Conformation and Permeability: Cyclic Hexapeptide Diastereomers

Abstract

Conformational ensembles of eight cyclic hexapeptide diastereomers in explicit cyclohexane, chloroform, and water were analyzed by multicanonical molecular dynamics (McMD) simulations. Free-energy landscapes (FELs) for each compound and solvent were obtained from the molecular shapes and principal component analysis at T = 300 K; detailed analysis of the conformational ensembles and flexibility of the FELs revealed that permeable compounds have different structural profiles even for a single stereoisomeric change. The average solvent-accessible surface area (SASA) in cyclohexane showed excellent correlation with the cell permeability, whereas this correlation was weaker in chloroform. The average SASA in water correlated with the aqueous solubility. The average polar surface area did not correlate with cell permeability in these solvents. A possible strategy for designing permeable cyclic peptides from FELs obtained from McMD simulations is proposed.

Figure 1.

Schematic view of conformational space and potential energy. Filled circles indicate initial structures. (a) Conventional MD performed at low temperature would be trapped at a local minimum and could not overcome the large potential energy barrier. High temperature MD samples a wider conformational space and overcomes large barriers; however, the structures are unrealistic. (b) McMD can equally sample a full potential energy space, easily overcome large barriers, and sample any local minima. Therefore, the staring conformation does not affect the results. After a production McMD run, canonical ensembles between low and high temperature states are easily obtained by reweighting.

Figure 2.

Cyclic hexapeptide diastereomers.

Figure 3.

Flat potential energy distribution of compound 8 for virtual states (v₀ to v₇) and reweighted canonical ensembles at T = 300, 700, and 1500 K. (a) in cyclohexane, (b) in chloroform and (c) in water. The exchange among virtual states for trajectories 1 to 3 out of 336 trajectories are shown for (d) in cyclohexane, (e) in chloroform and (f) in water. The following virtual state ranges were used: v₀ = [0.0, 0.2], v₁ = [0.1, 0.3], v₂ = [0.2, 0.4], v₃ = [0.3, 0.5], v₄ = [0.4, 0.6], v₅ = [0.5, 0.7], v₆ = [0.6, 0.8], and v₇ = [0.7, 1.0].

Figure 4.

(a) Backbone hydrogen bond patterns and representative structures. Cage-like pattern (type A and B), β-turn pattern (type C), and collapsed β-turn pattern (types D and E). Structures 2_C1, 3_C1, 7_C1, 2_X1, and 8_C1 correspond to types A, B, C, D, and E, respectively. The subscript indicates the solvent and cluster names, where C1 is the first cluster in chloroform and X1 is the first cluster in cyclohexane. The color fade is defined by the occurrence of H-bonds obtained by the VMD H-bond plug-in for each cluster. (b) Backbone RMSD matrix between the representative structures. Highlights by red shades are larger than 1.00 Å. (c) Example of nIMHB = 0 and disk-like conformation 8 found in water.

Figure 5.

FEL of molecular shape at T = 300 K for each compound and solvent. Each vertex, top left, top right and bottom represents a rod, sphere and disk, respectively. Annotated above for the permeability class defined in Table 1. (a) is in cyclohexane, (b) in chloroform, and (c) in water. The contour lines for PMF = 1.0, 2.0, 3.0, and 4.0 kcal/mol are plotted as white, yellow, sky-blue, and black lines, respectively. (d) Flex_FEL values for each compound and solvent defined by the molecular shape plane.

Figure 6.

FEL by PCA axis PC-1 vs. PC-2 at T = 300 K for each compound and solvent. Annotated above for the permeability class defined in Table 1. (a) is in cyclohexane, (b) in chloroform, and (c) in water. The contour lines for PMF = 1.0, 2.0, 3.0, and 4.0 kcal/mol are plotted as white, yellow, sky-blue, and black lines, respectively. (d) A representative box showing the locations of each pattern. See main text for details. (e) Flex_FEL values for each compound and solvent defined by PC-1 and PC-2 planes.

Figure 7.

Cell permeability vs. average PSA and SASA. (a) and (d) are in cyclohexane, (b) and (e) in chloroform, and (c) and (f) in water. Dashed lines are fitted for each point.

Figure 8.

LogD_dec/w vs. average SASA and PSA. (a) and (d) are in cyclohexane, (b) and (e) in chloroform, and (c) and (f) in water. Dashed lines are fitted for each point.

Figure 9.

Aqueous solubility vs. average SASA in water. Dashed lines are fitted for each point.

Figure 10.

Possible membrane permeation mechanisms. (a) Mechanism for compound 8. Character C, E, and H denote conformation patterns in Figure 6d. (b) Mechanism for compound 7. Note that pattern E could not form in water. (c) Flow chart of proposed strategy for designing permeable cyclic peptides.