Design, synthesis and DNA-cleavage of Gly-Gly-His-naphthalene diimide conjugates

DNA Cleaving "Tandem-Array" Metallopeptides Activated With KHSO5: Towards the Development of Multi-Metallated Bioactive Conjugates and Compounds

Amino terminal peptides of the general form Gly-Gly-His have been used to introduce single sites of metal binding and redox activity into a wide range of biomolecules to create bioactive compounds and conjugates capable of substrate oxidation. We report here that Gly-Gly-His-like peptides linked in a tandem fashion can also be generated leading to multi-metal binding arrays. While metal binding by the native Gly-Gly-His motif (typically to Cu²⁺, Ni²⁺, or Co²⁺) requires a terminal peptide amine ligand, previous work has demonstrated that an ornithine (Orn) residue can be substituted for the terminal Gly residue to allow solid-phase peptide synthesis to continue via the side chain N-δ. This strategy thus frees the Orn residue N-α for metal binding and permits placement of a Gly-Gly-His-like metal binding domain at any location within a linear, synthetic peptide chain. As we show here, this strategy also permits the assembly of tandem arrays of metal binding units in linear peptides of the form: NH₂-Gly-Gly-His-[(δ)-Orn-Gly-His]_n-(δ)-Orn-Gly-His-CONH₂ (where n = 0, 1, and 2). Metal binding titrations of these tandem arrays monitored by UV-vis and ESI-MS indicated that they bind Cu²⁺, Ni²⁺, or Co²⁺ at each available metal binding site. Further, it was found that these systems retained their ability to modify DNA oxidatively and to an extent greater than their parent M(II)•Gly-Gly-His. These findings suggest that the tandem array metallopeptides described here may function with increased efficiency as "next generation" appendages in the design of bioactive compounds and conjugates.

Influence of Stereochemistry and Redox Potentials on the Single- and Double-Strand DNA Cleavage Efficiency of Cu(II)· and Ni(II)·Lys-Gly-His-Derived ATCUN Metallopeptides

The DNA cleavage chemistry of a series of metallopeptides based on the amino-terminal Cu and Ni (ATCUN) binding motif of proteins has been studied. Specifically, the impact of the positioning of charged Lys side chains and their stereochemistry on metal reduction potentials and DNA cleavage reactivity have been quantitatively evaluated. Both Cu and Ni metallopeptides show a general increase in reactivity toward DNA with an increasing number of Lys residues, while a corresponding decrease in complex reduction potential reflects the enhanced sigma-donor character of the Lys side chain relative to that of Gly. Placement of Lys at the first position in the tripeptide ligand sequence resulted in a greater increase in DNA cleavage reactivity, relative to placement at the second position, while a switch from an l-Lys to a d-Lys typically resulted in enhanced reactivity, as well as perturbations of reduction potential. In the case of Cu peptides, reactivity was enhanced with both increasing positive charge density on the peptide and stabilization of the Cu3+ state. However, for Ni peptides, while the general trends are the same, the correlation with redox behavior was less pronounced. Most likely these differences in specific trends for the Cu and Ni complexes reflect the distinct coordination preferences for Cu3+/2+ and Ni3+/2+ oxidation states, and the consequent distinct positioning of metal-associated reactive oxygen species, as well as the orientation of the DNA-associated complex. Thus, the amino acid composition and stereochemistry of ATCUN metallopeptides can tune the intrinsic reactivities of these systems (their ability to promote formation and activity of metal-associated ROS) as well as their overall structural features, and both of these aspects appear to influence their reactivity and efficiency of DNA strand scission.

Diastereoselective DNA cleavage recognition by Ni(II) x Gly-Gly-His-derived metallopeptides

Site-selective DNA cleavage by diastereoisomers of Ni(II) x Gly-Gly-His-derived metallopeptides was investigated through high-resolution gel analyses and molecular dynamics simulations. Ni(II) x L-Arg-Gly-His and Ni(II) x D-Arg-Gly-His (and their respective Lys analogues) targeted A/T-rich regions; however, the L-isomers consistently modified a subset of available nucleotides within a given minor groove site, while the D-isomers differed in both their sites of preference and their ability to target individual nucleotides within some sites. In comparison, Ni(II) x L-Pro-Gly-His and Ni(II) x D-Pro-Gly-His were unable to exhibit a similar diastereoselectivity. Simulations of the above systems, along with Ni(II) x Gly-Gly-His, indicated that the stereochemistry of the amino-terminal amino acid produces either an isohelical metallopeptide that associates stably at individual DNA sites (L-Arg or L-Lys) or, with D-Arg and D-Lys, a noncomplementary metallopeptide structure that cannot fully employ its side chain nor amino-terminal amine as positional stabilizing moieties. In contrast, amino-terminal Pro-containing metallopeptides of either stereochemistry, lacking an extended side chain directed toward the minor groove, did not exhibit a similar diastereoselectivity. While the identity and stereochemistry of amino acids located in the amino-terminal peptide position influenced DNA cleavage, metallopeptide diastereoisomers containing L- and D-Arg (or Lys) within the second peptide position did not exhibit diastereoselective DNA cleavage patterns; simulations indicated that a positively charged amino acid in this location alters the interaction of the metallopeptide equatorial plane and the minor groove leading to an interaction similar to Ni(II) x Gly-Gly-His.

Ni(II)·Arg-Gly-His−DNA Interactions: Investigation into the Basis for Minor-Groove Binding and Recognition

A study of the minor-groove recognition of A/T-rich DNA sites by Ni(II).L-Arg-Gly-His and Ni(II).D-Arg-Gly-His was carried out with a fluorescence-based binding assay, one- and two-dimensional (1D and 2D) NMR methodologies, and molecular simulations. Fluorescence displacement titrations revealed that Ni(II).L-Arg-Gly-His binds to A/T-rich sequences better than the D-Arg diastereomer, while NMR investigations revealed that both metallopeptides bind to the minor groove of an AATT core region as evidenced by an intermolecular nuclear Overhauser effect (NOE) between each metallopeptide His imidazole C4 proton and the C2 proton of adenine. Results from molecular dynamics simulations of these systems were consistent with the experimental data and indicated that the His imidazole N-H, the N-terminal peptide amine, and Arg side chains of each metallopeptide are major determinants of minor-groove recognition by functioning as H-bond donors to the O2 of thymine residues or N3 of adenine residues.

Reactivities of Carboxyalkyl-Substituted 1,4,5,8-Naphthalene Diimides in Aqueous Solution

A series of water-soluble 1,4,5,8-naphthalene diimide derivatives has been prepared and their redox and photophysical properties characterized. From laser flash photolysis studies, the triplet excited state of N,N'-bis[2-(N-pyridinium)ethyl]-1,4,5,8-naphthalene diimide (NDI-pyr) was found to undergo oxidative quenching with the electron donors DABCO, tyrosine, and tryptophan as expected from thermodynamics. Interestingly, the reactivities of naphthalene diimides (NDI) possessing alpha- and beta-carboxylic acid substituents (R = -CH2COO-, -C(CH3)2COO-, and -CH2CH2COO-) were strikingly different. In these compounds, the transient produced upon 355 nm excitation did not react with the electron donors. Instead, this transient reacted rapidly (k > 10(8)-10(9) M-1 s-1) with known electron acceptors, benzyl viologen and ferricyanide. The transient spectrum of the carboxyalkyl-substituted naphthalimides observed immediately after the laser pulse was nearly identical to the one-electron-reduced form of 1,4,5,8-naphthalene diimide (produced independently using the bis-pyridinium-substituted naphthaldiimide). From our studies, we conclude that the transient produced upon nanosecond laser flash photolysis of NDI-(CH2)nCOO- is the species produced upon intramolecular electron transfer from the carboxylate moiety to the singlet excited state of NDI. In separate experiments, we verified that the singlet excited state of NDI-pyr does, indeed, react intermolecularly with acetate, alanine, and glycine. The process is further substantiated using thermodynamic driving force calculations. The results offer new prospects of the efficient photochemical production of reactive carbon-centered radicals.

Plasmid relaxation induced by copper metalated diglycine conjugates under heterogeneous reaction conditions

This paper reports synthesis and plasmid modification activities of a new class of insoluble copper-metalated diglycine conjugates, containing aliphatic linkers of varying length. Besides providing significant rate enhancement for model phosphate ester cleavage, these constructs also displayed efficient supercoiled plasmid scission, in the absence of co-oxidants, under heterogeneous catalytic conditions.