Visualized and Quantitative Conformational Analysis of Peptidomimetics

Abstract

Protein-protein interactions (PPIs) are fundamentally important and challenging drug targets. Peptidomimetic molecules of various types have been developed to modulate PPIs. A particularly promising drug discovery strategy, structural peptidomimetics, was designed based on special mimicking of side-chain C_α-C_β bonds. It is simple and versatile. Nevertheless, no quantitative method has been established to evaluate its similarity to a target peptide motif. We developed two methods that enable visual, comprehensive, and quantitative analysis of peptidomimetics: peptide conformation distribution (PCD) plot and peptidomimetic analysis (PMA) map. These methods specifically examine multiple side-chain C_α-C_β bonds of a peptide fragment motif and their corresponding bonds (pseudo-C_α-C_β bonds) in a mimetic molecule instead of φ and ψ angles of a single amino acid in the traditional Ramachandran plot. The PCD plot is an alignment-free method, whereas the PMA map is an alignment-based method providing distinctive and complementary analysis. Results obtained from analysis using these two methods indicate our multifacial α-helix mimetic scaffold 12 as an excellent peptidomimetic that can precisely mimic the spatial positioning of side-chain functional groups of α-helix. These methods are useful for visualized and quantified evaluation of peptidomimetics and for the rational design of new mimetic scaffolds.

Figure 1

“Pseudo-C_α–C_β bond” and pharmacophore mimetics. (a) Pseudo-C_α–C_β bond (stick in red) is a bond of a mimetic molecule, which corresponds exactly to the side-chain C_α–C_β bond (ball-and-stick in red) of a peptide fragment (ribbon in pink). In pharmacophore mimetics, a side-chain pharmacophore is connected to a linkage (stick in blue) other than a pseudo-C_α–C_β bond. (b) Example of 5a. The i side chain is pharmacophore mimetics, whereas the i+4 and i+7 side chains are pseudo-C_α–C_β bonds.

Figure 2

Lists of structural peptidomimetics (a) single-facial mimetics and (b) double-facial and multifacial mimetics. Chemical structures, mimetic amino acids/motifs, target proteins and activities, the number of rotatable bonds involved in the scaffolds, and references are shown. Substituents highlighted in gray are “pseudo-C_α–C_β bonds”, which are designed to project side-chain C_α–C_β bonds. The pseudo-C_α–C_β bonds in these structural mimetics were assigned according to the description in the references. The i substituent of 5 and the i + 4 substituent of 6 are not pseudo-C_α–C_β bonds but pharmacophore mimetics (Figure 1 and its legend present the details). The rotational bonds are counted in the scaffolds inside the pseudo-C_α–C_β bonds.

Figure 3

(a) Calculation workflow for PCD-plot[0123]. (b) Calculation workflow on the analysis of mimetic compounds: conformation generation, projection to the PCD plot, and illustration of the PMA map.

Figure 4

PCD-plot[0123]: principal component analysis map of conformational distribution on the peptide fragments extracted from nonredundant 118 proteins (Method 1). The continuous “i, i+1, i+2, and i+3” side chains were used for analysis. Each dot represents a peptide fragment. Helix (red), Turn (orange), Sheet (green), Others (gray), and the standard α-helix (blue triangle). Numbers in parentheses are numbers of shown data.

Figure 5

PCD-plot[0123] with the projection of multifacial peptidomimetic scaffolds 10 (a), 11 (b), and 12 (c). Each conformer is represented by a black dot. The Turn layer (orange) is sent to the back for clarification. The Other notation is the same as that shown in Figure 3.

Figure 6

(a–d) PCD-plot[047]: PCA analysis using the i, i+4, and i+7 side chains and projection of single-facial mimetic compounds 1–4. (e–g) PCD-plot[034]: PCA analysis using i, i+3, and i+4 side chains and projection of double-facial mimetic compounds 7–9. Notations are the same as those used in Figure 3.

Figure 7

(a) Helix mimetics analyzer (HMA) map. The x-axis and y-axis, respectively, denote the average of position difference (APD, Å) and the average of vector difference (AVD). Error bars show the standard deviation. (b) Detailed helix mimetic analysis of 12 for each pseudo-C_α–C_β bond. (c) Orientational distribution of the i pseudo-C_α–C_β bond of 12. (d) Superposed views with α-helix and mimetic compounds. Yellow and red denote each conformer and C_α–C_β bond, respectively. Chemical structures, all conformers (left), and a representative conformer for clarification (right).