Synthesis of polypyrrolinones on solid support

[reaction: see text] An efficient, three-step iterative synthesis of polypyrrolinones has been achieved on solid support, setting the stage for the construction of a wide variety of libraries based on the pyrrolinone scaffold. Central to the approach is an effective end-game sequence featuring pyrrolinone ring construction with traceless release from the solid support.     

Synthesis of somatostatin mimetics based on the 1-deoxymannojirimycin scaffold

A novel synthesis of somatostatin mimetics based on the 1-deoxymannojirimycin (DMJ) scaffold has been developed. This involved development of a route suitable for the strategic grafting of pharmacophoric tryptophan and lysine side chains to the nitrogen atom of the piperidine ring and to the primary hydroxyl group of DMJ, respectively. The novel peptidomimetics were found to bind with higher affinity to sst4 receptors than to sst5 receptors.     

Novel pyrrolopyrimidine-based α-helix mimetics: cell-permeable inhibitors of protein−protein interactions

There is considerable interest in developing non-peptidic, small-molecule α-helix mimetics to disrupt α-helix-mediated protein?protein interactions. Herein, we report the design of a novel pyrrolopyrimidine-based scaffold for such α-helix mimetics with increased conformational rigidity. We also developed a facile solid-phase synthetic route that is amenable to divergent synthesis of a large library. Using a fluorescence polarization-based assay, we identified cell-permeable, dual MDMX/MDM2 inhibitors, demonstrating that the designed molecules can act as α-helix mimetics.     

Small multivalent architectures mimicking homotrimers of the TNF superfamily member CD40L: delineating the relationship between structure and effector function

Synthetic multivalent ligands, owing to the presence of multiple copies of a recognition motif attached to a central scaffold, can mediate clustering of cell surface receptors and thereby function as effector molecules. This paper dissects the relationship between structure and effector function of synthetic multivalent ligands targeting CD40, a cell surface receptor of the tumor necrosis factor receptor (TNF-R) superfamily. Triggering CD40 signaling in vivo can be used to enhance immunity against intracellular pathogens or tumors. A series of multimeric molecules has been prepared by systematically varying the shape and the valency of the central scaffold, the nature and the length of the linker as well as the sequence of the receptor binding motif. The data reported here (i) suggest that radial distribution of CD40-binding units and C3-symmetry are preferred for optimal binding to CD40 and signaling, (ii) underscore the importance of choosing an appropriate linker to connect the receptor binding motif to the central scaffold, and (iii) show the versatility of planar cyclic alpha- and beta-peptides as templates for the design of CD40L mimetics. In particular, the (Ahx)3-B trimeric scaffold-linker combination equally accommodated binding elements derived from distinct CD40L hot-spot regions including AA" loop and beta-strand E. The use of miniCD40Ls such as those reported here is complementary to other approaches (recombinant ligands, agonistic anti-receptor antibodies) and may find interesting therapeutic applications. Furthermore, the results disclosed in this paper provide the basis for future design of other TNF family member mimetics.     

A modular approach for the synthesis of oligosaccharide mimetics

To allow modular syntheses of oligosaccharide mimetics, the potentially trifunctional glycoside 7 was synthesized and used as a scaffold for the successive attachment of further monosaccharide derivatives to lead to the di-, tri-, and tetrasaccharide mimetics 11, 13, and 16. This synthetic strategy can also be used to prepare oligovalent neoglycoconjugates, e.g., 18, which contains nine mannosyl units. The applied concept implies numerous options for the synthesis of a wide array of structural variations, biolabeling, or solid-phase synthesis as well as combinatorial approaches.     

The new science of protein mimetics

New chemistries have been developed for de novo protein design. Protein mimetics of different structural and functional properties such as synthetic peptide ligases and Dn symmetrical helical bundles have been reported. The Template-Assembled Synthetic Protein (TASP) method (as well as the ßMolecular Kit' approach) has also been utilized to prepare protein-like molecules. Here we report the synthesis of single chain, scaffold (TRIS)- and dendrimer-assembled collagen mimetics composed of the Gly-Nleu-Pro sequence where Nleu denotes N-isobutyl glycine. From the CD spectra and the thermal denaturation studies it can be seen that the collagen mimetics prepared form stable triple helices except the single chain structure. Furthermore, the 162-residue collagen mimetic dendrimer exhibits enhanced triple helical stability compared to the equivalent scaffold-terminated structure by an increase in the melting temperature in both H₂O and 2:1 ethylene glycol/H₂O (4°C and 12°C respectively). The concentration dependence for the melting transition of the collagen mimetic dendrimer was measured from which it was determined that the stabilization effect arises from the intramolecular clustering of the triple helical arrays about the core structure. This ensemble excludes solvent from the interior portion of the array which stabilizes the triple helix cluster.     

Collagen mimetic dendrimers

The synthesis of single-chain, scaffold (TRIS)- and dendrimer-assembled collagen mimetics (both Gly-Pro-Nleu and Gly-Nleu-Pro sequences) is reported. From the CD spectra and the thermal denaturation studies it can be readily seen that mimetics prepared from the Gly-Nleu-Pro sequence form more thermally stable triple helices than the Gly-Pro-Nleu sequence. Furthermore, the 162-residue collagen mimetic dendrimers exhibit enhanced triple helical stability compared to equivalent scaffold-terminated structures by a substantial increase in the melting temperature in H2O and 2:1 EG/H2O. The concentration dependence for the melting transition was measured which determined that the stabilization effect arises from the intramolecular clustering of the triple helical arrays about the core structure. This ensemble excludes solvent from the interior portion of the array which stabilizes the triple helical bundle.     

Improved synthesis of the valuable peptidomimetic intermediate 3-azido-4-hydroxy cyclopentanoic acid

An improved synthesis of 3-azido-4-hydroxy cyclopentanoic acid 2 is presented. This molecule is useful as a synthetic scaffold for β-turn mimetics on solid phase, with the selectivity of the turns being dependent on the diastereomer employed. A high diastereoselectivity in the synthesis of this molecule in solution is reported, which may then be attached to the solid phase for the synthesis of peptidomimetic libraries.     

Glucuronic acid derivatives as branching units for the synthesis of glycopeptide mimetics

Natural glycopeptides and glycoproteins exhibit a large structural diversity, which can be mimicked by synthetic glycopeptide derivatives to assist the investigation of biological functions and structure-activity relationships. Here, dendronized saccharides were synthesized to provide glycosyl amino acids, equipped with a branching element for the preparation of branched glycopeptide mimetics. An optimized Staudinger-type reaction served as key reaction en route to the complex glycopeptide 14, in which three mannose moieties were connected to the branched glucuronyl scaffold.     

α‐O‐Linked Glycopeptide Mimetics: Synthesis,Conformation Analysis,and Interactions with Viscumin,a Galactoside‐Binding Model Lectin

Efficient cycloaddition of a silylidene‐protected galactal with a suitable heterodiene yielded the basis for a facile diastereoselective route to a glycopeptide‐mimetic scaffold. Its carbohydrate part was further extended by β1–3‐linked galactosylation. The pyranose rings retain their ⁴C₁ chair conformation, as shown by molecular modeling and NMR spectroscopy, and the typical exo‐anomeric geometry was observed for the disaccharide. The expected bioactivity was ascertained by saturation‐transfer‐difference NMR spectroscopy by using the galactoside‐specific plant toxin viscumin as a model lectin. The experimental part was complemented by molecular docking. The described synthetic route and the strategic combination of computational and experimental techniques to reveal conformational properties and bioactivity establish the prepared α‐O‐linked glycopeptide mimetics as promising candidates for further exploitation of this scaffold to give O‐glycans for lectin blocking and vaccination.     

Synthesis and Solution Conformation of β‐Hairpin Mimetics Utilizing a Template Derived from (2S,3R,4R)‐Diaminoproline

A novel template was synthesized for stabilizing β‐hairpin conformations in cyclic peptide mimetics. The template is a diketopiperazine derived formally from L ‐aspartic acid and (2S,3R,4R)‐diaminoproline, the latter being available by an efficient synthetic route from vitamin C. The template was incorporated by solid‐phase peptide synthesis into a cyclic loop mimetic containing the sequence (‐Ala‐Asn‐Pro‐Asn‐Ala‐Ala‐template‐). This mimetic was shown by NMR to adopt a stable β‐hairpin conformation in (D₆)DMSO solution. The template may prove to be generally useful for creating small‐molecule mimetics of hairpin loops on proteins of diverse function.     

An optimised small-molecule stabiliser of the 14-3-3-PMA2 protein-protein interaction

Modulation of protein-protein interactions (PPIs) is a highly demanding, but also a very promising approach in chemical biology and targeted drug discovery. In contrast to inhibiting PPIs with small, chemically tractable molecules, stabilisation of these interactions can only be achieved with complex natural products, like rapamycin, FK506, taxol, forskolin, brefeldin and fusicoccin. Fusicoccin stabilises the activatory complex of the plant H(+)-ATPase PMA2 and 14-3-3 proteins. Recently, we have shown that the stabilising effect of fusicoccin could be mimicked by a trisubstituted pyrrolinone (pyrrolidone1, 1). Here, we report the synthesis, functional activity and crystal structure of derivatives of 1 that stabilise the 14-3-3-PMA2 complex. With a limited compound collection three modifications that are important for activity enhancement could be determined: 1) conversion of the pyrrolinone scaffold into a pyrazole, 2) introduction of a tetrazole moiety to the phenyl ring that contacts PMA2, and 3) addition of a bromine to the phenyl ring that exclusively contacts the 14-3-3 protein. The crystal structure of a pyrazole derivative of 1 in complex with 14-3-3 and PMA2 revealed that the more rigid core of this molecule positions the stabiliser deeper into the rim of the interface, enlarging especially the contact surface to PMA2. Combination of the aforementioned features gave rise to a molecule (37) that displays a threefold increase in stabilising the 14-3-3-PMA2 complex over 1. Compound 37 and the other active derivatives show no effect on two other important 14-3-3 protein-protein interactions, that is, with CRaf and p53. This is the first study that describes the successful optimisation of a PPI stabiliser identified by screening.     

Simple mimetics of a nuclear localization signal (NLS)

[reaction: see text] Molecular modeling was used to design mimetics of the HIV-1 matrix protein nuclear localization signal (NLS) in which a scaffold of two resorcinol units joined by a diamide linker presents 3-aminopropyl ethers in place of lysine side chains. Prospective mimetics with linkers of 6, 8, 10, or 12 atoms were synthesized and compared in a competition assay for binding to the nuclear import receptor subunit karyopherin alpha, showing the 10-atom linker to be best and shorter ones ineffective.     

A practical synthesis of (1S,4S)-2,5-diazabicyclo[2.2.1]heptane

The rigid piperazine homologue 2,5-diazabicyclo[2.2.1]heptane (DBH) finds extensive application in medicinal chemistry and pharmaceutical research, but access to this scaffold is non-trivial. This letter details a concise synthetic sequence that gives ready access to DBH on gram scale. The route features a Staudinger reduction of an azide to facilitate a transannular cyclisation     

Design, synthesis, and bioactivity of the first nonsteroidal mimetics of brassinolide

Ten novel compounds, each consisting of two subunits and a linker, were designed with the aid of molecular modeling to resemble the natural steroidal phytohormone brassinolide. The mimetics were synthesized and subjected to the rice leaf lamina inclination bioassay to test for brassinosteroid activity. Most of the mimetics displayed very weak or no bioactivity, but two were strongly active when coapplied with the auxin indole-3-acetic acid (IAA), which synergizes the activity of brassinosteroids. Thus, 1-(4,6 alpha,7 alpha-trihydroxy-5,6,7,8-tetrahydronaphthyl)-2-(6 alpha',7 alpha'-dihydroxy-5',6',7',8'-tetrahydronaphthyl)ethyne (4) and (E)-1,2-bis[trans-(4a alpha,8a beta)-4-oxo-6 alpha,7 alpha-dihydroxy-4a,5,6,7,8,8a-hexahydro-(3H)-naphthyl]ethylene (11) showed exceptional activity at doses as low as 0.01 ng and 0.001 ng/plant, respectively. These compounds are the first biologically active nonsteroidal brassinolide mimetics.     

The first synthetic receptor for the RGD sequence

[structure: see text] The combination of an optimized arginine receptor unit with a semirigid linker carrying a strategically placed primary ammonium group leads to the first synthetic RGD receptor. It binds to the free RGD peptide as well as to cyclo(RGDfV) in water with association constants around 1000 M(-1). RGD mimetics such as benzamidine 6 are not recognized, rendering the new host a prototype of a new class of receptors selective for the true RGD sequence in peptides.     

Circular DNA and DNA/RNA hybrid molecules as scaffolds for ricin inhibitor design

Ricin Toxin A-chain (RTA) catalyzes the hydrolytic depurination of A4324, the first adenosine of the GAGA tetra-loop portion of 28S eukaryotic ribosomal RNA. Truncated stem-loop versions of the 28S rRNA are RTA substrates. Here, we investigate circular DNA and DNA/RNA hybrid GAGA sequence oligonucleotides as minimal substrates and inhibitor scaffolds for RTA catalysis. Closing the 5'- and 3'-ends of a d(GAGA) tetraloop creates a substrate with 92-fold more activity with RTA (kcat/Km) than that for the d(GAGA) linear form. Circular substrates have catalytic rates (kcat) comparable to and exceeding those of RNA and DNA stem-loop substrates, respectively. RTA inhibition into the nanomolar range has been achieved by introducing an N-benzyl-hydroxypyrrolidine (N-Bn) transition state analogue at the RTA depurination site in a circular GAGA motif. The RNA/DNA hybrid oligonucleotide cyclic GdAGA provides a new scaffold for RTA inhibitor design, and cyclic G(N-Bn)GA is the smallest tight-binding RTA inhibitor (Ki = 70 nM). The design of such molecules that lack the base-paired stem-loop architecture opens new chemical synthetic approaches to RTA inhibition.     

An Optimised Small‐Molecule Stabiliser of the 14‐3‐3–PMA2 Protein–Protein Interaction

Modulation of protein–protein interactions (PPIs) is a highly demanding, but also a very promising approach in chemical biology and targeted drug discovery. In contrast to inhibiting PPIs with small, chemically tractable molecules, stabilisation of these interactions can only be achieved with complex natural products, like rapamycin, FK506, taxol, forskolin, brefeldin and fusicoccin. Fusicoccin stabilises the activatory complex of the plant H⁺‐ATPase PMA2 and 14‐3‐3 proteins. Recently, we have shown that the stabilising effect of fusicoccin could be mimicked by a trisubstituted pyrrolinone (pyrrolidone1, 1 ). Here, we report the synthesis, functional activity and crystal structure of derivatives of 1 that stabilise the 14‐3‐3–PMA2 complex. With a limited compound collection three modifications that are important for activity enhancement could be determined: 1) conversion of the pyrrolinone scaffold into a pyrazole, 2) introduction of a tetrazole moiety to the phenyl ring that contacts PMA2, and 3) addition of a bromine to the phenyl ring that exclusively contacts the 14‐3‐3 protein. The crystal structure of a pyrazole derivative of 1 in complex with 14‐3‐3 and PMA2 revealed that the more rigid core of this molecule positions the stabiliser deeper into the rim of the interface, enlarging especially the contact surface to PMA2. Combination of the aforementioned features gave rise to a molecule ( 37 ) that displays a threefold increase in stabilising the 14‐3‐3–PMA2 complex over 1 . Compound 37 and the other active derivatives show no effect on two other important 14‐3‐3 protein–protein interactions, that is, with CRaf and p53. This is the first study that describes the successful optimisation of a PPI stabiliser identified by screening.     

Bispidine as a β-strand nucleator: from a β-arch to self-assembled cages and vesicles

The development of synthetic scaffolds that nucleate well-folded secondary structures is highly challenging. Herein, we designed and synthesized a series of core-modified peptides (F1, F2, F3, and F4) that fold into β-strand structures. These bispidine-scaffolded peptides were studied by CD, IR, NMR, single crystal XRD, and Molecular Dynamics (MD) simulations to investigate their conformational preferences. Solid-state and solution studies revealed that bispidine is a versatile scaffold that could be placed either at the terminal or at the middle of the peptide strand for nucleating the β-strand structure. Scaffolds that nucleate an isolated β-strand conformation are rare. Bispidine placed at the C-terminus of the peptide chain could nucleate a β-strand conformation, while bispidine placed at the middle resulted in a β-arch conformation. This nucleation activity stems from the ability to restrict the psi torsion angle (ψ) through intramolecular C5 hydrogen bonding between the equatorial hydrogen(s) of bispidine and the carbonyl oxygen(s) of the amino acid close to the scaffold. Furthermore, the bispidine peptidomimetic with a super secondary structure, namely β-arch, assembled into single-hole submicron cages and spherical vesicles as evident from microscopic studies. The design logic defined here will be a significant strategy for the development of β-strand mimetics and super secondary structures.

Bispidine is a versatile scaffold that could be placed either at the terminal or at the middle of the peptide strand for nucleating β-strand structures. These β-strand mimetics self-assemble to single hole submicron cages and vesicles.