During the last decade, it has been a renaissance of the peptides as drugs. This phenomenon has been accompanied by an evolution in the structure of peptides, which are evaluated by the pharmaceutical industry as potential API’s. Thus, in the past, peptide-based drugs were natural sequences with low molecular weight. Right now, the peptides that are being investigated by both the academic and industrial groups show more sophisticated sequences. Thus, they present longer amino acid sequences and with aggregation tendency. Furthermore, in many cases some amino function is capped with a fatty acid chain, which increases its aggregation tendency. Some researchers have been claiming that nowadays it is easier to prepare medium size proteins, with the chemical ligation techniques, than medium size peptides.
In the '80s, the concept of "difficult peptides" was described. This refers to sequences that show inter- or intra-molecular β-sheet interactions significant enough to form aggregates. These structural associations occur during peptide synthesis using both solid-phase and solution-phase methodologies and they are stabilized and mediated by hydrogen bonds, which—depending on the sequence—are favored. These interactions arise on the backbone of the peptide, in particular between the hydrogen amides and the carbonyls. The tendency of peptide chains to aggregate is translated into a list of common behavioral features attributed to "difficult sequences". The main relevant synthetic evidence are the following: repetitive incomplete aminoacylations (<15%) despite re-couplings; accentuated difficulties when resin loading is high or when sterically hindered AAs are present in the sequence; and more importantly, slow or incomplete 9-fluorenylmethoxycarbonyl (Fmoc) removal.
This presentation summarizes the different strategies used in our laboratory for overcoming the inherent difficulties associated to the synthesis of the so-called “difficult peptides”: solvents, auxiliary protecting groups, non-conventional heating systems, use of additives such as salts and detergents, and others.