Peptides and Peptidomimetics - Drug Design and Discovery - page 126

8.3.1.1 Identifying Pharmacophore Elements
Identifying the pharmacophore elements plays a crucial role to develop a potent and optimized
design of peptides. (1) “Truncating” one amino acid at a time from the amino and/or carboxy termini
can lead to a minimum active fragment or sequence responsible for biological activity. (2) “Amino
acid scans” can reveal the binding afi nities and activities of a primary ligand. These scans help to
deduce the importance of the side chain groups required for biological activity that is responsible
for molecular recognition and signal transduction. Amino acid scans in peptide or protein design
include the following. (a) Alanine scans : For a given peptide each amino acid is replaced by an
l-alanine to evaluate the relative signii cance of the side chain group in the binding and biological
activity of the peptide. (b) D -Amino acid scans : Each l-amino acid is replaced by its corresponding
d-amino acid. Advantages of d-amino acid offer the stability of certain reverse (hairpin) turns or
destabilization of -helices, thus providing insights about the chirality of the amino acids in the

interested peptide sequence. “d-alanine scans” offer the dual-advantage of the aforementioned two
scans thus disclosing the crucial role of chirality and side chain group at the same time. (c) Proline
scans : Replacing a given amino acid by proline, or other N -alkylated amino acids provide specii c
insights into the importance of backbone conformations. Many GPCRs recognize

α

-turn structural
type of ligands and a judicious replacement by proline can, for example, induce turns and give rise to
conformers that may be crucial toward design of a ligand. (d) Bulky amino acid scans : Bulky amino
acids and aromatic amino acids can play important roles in peptide ligand binding with receptors/
acceptors because of their size or hydrophobicity. Often bulky amino acids will cause hindrance of
binding of the peptide to the receptor/acceptor binding site, or they can show vast differences
in binding to one receptor subtype over another to enhance selectivity for a particular receptor
subtype. (3) Cyclic scans : As discussed earlier in the global restriction section, side-chain-to-side-
chain, side-chain-to-backbone, C-terminal-to-N-terminal, backbone-to-backbone, and other com-
binations are employed to stabilize or favor segments of the peptide to adopt a global conformation.
Varying types of cyclized moieties and ring sizes are adapted to explore functional and biological
changes. Cyclization of peptides is often used to bias the peptide

β

-turn, and other hairpin
type conformations that may be crucial for the biological activity. (4) Other scans : Amide bond
replacement scans and aza scans (aza peptides adopt

α -helix, β

β -turn conformations) are additional methods

used for the design of peptides or peptidomimetics.

8.3.1.2 Conformation of the Pharmacophore
Most peptides are highly l exible in a conformational manner in aqueous solution, but upon inter-
acting with another biologically relevant molecule they adapt a preferred conformation. Thus,
the reduction of conformational freedom may eventually lead to insights regarding the receptor/
acceptor-bound conformation, and can also result in selective interaction of a ligand with a recep-
tor. Conformationally constrained peptides can provide crucial information about biologically
active conformations. A major goal of using conformational constraints is to determine which pep-
tide conformation is required for binding to the receptor. Conformational constraint of l exible
bioactive peptides can signii cantly improve potency, selectivity, stability, and bioavailability com-
pared with endogenous peptides. The determination of a biologically active conformation of peptide
is a tedious process. However, general strategies have been developed and tested in many laborato-
ries. In many cases, the relevant conformation would be one from the major low energy secondary
structures such as -turns) or extended structures.

Turns are important conformational motifs of peptides and proteins, besides

α -helix, β -sheet, a reverse ( β -turns or γ

-sheets.
Reverse turns contain a diverse group of structures with well-dei ned three-dimensional (3D) orien-
tation of amino acid side chains. Turns represent the most important subgroup. A

α -helix and β

-turn is formed
from four amino acids and is stabilized by a hydrogen bond between the carbonyl group of the i rst
amino acid residue and the amino group of the fourth amino acid residue (Figure 8.3).
The correlation of biological activity with peptide conformation provides useful information
about the best i t to the corresponding i nding region of the receptor. Once the primary structure of

β