Macrocycle synthesis strategy based on step-wise "adding and reacting" three components enables screening of large combinatorial libraries.

Macrocycles provide an attractive modality for drug development, but generating ligands for new targets is hampered by the limited availability of large macrocycle libraries. We have established a solution-phase macrocycle synthesis strategy in which three building blocks are coupled sequentially in efficient alkylation reactions that eliminate the need for product purification. We demonstrate the power of the approach by combinatorially reacting 15 bromoacetamide-activated tripeptides, 42 amines, and 6 bis-electrophile cyclization linkers to generate a 3780-compound library with minimal effort. Screening against thrombin yielded a potent and selective inhibitor (K i = 4.2 ± 0.8 nM) that efficiently blocked blood coagulation in human plasma. Structure-activity relationship and X-ray crystallography analysis revealed that two of the three building blocks acted synergistically and underscored the importance of combinatorial screening in macrocycle development. The three-component library synthesis approach is general and offers a promising avenue to generate macrocycle ligands to other targets.

Cyclization of peptides with two chemical bridges affords large scaffold diversities.

Successful screening campaigns depend on large and structurally diverse collections of compounds. In macrocycle screening, variation of the molecular scaffold is important for structural diversity, but so far it has been challenging to diversify this aspect in large combinatorial libraries. Here, we report the cyclization of peptides with two chemical bridges to provide rapid access to thousands of different macrocyclic scaffolds in libraries that are easy to synthesize, screen and decode. Application of this strategy to phage-encoded libraries allowed for the screening of an unprecedented structural diversity of macrocycles against plasma kallikrein, which is important in the swelling disorder hereditary angioedema. These libraries yielded inhibitors with remarkable binding properties (subnanomolar Ki, >1,000-fold selectivity) despite the small molecular mass (~1,200 Da). An interlaced bridge format characteristic of this strategy provided high proteolytic stability (t1/2 in plasma of >3 days), making double-bridged peptides potentially amenable to topical or oral delivery.

Polar Hinges as Functionalized Conformational Constraints in (Bi)cyclic Peptides.

Two polar hinges for cyclization of peptides have been developed, leading to bicyclic peptides and cyclized peptides with improved solubility and biological activity. Increasingly, we note that a good aqueous solubility of peptides is an absolute prerequisite, not only to allow handling and purification of our target peptides but also being crucial for biological activity characteristics. Compared to earlier hinges, the 1,1',1"-(1,3,5-triazinane-1,3,5-triyl)tris(2-bromoethanone) (TATB) and 2,4,6-tris(bromomethyl)-s-triazine (TBMT), each containing three nitrogen atoms are structurally similar but chemically very different. Both were accessible in a one-step fashion from bromoacetonitrile. TATB and TBMT are very suitable for the preparation of more soluble bicyclic peptides. Azide-modified TATB and TBMT derivatives provide hinges for the preparation of cyclized peptides for incorporation on scaffolds to afford protein mimics.

Self-assembled vesicles of urea-tethered foldamers as hydrophobic drug carriers.

Molecular self-assembly of nonamphiphilic α,ß-hybrid foldamers based on urea-tethered anthranilic acid-proline (Ant-Pro) foldamers is reported. These self-assembled hollow vesicular architectures can take up and release the anticancer hydrophobic drug curcumin.

Novel hybrid nocodazole analogues as tubulin polymerization inhibitors and their antiproliferative activity.

We describe the design, synthesis and SAR profiling of a series of novel combretastatin-nocodazole conjugates as potential anticancer agents. The thiophene ring in the nocodazole moiety was replaced by a substituted phenyl ring from the combretastatin moiety to design novel hybrid analogues. The hydroxyl group at the ortho position in compounds 2, 3 and 4 was used as the conformationally locking tool by anticipated six-membered hydrogen bonding. The bioactivity profiles of all compounds as tubulin polymerization inhibitors and as antiproliferative agents against the A-549 human lung cancer cell line were investigated Compounds 1 and 4 showed µM IC50 values in both assays.

Conformational modulation of peptide secondary structures using ß-aminobenzenesulfonic acid.

This communication describes the influence of ß-aminobenzenesulfonic acid ((S)Ant) on the conformational preferences of hetero foldamers. The designed (Aib-(S)Ant-Aib)n and (Aib-(S)Ant-Pro)n oligomers display a well-defined folded conformation featuring intramolecular mixed hydrogen bonding (7/11) and intra-residual (6/5) H-bonding interactions, respectively.

Carboxamide versus sulfonamide in peptide backbone folding: a case study with a hetero foldamer.

Strikingly dissimilar hydrogen-bonding patterns have been observed for two sets of closely similar hetero foldamers containing carboxamide and sulfonamides at regular intervals. Although both foldamers maintain conformational ordering, the hydrogen-bonding pattern and backbone helical handedness differ diametrically.

Orthanilic acid-promoted reverse turn formation in peptides.

Orthanilic acid (2-aminobenzenesulfonic acid, (S)Ant), an aromatic ß-amino acid, has been shown to be highly useful in inducing a folded conformation in peptides. When incorporated into peptide sequences (Xaa-(S)Ant-Yaa), this rigid aromatic ß-amino acid strongly imparts a reverse-turn conformation to the peptide backbone, featuring robust 11-membered-ring hydrogen-bonding.

Conformational modulation of Ant-Pro oligomers using chirality alteration of proline residues.

Structural modulation of Ant-Pro (anthranilic acid-proline) oligomers has been carried out by chirality alteration of the proline residues. The results suggest that the chirality altered oligomers show well-defined helical conformation featuring nine-membered hydrogen bonding interactions - without compromising conformational rigidity.

Bicyclic amino acid-carbohydrate-conjugates as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres.

This communication describes a general synthetic route to bicyclic amino acid-carbohydrate-conjugates, which would be useful as conformationally restricted hydroxyethylamine (HEA) transition-state isosteres. The synthesis was achieved in 12 steps starting from D-glucose. The striking features of this system are the bicyclic rigid core displaying an α-amino acid side chain and hydroxyethylamine moiety--both of which would be potentially important for receptor interactions, leading to various biomedical responses, as described in the literature. Crystal structure investigation suggested extensive intermolecular hydrogen-bonding interactions in this system, involving the backbone amide and hydroxyl groups.

Sequence-specific unusual (1-->2)-type helical turns in alpha/beta-hybrid peptides.

This article describes novel conformationally ordered alpha/beta-hybrid peptides consisting of repeating l-proline-anthranilic acid building blocks. These oligomers adopt a compact, right-handed helical architecture determined by the intrinsic conformational preferences of the individual amino acid residues. The striking feature of these oligomers is their ability to display an unusual periodic pseudo beta-turn network of nine-membered hydrogen-bonded rings formed in the forward direction of the sequence by 1-->2 amino acid interactions both in solid-state and in solution. Conformational investigations of several of these oligomers by single-crystal X-ray diffraction, solution-state NMR, and ab initio MO theory suggest that the characteristic steric and dihedral angle restraints exerted by proline are essential for stabilizing the unusual pseudo beta-turn network found in these oligomers. Replacing proline by the conformationally flexible analogue alanine (Ala) or by the conformationally more constrained alpha-amino isobutyric acid (Aib) had an adverse effect on the stabilization of this structural architecture. These findings increase the potential to design novel secondary structure elements profiting from the steric and dihedral angle constraints of the amino acid constituents and help to augment the conformational space available for synthetic oligomer design with diverse backbone structures.