Going Out on a Limb: Delineating The Effects of β-Branching, N-Methylation, and Side Chain Size on the Passive Permeability, Solubility, and Flexibility of Sanguinamide A Analogues

Abstract

It is well established that intramolecular hydrogen bonding and N-methylation play important roles in the passive permeability of cyclic peptides, but other structural features have been explored less intensively. Recent studies on the oral bioavailability of the cyclic heptapeptide sanguinamide A have raised the question of whether steric occlusion of polar groups via β-branching is an effective, yet untapped, tool in cyclic peptide permeability optimization. We report the structures of 17 sanguinamide A analogues designed to test the relative contributions of β-branching, N-methylation, and side chain size to passive membrane permeability and aqueous solubility. We demonstrate that β-branching has little effect on permeability compared to the effects of aliphatic carbon count and N-methylation of exposed NH groups. We highlight a new N-methylated analogue of sanguinamide A with a Leu substitution at position 2 that exhibits solvent-dependent flexibility and improved permeability over that of the natural product.

Conformational Restriction of Peptides Using Dithiol Bis-Alkylation

“…One of the largest limitations of peptide drugs is poor membrane permeability, making delivery to intracellular targets difficult (Hill, Shepherd, Diness, & Fairlie, 2014). Chemical modification of peptides, such as isosteric backbone replacement and N-methylation, has substantial promise as a solution to many of these drawbacks (Avan, Hall, & Katritzky, 2014; Bockus et al, 2015; Brust et al, 2013; Chatterjee, Gilon, Hoffman, & Kessler, 2008; Yamagishi et al, 2011). Many modification strategies have been pursued in the effort to transform linear peptides into more natural product-like molecules with high potency, selectivity, cell penetration, and even oral bioavailability (Bock, Gavenonis, & Kritzer, 2013; Clark et al, 2010; Dahan, Tsume, Sun, Miller, & Amidon, 2011; Renukuntla, Vadlapudi, Patel, Boddu, & Mitra, 2013).…”

Targeting intracellular protein–protein interactions with cell-permeable cyclic peptides

“…These methods decrease the solvent-accessible polar surface area, thus reducing the desolvation energy associated with membrane crossing. Using Sanguinamide A (Figure 2) as a model system, Bockus et al noted the importance of conformational flexibility when designing cyclic peptides with favourable balance between solubility and permeability [40]. Kihlberg and co-workers performed NMR- and computer-based conformational analysis of orally administered macrocycle drugs (e.g.…”

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

“…37 The number of solvent-exposed NH groups has been shown to negatively correlate with cell permeability in a number of model systems. 17,23,24,35,36 To compare two matched pairs we conducted temperature coefficient experiments on 1, 3, 5, and 7 in chloroform. For both compounds with natural stereochemistry, 1 and 3, only one or two amide protons showed significant solvent exposure.…”

“…28 We also observed a very large solvent-dependent conformational effect on aqueous solubility among synthetic analogues of the natural product sanguinamide A. 24 Yet although conformational flexibility has been observed in CSA as well as some other natural products, 29 the effect of flexibility per se on physicochemical properties has not been studied in these natural systems.…”

“…A variety of factors have been shown to affect membrane permeability in cyclic peptides, including side chain composition, 16,19,20 N-methylation, 21−23 β-branching, 24,25 and the introduction of nonproteinogenic residues such as peptoid, 26 statine, and vinylogous residues. 27 All of these modifications appear to improve permeability at least in part by increasing lipophilicity.…”