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Sequence-selective Recognition of Peptides by Aminopyrazoles

A formidable challenge in the artificial recognition of peptides is the achievement of sequence selectivity. The contributions of Schmuck (Chapter 2.3), Nestler (Chapter 3.1), or Wennemers (Chapter 5.4) in this book demonstrate the power of the combinatorial approach, originally introduced by Still et al. [12]. With our aminopyrazoles available we chose an alternative route, i.e. rational design of modular peptide receptors tailored for recognition of the main classes of amino acids [13]. The concept is that because complexation of a peptide in its ¿-sheet conformation brings all side-chains into a horizontal orientation, their specific recognition can only be achieved by introduction of an additional binding site coming from the top. To this end we connected to the aminopyrazole a U-turn in the form of Kemp's triacid, and attached to its opposite end an interchangeable tip with binding sites for polar, aromatic or basic side amino acid chains. As soon as the aminopyrazole docks on to the peptide's backbone, the additional binding site is lowered from above on to the respective side-chain and forms an additional interaction specific for the class to which this amino acid belongs (Figure 2.4.3).

Monotrifluoroacetylated diaminopyrazole was first reacted with the free Kemp's triacid to produce the imide, followed by N-Boc protection and amide-coupling with a m-substituted aniline derivative. Final Boc-deprotection occurred on the chromatography column leading directly to the new receptor modules. The recognition site X was chosen to be ethyl as a neutral reference, acetyl for polar side-chains, nitro for electron-rich aromatic residues and carboxylate for basic amino acids (Figure 2.4.4).

The structures of 3-6 show a high degree of preorientation, a prerequisite for the highly selective recognition of amino acid side-chains. Intramolecular hydrogen bonding locks the imide and the neighboring aminopyrazole in the same plane, whereas the sub-van der Waals distance between both aromatics keeps them parallel to each other. This was suggested by Monte Carlo conformational searches and proven by NOE measurements [14].

Fig. 2.4.3. Rational design of modular building blocks for the specific recognition of amino acid side-chains in the j-sheet conformation. Right: force-field calculation of the serine recognition event.

No self-association occurs between the receptor molecules of 4 in a concentration range between 10~2 m and 10~3 m, as was proven with a dilution experiment. Hence, all complexation studies were performed with alanine-containing dipep-tides in this concentration range. As usual, the peptide's top face NH proton shows a downfield shift on complexation with the aminopyrazole. In almost every exam-

Fig. 2.4.4. Synthesis of hosts 3-6 from Kemp's triacid and monotrifluoroacetylated diaminpyrazole 1; (a) 110 °C; (b) Boc2O; (c) m-substituted aniline derivative, PyCloP; (d) silica gel. Right: Productive conformation of the receptor modules found in Monte Carlo simulations (MacroModel 7.0).

Fig. 2.4.4. Synthesis of hosts 3-6 from Kemp's triacid and monotrifluoroacetylated diaminpyrazole 1; (a) 110 °C; (b) Boc2O; (c) m-substituted aniline derivative, PyCloP; (d) silica gel. Right: Productive conformation of the receptor modules found in Monte Carlo simulations (MacroModel 7.0).

Tab. 2.4.1. Association constants Ka [m 1] for complex formation between hosts 3-6 and various dipeptides, determined by NMR titrations in CDCI3.

Host

Standard

Selective binding

Special

triflAMPa

Ala-Ala: 50

-

Phe-Ala: 40

Reference 3

Orn-Ala: 280

Ala-Ala: 70

Phe-Ala: <40

XH-binder 4

Ala-Ala: 80

Ser-Ala: 900

Ser-Val: no shifts

Arene-binder 5

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