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Ψ[CH 2O], 5; thioether or Ψ[CH 2S], 6; tetrazole or Ψ[CN 4], 7; thiazole or Ψ[thz], 8; retroamide or
Ψ[NHCO], 9; thioamide or Ψ[CSNH], 10; and ester or Ψ[CO 2], 11. These amide bond surrogates
provide insight into the conformational and H-bonding properties that may be requisite for peptide
molecular recognition and/or biological activity at receptor targets. Furthermore, such backbone
replacements can impart metabolic stability towards peptidase cleavage relative to the parent peptide.
The discovery of yet other nonhydrolyzable amide bond isosteres has particularly impacted the design of
protease inhibitors, and these include: hydroxymethylene or Ψ[CH(OH)], 12; hydroxyethylene or
Ψ[CH(OH)CH 2] and Ψ[CH 2CH(OH)], 13 and 14, respectively; dihydroxyethylene or
(Ψ[CH(OH)CH(OH)], 15, hydroxyethylamine or Ψ[CH(OH)CH 2N], 16, dihydroxyethylene 17 and C 2symmetric
hydroxymethylene 18. In the specific case of aspartyl protease inhibitor design (see below)
such backbone modifications have been extremely effective, as they may represent transition state
mimics or bioisosteres of the hypothetical tetrahedral intermediate (e.g., Ψ[C(OH) 2NH] for this class of
proteolytic enzymes.
Both peptide backbone and side chain modifications may provide prototypic leads for the design of
secondary structure mimicry [11, 22–31] as typically suggested by the fact that substitution of D-amino
acids, Nα-Me-amino acids, Cα-Me-amino acids, and/or dehydroamino acids within a peptide lead may
induce or stabilize regiospecific β-turn, γ-turn, β-sheet, or α-helix conformations. To date, a variety of
secondary structure mimetics have been designed and incorporated in peptides or peptidomimetics
(Figure 5). The β-turn has been of particular interest to the area of receptor-targeted peptidomimetic
drug discovery. This secondary structural motif exists within a tetrapeptide sequence in which the first
and fourth Cα atoms are < 7 Å separated, and they are further characterized as to occur in a nonhelical
region of the peptide sequence and to possess a ten-membered intramolecular H-bond between the i and
i+4 amino acid residues. On of the initial approaches of significance to the design of β-turn mimetics
was the monocyclic dipeptide-based template 19 [22] which employs side chain to backbone constraint
at the i+1 and i+2 sites. Over the past decade a variety of other monocyclic or bicyclic templates have
been developed as β-turn mimetics, and specific examples include 20 [23], 21 [24], 22 [25], 23 [26] and
24 [27]. Most recently, the monocyclic β-turn mimetic 25 has been described [28] and illustrates the
potential opportunity to design scaffolds that may incorporate each of the side chains (i, i+1, i+2 and i+3
positions), as well as five of the eight NH or C=O functionalities, within the parent tetrapeptide
sequence. tetrapeptide sequence modeled in type I–IV β-turn conformations. Similarly, the
benzodiazepine template 26 has shown [29, 30] utility as a β-turn mimetic scaffold which also may be
multisubstituted to simulate side chain functionalization, particularly at the i and i+3 positions of the
corresponding tetrapeptide sequence modeled in type I–VI β-turn conformations. A recently reported
[31]
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