Stereochemistry Balances Cell Permeability and Solubility in the Naturally Derived Phepropeptin Cyclic Peptides

Abstract

Cyclic peptide (CP) natural products provide useful model systems for mapping "beyond-Rule-of-5" (bRo5) space. We identified the phepropeptins as natural product CPs with potential cell permeability. Synthesis of the phepropeptins and epimeric analogues revealed much more rapid cellular permeability for the natural stereochemical pattern. Despite being more cell permeable, the natural compounds exhibited similar aqueous solubility as the corresponding epimers, a phenomenon explained by solvent-dependent conformational flexibility among the natural compounds. When analyzing the polarity of the solution structures we found that neither the number of hydrogen bonds nor the total polar surface area accurately represents the solvation energies of the high and low dielectric conformations. This work adds to a growing number of natural CPs whose solvent-dependent conformational behavior allows for a balance between aqueous solubility and cell permeability, highlighting structural flexibility as an important consideration in the design of molecules in bRo5 chemical space.

Keywords: bRo5; cyclic peptide; epimer; phepropeptin.

Figure 1

Structure, physiochemical, and ADME properties of the phepropeptins and their proline–epimeric isomers, the epiphepropeptins. ^aThermodynamic aqueous solubility pH 7.4. ^bAverage of A–B and B–A transport reported in cm/s × 10^–6.

Figure 2

In vitro cell permeability and solubility for the phepropeptins and epimeric analogues.

Figure 3

Temperature shift experiments for 1, 3, 5, and 7 in chloroform. Using the cutoff of −4 ppb/K peaks that are solvent exposed are noted in red, while those that are hidden from solvent are noted in green. Peaks that disappear and reappear are highlighted with a red line Note: only four peaks were observable for compounds 5 and 7, with the fifth amide NH likely hidden under the phenylalanine side chain protons at 7.2–7.3 ppm.

Figure 4

(a) Table of NMR data for the NH protons of compound 3 in CDC_l3; (b) solution structure of 3 as found by molecular dynamics, ROESY, and ³J HNHA; (c) surface showing solvent accessible polarity of the structure in b, with the solvent exposed NH of phenyalanine 2 highlighted with a dashed circle.

Figure 5

(a) Table of NMR data for the NH protons of compound 3 in DMSO; (b) two views of the solution structure of 3 in DMSO; (c) box plots of solvation energy of the 10 best NMR structures in DMSO and chloroform.