Approaches to target WD40 proteins and synthesis and evaluation of chemical tools for on-bead screening
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A database consisting of information on human WD40 domains was compiled from literature sources. Data collected included information on function, structure, links to disease and information on molecules known to bind to WD40 domain containing proteins. Curation of the data collected suggested that 21% of WD40 domain containing proteins are linked to cancer, and that only 6% had known small molecule binders. From the database a shortlist of WD40 domain containing proteins that were considered of interest as research targets was produced. It was determined that WD40 Domain Containing Protein 5 (WDR5) was a potential cancer target open to several targeting methods. WDR5 normally plays a structural roll in the formation of a complex containing WDR5, RbBP5, ASH2L, and DPY-30. This complex is required for methylation of H3K4, when MLL1 joins the complex it is able to methylate H3K4me2. It was also recently determined that WDR5 complexes with MYC, another protein with roles in transcriptional control. Both MLL1 and MYC are known to be prominent cancer targets. His-tagged WDR5 was successfully expressed in BL21 (DE3) cell line and purified by a 2 step method. First the protein was purified via His tag - Ni-NTA agarose affinity chromatography, the eluted protein was then further purified via Size Exclusion Chromatography. The first approach targeting WDR5 consisted of a combination of an in-silico approach and a small molecule binder screen. Two in-silico methods, Q-mol and USRCAT, were used to determine small molecules that would potentially bind to WDR5. From this suggested set, 81 compounds were screened against WDR5. Thermal denaturation fluorescence (TDF) was chosen as assay technique. A single compound increased the thermal stability of WDR5 in repeated experiments. This compound, NCI292249, was further characterised in microdialysis experiments where it was determined to have a low affinity of 564 μM to WDR5. In a second approach, in order to target the MYC-WDR5 interaction, a series of truncated peptides derived from the WDR5 binding motif from MYC were produced testing a variation of the One-Bead One-Compound (OBOC) synthesis method derived in this work. These peptide fragments were synthesised using Fmoc solid phase peptide synthesis on TentaGel micobeads experimenting with the SOBOC technique (Scanning OBOC) adapted to produce all possible fragments of a peptide in parallel. The peptide fragments were fluorescently labelled with tetramethylrhodamine and screened against 6XHis-WDR5 isolated on Ni-NTA functionalised agarose beads. The peptide fragments were ranked based on their affinity to the WDR5-coated micro-beads assayed by Confocal Scanning (CONA). The highest affinity peptide found in the CONA screen was further tested for WDR5 binding in solution by fluorescence anisotropy which resulted in an affinity of 96 μM to WDR5. This 7-mer truncate of the MYC peptide was used as input for an in-silico method of peptide optimisation named MorPH. MorPH is a technique developed in the Auer Lab in which amino acids in a peptide are systematically replaced by all commercially available non-natural amino acids in a sequential manner. Each of ~ 1000 modified peptidomimetics are docked in-silico to the target structure. The suggestions from MorPH for the MYC peptide truncate were analysed and the potential replacements discussed in order to plan a possible future synthesis. The MorPH technique was tested experimentally in this thesis in a second example, targeting of Survivin. Survivin is followed as cancer target in the Auer lab and it is found in significantly high concentrations in cancer cell lines and in stem cells. Increased Survivin expression has also been linked to a poor prognosis and reduced patient survivability in the clinic. Several suggestions resulting from the MorPH in-silico screen were synthesised and screened against Survivin. The best-in-series peptide was shown to have a Kd of 2.5 μM, with significantly increased plasma stability. Several chemical tools were developed and characterised for use with on-bead synthesis methods. A contribution was made to a novel synthetic method for isomerically pure rhodamine dyes and their functionalisation (Tetramethylrhodamine was azide-functionalised for use in peptide labelling, based on the azide-alkyne Huisgen cycloaddition reaction). The Auer lab synthesises many of its compounds and libraries using solid phase synthesis techniques. Several compounds exist in literature for the linking of chemicals to a solid-support, all of which are stable to different chemistries and require different conditions to cleave the reaction product from the solid phase. The use of methionine as a linker is described in literature as being highly specific in its cleavage conditions. A series of literature cleavage conditions were tested, the method that offered the highest purity was selected to be improved through further testing. The improved cleavage method was then characterised by cleaving the 20 natural amino acids from the methionine linker. In this experiment it was determined that all amino acids tolerated the new conditions with the exception of methionine, cysteine and tryptophan, which were expected to react poorly to the harsh conditions. This verified that methionine was a suitable alternative to current lab standards for bead linkage.