Peptide-Based Drug Design

58 Winkler and Campbell
A)
wt A C D E ... W Y
PEPTIDE AEPTIDE CEPTIDE DEPTIDE EEPTIDE ... WEPTIDE YEPTIDE
PEPTIDE PAPTIDE PCPTIDE PDPTIDE PEPTIDE ... PWPTIDE PYPTIDE
PEPTIDE PEATIDE PECTIDE PEDTIDE PEETIDE ... PEWTIDE PEYTIDE
PEPTIDE PEPAIDE PEPCIDE PEPDIDE PEPEIDE ... PEPWIDE PEPYIDE
PEPTIDE PEPTADE PEPTCDE PEPTDDE PEPTEDE ... PEPTWDE PEPTYDE
PEPTIDE PEPTIAE PEPTICE PEPTIDE PEPTIEE ... PEPTIWE PEPTIYE
PEPTIDE PEPTIDA PEPTIDC PEPTIDD PEPTIDE ... PEPTIDW PEPTIDY
B)
Fig. 4. Example of a substitution analysis. (A) Sequences resulting from substitution
analysis of a peptide with the sequence PEPTIDE (wild type, wt). (B) Resulting image
of the substitution analysis after incubation with a protein and detection of the bound
protein (fictive).
with the entire pool of possible peptide sequences. Due to the impossibility of
synthesizing all peptides as single sequences (e.g., all 6-mers of the common
20 l-amino acids would be 64,000,000 peptides), during the synthesis coupling
at most positions introduces a mixture of all possible amino acids and building
blocks of interest (amino acids (54), PNA(23), peptoids (55)). As a result one
can synthesize a mixture of all possible peptides on each spot. In practice, for
the first round of synthesis and screening one or two positions have defined
amino acids or building blocks of interest (see Notes 11 and 12). Following
that, each peptide consists of a sequence with several mixed positions and one
or two defined amino acids. The advantage of substituting two mixed positions
at once is the possibility of obtaining stronger signals during the screening. If
one wants to substitute two mixture positions systematically, one has to combine
the exchanges. For instance, if two mixture positions are exchanged with the
common 20 l-amino acids one would obtain 20 × 20 = 400 possibilities. For
a better overview the spots in an array can be arranged in a chessboard pattern
with 20 rows and 20 columns. In each single row synthesize all substitutions
at one mixture position and combine it with the column-wise substitution for
the other mixture position (see Fig. 5). By screening one would obtain signals
on spots with active sequence patterns (see Note 13). These sequence patterns
represent the groups of all possible peptides of distinct length with one or two