Peptide-Based Drug Design

132 Hilpert et al.
different naturally occurring peptides have been discovered so far; about
900 of these are described in a database for eukaryotic host defense
peptides (http://www.bbcm.units.it/∼tossi/pag1.htm). Selected examples of
natural cationic antimicrobial peptides are provided in Table 1. For all these
peptides it was proposed that permeabilization of the cytoplasmic membrane
of the microbe was the cause of the antimicrobial activity. There are many
different models that try to explain the detailed steps of the interaction of
cationic antimicrobial peptides with microbial membranes. The most prominent
ones are barrel-stave, carpet, toroidal pore, and aggregate models (14). Charge
and hydrophobicity of the peptides support the interaction with the microbial
cytoplasmic membrane: the positive charge amino acids interact with the anionic
lipid head and the hydrophobic amino acids with the lipid core (17). Solid-state
NMR and attenuated total reflectance–Fourier transform infrared spectroscopy
(ATR-FTIR) studies showed that peptides bind in a membrane parallel orientation,
interacting only with the outer membrane layer. Only at higher concentrations
(more than needed for killing the microbes) can membrane disruptions or
pore formations be detected (18–20). However, in the last decade it has become
evident that some antimicrobial peptides are not disrupting the cytoplasmic
membrane, but seem to interact with different internal targets, e.g., protein or
RNA synthesis (21).
2. Screening and Optimizing Peptides for Antimicrobial Activity
Biological or chemical libraries can be used to synthesize and screen large
numbers of peptides. Using biological techniques, such as phage (22), bacterial
(23), or ribosome display (24), screening peptide libraries for antimicrobial
activity is applicable and led, for example, to moderately active peptides with
minimal inhibitory concentrations (MIC) against Escherichia coli of 500 �g/mL
for linear 10mer peptides obtained from a phage display (25) or 25 �g/mL from
ribosomal display (26). One main advantage to these approaches is that the
peptides are synthesized by a biological process and, therefore, the cost of the
peptides is low. In addition, repetitive rounds of enrichment may increase the
chance of discovering highly active peptides. On the other hand, using biological
approaches, only the gene-encoded amino acids can be used, limited numbers
of sequences permit only partial information, the biological peptide libraries are
tricky to handle, and fusion peptides rather than isolated molecules are created.
To synthesize large amounts of peptide chemically, several different modified
peptide synthesis procedures have been developed, e.g., tea bag synthesis (27),
digital photolithography (28), pin synthesis (29), andSPOTTM synthesis on
cellulose (30). All these methods can incorporate more than 600 commercially
available building blocks, and it is possible to systematically investigate the