Current challenges in peptide-based drug discovery.

Abstract

The central event of each signaling step in biology is biomolecular recognition. Notwithstanding the importance of nucleic acids, carbohydrates, or lipids in ligand-target interactions, the effectors of most signal transduction processes are peptides. These can be fragments of proteins or stand-alone hormones, cytokines, toxins, antimicrobials, and many other types of peptides. At this point there is no good reason to classify peptides by the number of amino acid residues. We consider peptides as any polyamide (or even biopolymer with ester, thioester, or otherwise modified backbone) that can be made on a contemporary chemical peptide synthesizer. The limit in size is greater than the arbitrary cutoff of 50 amino acids set up by the US Food and Drug Administration (Carton and Strohl, 2013) for proteins and far exceeds that of biological recognition elements. While target recognition can occur with as low as a few residues (Ertl et al., 1991), even wide binding groves can be bound by 30–40 residue long peptides. Thus, in principle synthetic peptides can be used to regulate almost all receptor responses. The high specificity and low toxicity of peptide drugs derive from their extremely tight binding to their targets. This is due to the large chemical space the side-chain variations of native amino acids cover. Current databases estimate the total number of valid protein-ligand binding sites at 7700 (Khazanov and Carlson, 2013). Calculation based on 17 variable residues (Cys, Met, and Trp are significantly underrepresented in known ligands), show that an 83,000-member tetrapeptide library can be prepared that will essentially cover all unique protein binding regions. As the median length of an active site is 11 amino-acid residues (Khazanov and Carlson, 2013), designed ligands should also be longer. While historically six-residue positional scanning could identify ligands of receptors or epitopes of monoclonal antibodies (Dooley and Houghten, 1993), in our experience receptor agonists are 9–12 residue long (Otvos et al., 2008, 2011a) much like major histocompatibility complex binding peptides (Appella et al., 1995). Antagonists acting on the same receptor binding sites are somewhat shorter (vide infra). If it is assumed that conformational preferences improve the binding kinetics but only rarely thermodynamics, then the tremendous specificity of side-chain combinations of peptides over six residues in length can be even further expanded by using non-natural residues. Hundreds of appropriately protected and activated non-natural amino acid derivatives, ready for incorporation into synthetic peptides, are commercially available and indeed are frequently explored in peptidebased drug design. Importantly, chemical biology has provided both backbone and side-chain combinations for exploring an enormous chemical space and is expected to supply peptide chemists with further building blocks suitable for identifying close-to-ideal agonists and antagonists of any biologically important target. The selectivity of peptide drugs for their target is highlighted by the elevated success rate in clinical trials. According to a biotechnology report (Thomas, 2013), of the 40 approved drugs in 2012, five (12.5%) were peptides compared to 28 small molecule drugs and two monoclonal antibodies (in addition to three enzymes, a cell-based drug and a vaccine). However, in a recent report, the total number of peptide approvals between 2001 and 2012 was 19 (Kaspar and Reichert, 2013). Due to the low number of drug approvals, any particularly successful year can bias the ratios significantly. According to another report, the overall success rate of all drugs entering clinical trials is just 10.4% (Hay et al., 2014). Sixty-five percent of small molecules proceed from Phase I to Phase II in non-oncology applications, a figure identical for peptide/protein drugs. Interestingly peptides/proteins outperform small molecules at the Phase II → Phase III transition stage with 29% for small molecules and 42% for the larger drug candidates. While peptides have traditionally been considered safe in Phase I clinical trials, the public perception is that they are less beneficial in late clinical trials when they are compared side-by-side with different types of treatment modalities. It must be mentioned that peptides are less successful in oncology than in other applications. The cost of large scale peptide production might well-exceed those of small molecule drugs, but if one considers the total cost of the drug development process, the active pharmaceutical ingredient expense will remain under 3% (Otvos, 2014a). In direct opposition to concerns with expensive peptides, the increased clinical success rate, and thus, overall expense/approved drug ratio compared to small molecule chemical entities, make peptide drug development particularly attractive. The biochemical processes that activated receptors directly or indirectly regulate include protein phosphorylation, nucleic acid transcription, ion transport, and a series of enzyme activities (Yan