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Abstract
This thesis reports the application of dynamic combinatorial chemistry (DCC)
to identify new DNA-binding compounds, and provide insight into the factors
that are important in DNA recognition. The discovery of new binding motifs
and DNA-binding compounds are important to understanding the rules of
DNA recognition, and in the long term has the potential to assist on the design
of new compounds with therapeutic and biotechnological applications.
DCC was used to generate heterocycles functionalised with amidines and
carbohydrates in the presence of different oligonucleotides, in order to identify
functionality that would increase the affinity of the heterocycles for DNA.
Water soluble heterocycle building blocks of quinolines, imidazoles and
naphthalamide were synthesised as thiol and disulfide derivatives. The thiol
substitution on the quinoline ring was varied in these building blocks, and in
the case of 4-thioquinoline, included an electron withdrawing trifluoromethyl
group. The carbohydrates included glucose and aryl derivatives of the
deoxysugar fucose, while the amidines included alkyl, benzyl and aryl groups.
Flexible bisamine and bisthiol derivatives with the potential to form DNA
bisintercalators were also studied.
DCC experiments were conducted using thiol disulfide chemistry in aqueous
methanol using either GSSG/GSH at neutral pH or disulfide exchange at basic
pH, conditions that have not been used previously for studies with nucleic
acids. DCC experiments were conducted to assess the effect of overall charge,
substitution of the quinoline ring, the importance of deoxysugars versus
glucose, aryl and imidazole rings on DNA-binding. Analysis of both the DNA
bound and unbound solutions provided important insights into the features
that are important for DNA recognition and allowed the effect of subtle
structural features on DNA-binding to be identified. Molecular visualisation of
the selected DNA-bound and unbound compounds were used to rationalise
the results and propose minor groove and intercalation binding motifs.
Flexible amino quinoline Q4-Y and guanidine disulfides Q4-A1 and Q4-A2
interacted with DNA. In contrast, neither of the aromatic guanidine disulfides
Q4-A2 and Q4-A3 interacted with DNA, suggesting that the aryl groups may
interfere with positioning of the amidine near the phosphate backbone. In the
case of 7-trifluoromethyl-4-thioquinoline Q2, the thioglucose derivate Q2-S1
was amplified with DNA, and the relative binding affinity Q2-Cys>Q2-A1>Q2-
S1 was determined. This result is consistent with proposed models of
intercalation of the structurally related compound, chloroquine, with DNA. In
contrast, the rigid arylfucose with 2-thio quinoline Q1-S2, was amplified in
preference to the corresponding benzylic disulfide or glucose derivative. The
fucose sugar was shown to be important for DNA-binding, consistent with
DNA minor groove binding. The flexible bisthiol derivatives failed to produce
any DNA-binding compounds, and experiments with naphthalimides were
unsuccessful due to precipitation during the course of the assay.
Biostable mimics of the two lead compounds Q1-S2 and Q2-S1 were studied.
The thioether analogue of Q1-S2 interacted more strongly with DNA compared
to the amide, consistent with minor groove binding. Both 1,4- and 1,5-triazole
analogues of Q2-S1 bound to DNA, with the similar binding profile of the 1,-4-
triazole to the parent disulfide supporting intercalation as the binding mode.