS), respectively. A score system is presented that ranks the binding preferences of Ru complexes with nucleotides and demonstrated the following trend of decreasing selectivity after 24h: RM175 (0.89)>RAPTA-C (0.78)>NKP-1339 (0.40). As expected, the organometallic drug candidates RM175 and RAPTA-C underwent a halido/aqua ligand exchange reaction at the metal center and showed distinct reactivity towards the biomolecules. In particular, the protein/DNA binding sites of RAPTA-C in a mixture of protein (ubiquitin) and oligonucleotide (5'-dATTGGCAC-3') were located at single-amino acid and single-nucleotide resolution, respectively. Activated RAPTA-C bound selectively to Met1, adenine and cytosine in this setting, which contrasts with the selectivity of RM175 for guanine. Finally, activation products of NKP-1339 were detected corresponding to Ru(Hind) fragments coordinated to the oligonucleotide, which represents one of the few examples of a directly observed Ru adduct.