Design, synthesis, and implementation of handles for solid-phase peptide synthesis

The recent popularity of methods of solid-phase peptide synthesis that use the 9-fluorenylmethyloxycarbonyl (Fmoc) group for {dollar}Nspalpha{dollar}-amino protection has created a need for compatible anchoring linkages and handles directed towards peptide amides and acids. This need has been met from our laboratory by the introduction of the acid-labile 5-(4-(9-fluorenylmethyloxycarbonyl)aminomethyl-3,5-dimethoxyphenoxy)valeric acid (PAL) handle for peptide amides, and the highly acid-sensitive (4-hydroxymethyl-3,5-dimethoxyphenoxy)valeric acid (HAL) handle for peptide acids. This thesis details essential improvements in the synthesis and use of the PAL and HAL handles, and the development of a number of novel related handles for preparation of C-terminal modified peptides.; Tris(alkoxy)benzylamide (PAL) anchoring is well established for the preparation of C-terminal peptide amides, and is commercially available. Reductive amination and variations were explored as novel alternatives to the published synthesis. Thus, one-pot reductive amination of tritylamine with aldehyde precursors to PAL provided tritylated secondary amines, which were readily converted in three further steps to the target PAL compounds. The related hydroxymethyl-based handle, HAL, used to anchor peptide acids, is cleaved with very dilute acid, enabling preparation of protected peptides. The published synthesis of HAL was rigorously optimized, and alternative preparative routes were developed. Additionally, nonstandard coupling approaches were studied where the handle, previously functionalized with an appropriate leaving group, was used to alkylate the C-terminal amino acid residue. A protocol was thus developed to transform the aminomethyl-based PAL into the hydroxymethyl-based HAL.; Lastly, peptides are often desired with C-terminal end-groups other than the more usual amide and acid functionalities, for example, peptide N-alkylamides, aldehydes, alcohols, and cyclic peptides. Reductive aminations with various alkylamines (e.g., methylamine, ethylamine) were used for the preparation of several handles of the general form: 5- (4-(N-Fmoc-N-alkyl)aminomethyl-3,5-dimethoxyphenoxy) valeric acid (Fmoc-(R)PAL-OH), designed to enable preparation of peptide N-alkylamides. In addition, a novel backbone amide linker (BAL) approach was developed, whereby the growing peptide is anchored through a backbone nitrogen, thus readily allowing for modification at the C-terminus. Although a general handle approach, initial efforts on BAL have adapted the chemistry of PAL similarly to the (R)PAL handles above.