Defense Date

2007

Document Type

Dissertation

Degree Name

Doctor of Philosophy

Department

Chemistry

First Advisor

Dr. Nicholas Farrell

Abstract

Ternary systems comprising DNA/RNA, proteins and one (or more) metal ion are generating increased interest due to its biological relevance. The knowledge gained from the study of these systems could provide important clues regarding the precise mechanism for transcription factors, repair proteins and metal complexes with anti-tumoral/anti-viral activities.The interactions occurring among the components of these ternary systems can be broadly grouped into covalent and non-covalent. The first kind of interactions can lead to the irreversible transformation of the components in the system, while the second is thought to be reversible leading to transient states and fluxionality. Both kinds of interaction are generally present in living systems, complementing the function of each other.Monofunetional Platinum-nucleobase complexes (MPNs) are synthesized via substitution of a chloride ligand by a nucleobase in platinum complexes with trans geometry. MPNs are particularly interesting for the study of ternary systems since they mimic the first step in the formation of a platinum-DNA adduct and their interaction with aminoacids/proteins provide a good first approach for more complex systems.The presence of the nucleobase as a ligand, significantly modifies the biological activity of these complexes by reducing its cytotoxicity and generating a promising anti-viral activity, especially against HIV-1 virus. The specific role of the nucleobase ligand on these complexes as a non-covalent motif, important for protein recognition, was explored in models involving tryptophan/N-acetyl tryptophan and a small protein domain called zinc finger, containing also a tryptophan residue.The coordination of the nucleobase to a metal ion such as Pt(II) or Pd(II) was found to increase its π-stacking interaction towards aromatic residues in proteins, specifically tryptophan. The enhancing effect was found to depend on the nature of the metal ion, nature of nucleobase and size/complexity of the protein model. Furthermore, DFT studies revealed an important change in the energy for the lowest unoccupied molecular orbital (LUMO) in the coordinated nucleobases, which could place this orbital in an favored position to interact with the highest occupied molecular orbital (HOMO) in the tryptophan residue. Results from calculations showed a good correlation with experimental evidence and could indicate an important role for the frontier molecular orbitals (HOMO/LUMO) of the species involved in the π-stacking interaction.This study was extended to a zinc finger domain from an essential protein in HIV-1 virus, i.e. nucleocapsid protein NCp7. Findings showed that the nucleobase ligand in addition to modulate hydrolysis and reaction rates for MPNs can also be responsible for an initial non-covalent recognition towards a specific protein. This initial recognition has been proposed as the first stage in a two-step mechanism of action for these platinum complexes that ultimately can lead to zinc ejection from the zinc finger domain in the viral NCp7. The significance of the data presented show that is possible to modulate the ligand coordination sphere in metal complexes to can result in great differences in terms of biological effects.The novel chemistry derived from DNA adducts with platinum complexes with a trans geometry was also explored in silico. The molecular dynamics of two free DNA 20-mer is compared with the corresponding metallated-adducts, namely monofunctional, 1,2-bifunctional interstrand and 1,3-bifunctional intrastrand. The differences in terms of structure and energy are compared for these systems, in general the monofunctional adduct exhibited the most interesting feature in terms of structural change in the DNA double strand causing the destacking of the metallated nucleobase. Bifunctional adducts exhibited loss of Watson-crick bonds and localized change in sugar puckering. These results showed that important differences can be found for platinated DNA even at short simulation times < 1 ns.

Rights

© The Author

Is Part Of

VCU University Archives

Is Part Of

VCU Theses and Dissertations

Date of Submission

June 2008

Included in

Chemistry Commons

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