Inhibition of protein-protein interactions: cyclic peptides targeting HIV-1 integrase/LEDGF binding

Over 34 million people worldwide are currently infected with human immunodeficiency virus 1 (HIV-1), which is the etiologic agent of acquired immunodeficiency syndrome (AIDS). This virus is becoming resistant to current drug therapy. Consequently, there is a need for new drugs, which work alone or in combination with existing therapies, to treat HIV-positive patients and limit the spread of the disease. More than 30 drugs are currently approved by the United States Food and Drug Administration (FDA) to treat HIV. These include inhibitors of HIV-1 enzymes reverse transcriptase and protease, as well as entry inhibitors and fusion inhibitors. However, there is currently only one drug on the market that targets HIV integrase. In recent years, new approaches to inhibit HIV replication have been sought. These have included attempts to prevent enzymes in the replication cycle from binding to endogenous cofactors important for enzyme activity. Lens epithelium-derived growth factor (LEDGF) is a cellular protein, essential for efficient integration of viral DNA into the host chromosome, and consequently for successful viral replication. LEDGF functions include aiding nuclear import of the pre-integration complex (PIC) and directing the PIC to active transcription sites on the chromatin. The tetrapeptide sequence Lys364-Ile365-Asp366-Asn367, present in LEDGF, has been shown to be crucial for LEDGF binding to integrase. This thesis describes the design, synthesis and binding analysis of cyclic peptides designed to mimic LEDGF binding to HIV integrase. The peptides incorporate the Lys-Ile-Asp-Asn sequence in conjunction with a turn-inducing scaffold and were designed to block the protein-protein interaction between LEDGF and integrase. Analysis of peptide binding to integrase was achieved using a combination of techniques including HSQC NMR, X-ray crystallography and SPR. The first body of work describes the initial design and synthesis of our cyclic peptides. Disulfide cyclised and head-to-tail cyclised peptides were initially explored. Head-to-tail cyclic peptides, incorporating the LEDGF tetrapeptide sequence and a D-Xaa-L-Pro dipeptide scaffold, showed the ability to readily mimic the conformation of LEDGF. These initial analogues spurred the development of a head-to-tail cyclic peptide library. The head-to-tail cyclic peptides were optimised through investigation of alternate turn-inducing motifs. These included a range of D-Xaa-L-Pro dipeptide scaffolds in addition to a selection of constrained β-amino acids. Additionally, the Ile365 side chain was known to protrude into a hydrophobic pocket on the surface of integrase. This provided an opportunity to increase hydrophobic interactions by substituting alternate residues at this position. Following development of the peptide library, a means to introduce conjugates to the peptides was sought. This involved the development of modified proline amino acids that included an alkyne linker, which allowed conjugation of the peptides using ‘click chemistry’ to couple any azide conjugate of our choice. A conjugate library was efficiently and rapidly developed, incorporating a mixture of carbohydrates, fluorophores and biotin labels to our peptides.