Degree Name

Doctor of Philosophy


Department of Chemistry


An important, yet unexploited potential therapeutic target against the human immunodeficiency virus is the integrase enzyme. To aid the structure-based based design of potential inhibitors, a model of HIV-1 integrase, which was composed of two catalytic core domains, was prepared. This dimeric model could accurately reproduce the crystallographically resolved orientation of the HIV-1 IN inhibitor 5CITEP.

A series of 10 naphthalene sulfonate derivatives, which were based on a previously identified lead Direct-Red 25, were prepared. Although there is a common consensus that the naphthalene sulfonate class of HIV-1 IN inhibitors may bind within a third and as yet unexploited binding site, docking simulations indicated that the derivatives inhibit the enzyme via binding within the active site. The two most active Direct-Red 25 analogues produced possessed IC50 values of 34 μM and 48 μM respectively. It was anticipated that the azo linker in analogues may be metabolically reduced to afford toxic aniline derivatives. Numerous attempts to synthesise starting materials required for the formation of non-azo derivatives were unsuccessful. Seven commercially available naphthalene sulfonate dyes were subjected to biological testing. The IC50 values of these analogues demonstrated that the critical elements required for anti-IN activity were ortho substituted phenol or naphthol functionalities. The anti-IN activity of other molecules containing ortho substituted phenol or naphthol motifs had been previously documented with the majority of these molecules being cytotoxic. For these reasons the development of the Direct-Red 25 analogues was abandoned.

A number of commercially available dyes which lacked the naphthalene sulfonate functionality were subjected to biological testing. Two active compounds, Cresyl-Blue (IC50 10 μM) and Disperse-Orange 30 (IC50 0.5 μM) were identified. Fourteen Disperse- Orange derivatives were synthesised. None of these derivatives possessed potent anti-IN activity. Subtle alterations to the Disperse-Orange 30 structure obliterated anti-IN activity demonstrating that the lead binding interactions were extremely specific. Extensive docking simulations failed to provide definitive insights into key Disperse-Orange features required to elicit anti-IN activity.

The structure-based design of peptidomimetic HIV-IN inhibitors was investigated following a lead from an associated project. A protocol for docking flexible peptidomimetic derivatives was established and utilised to dock 40 analogues into an inhibited and an uninhibited HIV-1 IN model. From analysis of the docking data an active second generation derivative, IC50 16 μM, with significantly reduced molecular mass was produced, and a third generation of inhibitors was designed.



Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong.