New Heterocyclic β-Sheet Ligands with Peptidic Recognition Elements

A detailed and comprehensive overview is presented about the design, modeling, and synthesis, as
well as spectroscopic characterization, of a new class of β-sheet ligands. The characteristic feature
of these compounds is a peptidic chimeric structure formed from a specific combination of
aminopyrazolecarboxylic acids with naturally occurring α-amino acids. These hybrid peptides are
designed with the aid of molecular modeling to exist mainly in an extended conformation. All their
hydrogen bond donors and acceptors can be aligned at the bottom face in such a way that a perfect
complementarity toward β-sheets is obtained. Thus the aminopyrazoles impart rigidity and a highly
efficient DAD sequence for the recognition of whole dipeptide fragments, whereas the natural
α-amino acids are designed to mimick recognition sites in proteins, ultimately leading to sequence-selective protein recognition. The synthetic protocols either rely upon solution phase peptide coupling
with a PMB protecting group strategy or solid-phase peptide coupling based on the Fmoc strategy,
using the same protecting group. In solution, a key building block was prepared by catalytic
reduction of a nitropyrazolecarboxylic acid precursor. Subsequently, it was (N-1)-protected with a
PMB group, and elongated by HCTU- or T3P-assisted peptide coupling with dipeptide fragments,
followed by PyClop-assisted coupling with another nitropyrazolecarboxylic acid building block. Final
simultaneous deprotection of all PMB groups with hot TFA completed the high-yield protocol, which
works racemization-free. After preparing a similar key building block with an Fmoc protection at
N-3, we developed a strategy suitable for automated synthesis of larger hybrid ligands on a peptide
synthesizer. Attachment of the first amino acid to a polystyrene resin over the Sieber amide linker
is followed by an iterative sequence consisting of Fmoc deprotection with piperidine and subsequent
coupling with natural α-amino acid via HATU/HOAt. High yields of free hybrid peptides are obtained
after mild acidic cleavage from the resin, followed by deprotection of the PMB groups with hot
TFA. The new aminopyrazole peptide hybrid compounds were characterized by various spectroscopic
measurements including CD spectra, VT, and ROESY NMR experiments. All these accumulated
data indicate the absence of any intramolecular hydrogen bonds and strongly support an extended
conformation in solution, ideal for docking on to solvent-exposed β-sheets in proteins. Initial results
from aggregation tests of pathological proteins with these and related ligands look extremely
promising.