Solution Structure Studies of the Cobalt Complex of a Bleomycin Functional Model Bound to d(CGCAATTGCG)₂ by Two-Dimensional Nuclear Magnetic Resonance Methods and Restrained Molecular Dynamics Simulation

Abstract

The interaction between the cobalt(III) complex of a bleomycin functional model (AMPHIS-NET) and the oligonucleotide d(CGCAATTGCG)2 and the structural features of the 1:1 ligand-DNA complex have been determined by high-resolution two-dimensional nuclear magnetic resonance methods and restrained molecular dynamics calculations. The intermolecular nuclear Overhauser effect (NOE) cross-peaks between ligand protons and the DNA minor groove protons suggest that the cobalt(III) complex of AMPHIS-NET binds in the minor groove of DNA at the central AATT site. The NOE connectivities also clearly indicate that the H8 pyridine proton and the H2 imidazole proton in the metal-binding domain interact with the H4' sugar proton of C19 and the H4' sugar proton of A5, respectively, which defines a structure where the metal binding moiety of Co(III).AMPHIS-NET participates in binding to the DNA and extends into the region two base pairs beyond the central AATT site in the minor groove. This binding model is in accord with the consistently observed nondiffusion DNA cleavage in locations two to three residues beyond the end of AT-rich binding sites induced by the corresponding iron(II) complexes of AMPHIS-NET and other AMPHIS-lexitropsin hybrids of the bleomycin functional model compounds.

Sequence-Specific DNA Minor Groove Binders. Design and Synthesis of Netropsin and Distamycin Analogues

“…Attachment of PYML (235,236) and AMPHIS (237)(238)(239)(240)(241) to lexitropsin carriers gave bleomycin-like conjugates such as compounds 65-68 endowed with interesting sequence-specific DNA recognition properties. For bleomycin, the whole molecule spanning from the pyrimidine region to the bithiazole terminus appears to be responsible for specific recognition of DNA (242)(243)(244).…”

Polyamide-Scorpion Cyclam Lexitropsins Selectively Bind AT-Rich DNA Independently of the Nature of the Coordinated Metal

“…While naturally-occurring netropsin has only two pyrroles, the two charged groups at either end of the structure (and analogs[58], [68]) can compensate by giving rise to favourable electrostatic interactions with the helix [16]…”

“…In contrast to previous results with an avidin/biotin couple,[76] it appears that binding of the DNA does not lead to altered metal coordination in the scorpion complex. In a report of a cobalt-bleomycin-lexitropsin compound the metal-free ligand had a binding affinity with its target (4.75×10 4 M −1 ) that was only slightly lower than that for the metalated version (2.26×10 5 M −1 ) and a similar “shielding” of the metal from the DNA backbone by bulky ligand substituents was proposed [58]. In contrast Li et al recently reported a Zn-lexitropsin conjugate based on the bis (2-benzimidazolyl-methyl)amine scaffold, in which the metal is available for coordination, and which exhibited a 3-fold enhancement of affinity for AT-rich oligonucleotides compared to the metal-free ligand [73]…”

“…The results above clearly show that three pyrroles are required for synthetic lexitropsins of this type to bind to AT-rich DNA, a figure that is consistent with the literature for related compounds. [1] , [79] While naturally-occurring netropsin has only two pyrroles, the two charged groups at either end of the structure (and analogs [58] , [68] ) can compensate by giving rise to favourable electrostatic interactions with the helix. [16] …”

“…Bleomycin analogs have also been attached to lexitropsins in conjunction with cobalt. [58] Copper- salen, [59] -phenanthroline, [60] – [61] –peptide [62] and –bipyridine [63] – [64] complexes have been conjugated to lexitropsins, as well as a copper complex consisting of an N -terminal peptide and C -terminal intercalator. [65] Other metal complexes associated with lexitropsins include manganese, [66] vanadium, [67] tungsten, [68] platinum [69] – [71] and the radionuclide technetium-99m.…”