New insights into the palladium-mediated selective hydrolysis of the His18–Thr19 peptide bond in cytochrome c: 1H NMR and density functional theory investigation for model compounds

Abstract

The peptides, CH₃CO-Met-His-GlyH, CH₃CO-CysMe-His-GlyH, CH₃CO-CysMe-His-Gly-OEt and its imidazole derivatives, N^τ-benzyl, N^τ-tosyl, N^τ-benzyl-N^π-phenacyl, have been synthesized and used as model compounds for the mechanistic study of the selective cleavage of cytochrome c promoted by Pd(II) complexes. The peptide bond cleavage of these substrates by cis-[Pd(en)(solvent)₂]²⁺ (solvent: D₂O or CD₃OD) was monitored by ¹H NMR spectroscopy. The results showed that the methionine-containing tripeptide differs from the S-methylcysteine-containing tripeptides in the mode of coordination to Pd(II). The former coordinates to Pd(II) through a sulfur atom, an amide nitrogen of methionine and an N^π atom of imidazole, forming a polycyclic chelate, and is resistant to hydrolysis. The latter, as a model compound for cleavage of the His18–Thr19 bond in cytochrome c with Pd(II) complexes, coordinates to Pd(II) via a sulfur atom, an amide nitrogen and a carbonyl oxygen of histidine to form a polycyclic chelate in which the His–Gly peptide bond is cleaved. Kinetic studies showed that protonation of the N^π atom of imidazole in the S-methylcysteine-containing tripeptides is one of the key factors in controlling the cleavage of the His–Gly bond. In order to obtain theoretical guidance on the cleavage reaction, the geometries of a representative N^π protonated tripeptide cation of CH₃CO-CysMe-His-GlyNMe and its Pd(II) complex with and without ancillary water molecules are optimized at the B3LYP density functional theory level using 3-21G, 6-31G(d) and LanL2DZ basis sets. Based on the experimental and theoretical results obtained from the model compounds, a mechanism is proposed for the first time to explain the nature of selective cleavage of the His18–Thr19 bond in cytochrome c promoted by Pd(II) complexes. Coordination of Pd(II) to the carbonyl oxygen of histidine and hydrogen bond formed between the CO and ancillary dimer water weaken and polarize the CO double bond of histidine, giving rise to cleavage of the peptide bond.