Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization

Peptides have recently regained interest as therapeutic
candidates,
but their development remains confronted with several limitations
including low bioavailability. Backbone head-to-tail cyclization,
i.e., setting a covalent peptide bond linking the last amino acid
with the first one, is one effective strategy of peptide-based drug
design to stabilize the conformation of bioactive peptides while preserving
peptide properties in terms of low toxicity, binding affinity, target
selectivity, and preventing enzymatic degradation. Starting from an
active peptide, it usually requires the design of a linker of a few
amino acids to make it possible to cyclize the peptide, possibly preserving
the conformation of the initial peptide and not affecting its activity.
However, very little is known about the sequence–structure
relationship requirements of designing linkers for peptide cyclization
in a rational manner. Recently, we have shown that large-scale data-mining
of available protein structures can lead to the precise identification
of protein loop conformations, even from remote structural classes.
Here, we transpose this approach to linkers, allowing head-to-tail
peptide cyclization. First we show that given a linker sequence and
the conformation of the linear peptide, it is possible to accurately
predict the cyclized peptide conformation. Second, and more importantly,
we show that it seems possible to elaborate on the information inferred
from protein structures to propose effective candidate linker sequences
constrained by length and amino acid composition, providing the first
framework for the rational design of head-to-tail cyclization linkers.
Finally, we illustrate this for two peptides using a limited set of
amino-acids likely not to interfere with peptide function. For a linear
peptide derived from Nrf2, the peptide cyclized starting from the
experimental structure showed a 26-fold increase in the binding affinity.
For urotensin II, a peptide already cyclized by a disulfide bond that
exerts a broad array of biological activities, we were able, starting
from models of the structure, to design a head-to-tail cyclized peptide,
the first synthesized bicyclic 14-residue long urotensin II analogue,
showing a retention of in vitro activity. Although
preliminary, our results strongly suggest that such an approach has
strong potential for cyclic peptide-based drug design.