All-cis cyclic peptides

Amide bonds -NH-CO- preferentially exist in trans conformations, the cis conformation being thermodynamically unfavored with respect to the trans by about 2 kcal/mol. Yet, the main reason most proteins or peptides cannot be made from cis-peptide plaques only lies in that connecting them into open chains appears to be sterically impracticable. It is possible, however, to build all-cis cyclic peptides in which all cis-plaques are efficiently locked. The present work examines, through quantum calculations, the structural and energetic issues associated with these peculiar arrangements. Systematic exploration at DFT-B3LYP level of the potential-energy surfaces for all-cis cyclopolyglycines cG(n)(c) (n = 2-10,15), and to a lesser extent, for all-cis cyclopolyalanines and all-cis cyclopolyphenylalanines confirms that all these structures are true minima. Optimal ring size occurs around eight peptide units, resulting in planar cG7(c), cG8(c), and cG9(c). In smaller systems, the ring strain is relieved through nonplanar cup-like distortions, particularly in cG6(c). From 10 peptide units and beyond, the ring framework distorts into a saddle-edge shape. These molecules disclose some molecular flexibility, as combinatorial tilting of the plaques may give sets of minima close in energy. Indexes based on isodesmic reactions are used to estimate the energy for joining all-cis or all-trans plaques into cyclic peptides. One of them, the mean plaque-junction energy (MPJE) suggests that within sensible sizes from six peptide units and beyond, all-cis plaque association is almost equally favorable as all-trans one. The frame of radiating cis-amide bonds can be considered as defining a new kind of peptidic material, endowed with specific self-assembling properties.     

Fragmentation of biotinylated cyclic peptides

Electrospray ionization coupled with tandem mass spectrometry (MS/MS) was used to determine the preferred binding site(s) of biotin NHS ester with a series of cyclic peptides with antibiotic properties. The peptides investigated are polymyxins, cyclic peptides produced by Bacillus polymyxa. In spite of the 1:1 stoichiometry used in the labeling reaction, multiple biotin molecules were incorporated into intact polymyxin peptides. Given the amine specificity of the activated biotin and the large number of amino acids with primary amines in the polymyxins, it was not clear by inspection which binding sites were more reactive than others. MS/MS was used to characterize the structure of the biotinylated peptides. MS/MS spectra of cyclic peptides often lead to ambiguous structure determinations due to the potential for multiple ring openings which result in the generation of multiple ion series. The MS/MS spectra of polymyxin peptides are especially difficult to characterize due to the lack of variety in their amino acids; however, the added complexity of the biotin aided the elucidation of the fragmentation pathways. MS/MS spectra of the species with biotin additions were used to rationalize the preferential binding sites of these molecules.     

Synthesis of cyclic endiamino peptides

Several building blocks for endiamino peptides, as well as several cyclic endiamino peptides themselves, and pyrazin-6-one, which embodies the endiamino group, were prepared. The variety of synthesized compounds shows the potential of this synthesis in the preparation of many different groups of compounds.     

Synthesis of reversible cyclic peptides

A novel approach for the synthesis of cyclic peptides that can exist in either linear or cyclized conformations is described. Synthesis of the peptides was achieved via a modified solid phase methodology. The reversible linear/cyclized (i.e., open/closed) states are controlled via the reduction/oxidation of a disulfide bond incorporated into the backbone of the peptide chain.     

Naturally occurring antitubercular cyclic peptides

The antibiotic pipeline has failed to keep pace with the rise of multidrug resistant tuberculosis and extensively drug-resistant tuberculosis pathogens. Naturally occurring peptides provide a rich source of lead compounds for developing novel pharmaceuticals with high selectivity and potency. Given the vast number of naturally-occurring bioactive cyclic peptides identified so far, the following digest highlights several cyclic peptides, discovered in the preceding decade, that exhibit promising activity against Mycobacterium tuberculosis.     

Amphiphilic Bistable Rotaxanes

Two molecular shuttles/switches—a slow one and a fast one—in the shape of amphiphilic, bistable [2]rotaxanes have been synthesized and characterized. Both [2]rotaxanes contain a hydrophobic, tetraarylmethane and a hydrophilic, dendritic stopper. They are comprised of two π‐electron‐rich stations—a monopyrrolotetrathiafulvalene unit and a 1,5‐dioxynaphthalene moiety—which can act as recognition sites for the tetracationic cyclophane, cyclobis(paraquat‐p‐phenylene), to reside around. In addition, a model [2]rotaxane, incorporating only a monopyrrolotetrathiafulvalene unit in the rod section of the amphiphilic dumbbell component and cyclobis(paraquat‐p‐phenylene) as the ring component, has been investigated. The dumbbell‐shaped components were constructed using conventional synthetic methodologies to assemble 1) the hydrophobic, tetraarylmethane stopper and 2) the hydrophilic, dendritic stopper. Next, 3) the hydrophobic stopper was fused to the 1,5‐dioxynaphthalene moiety and/or the monopyrrolotetrathiafulvalene unit by appropriate alkylations, followed by 4) attachment of the hydrophilic stopper, once again by alkylation to give the dumbbell‐shaped compounds. Finally, 5) the [2]rotaxanes were self‐assembled by using the dumbbells as templates for the formation of the encircling cyclobis(paraquat‐p‐phenylene) tetracations. The two [2]rotaxanes differ in their arrangement of the π‐electron‐rich units, one in which the SMe group of the monopyrrolotetrathiafulvalene unit points toward the 1,5‐dioxynaphthalene moiety ( 2 ?4 PF₆) and another in which it points away from the 1,5‐dioxynaphthalene moiety ( 3 ?4 PF₆). This seemingly small difference in the orientation of the monopyrrolotetrathiafulvalene unit leads to profound changes in the physical properties of these rotaxanes. The bistable [2]rotaxanes were both isolated as brown solids. ¹H NMR and UV‐visible spectroscopy, and electrochemical investigations, reveal the presence of both possible translational isomers at ambient temperature. As a consequence of the existence of both possible translational isomers in these bistable [2]rotaxanes, they exhibit a complex electrochemical behavior, which is further complicated by the presence of folded conformations wherein the monopyrrolotetrathiafulvalene unit is involved in an “alongside” interaction with the tetracationic cyclophane. In the molecular shuttle/switch 2 ?4 PF₆ a “knob”, in the shape of the SMe group, is situated between the monopyrrolotetrathiafulvalene and the 1,5‐dioxynaphthalene recognition sites, making it possible to isolate both translational isomers ( 2 ?4 PF₆?GREEN and 2 ?4 PF₆?RED) and to investigate the kinetics of the shuttling of the cyclobis(paraquat‐p‐phenylene) tetracation between the two recognition sites. The shuttling processes, which are accompanied by clearly detectable color changes, can be followed by ¹H NMR and UV‐visible spectroscopy, allowing the rate constants and energies of activation for the translation of the cyclobis(paraquat‐p‐phenylene) tetracations between the two recognition sites to be determined. In the molecular shuttle/switch 3 ?4 PF₆, there is no “knob” situated between the 1,5‐dioxynaphthalene and the monopyrrolotetrathiafulvalene recognition sites, resulting in a considerably faster shuttling of the cyclobis(paraquat‐p‐phenylene) tetracation between these two sites, making the separation of the two possible translational isomers of 3 ?4 PF₆ impractical. However, the shuttling of the cyclobis(paraquat‐p‐phenylene) tetracation can be followed by dynamic ¹H NMR spectroscopy. At low temperatures, the major translational isomer is 3 ?4 PF₆?RED, while 3 ?4 PF₆?GREEN is the major isomer at higher temperature. In the bistable [2]rotaxanes shuttling of the cyclobis(paraquat‐p‐phenylene) tetracations can be driven by electrochemical oxidation of the monopyrrolotetrathiafulvalene unit. In complexes in which one of the two dumbbell stoppers is missing, electrochemical oxidation causes dethreading.     

Improbable Rotaxanes Constructed From Surrogate Malonate Rotaxanes as Encircled Methylene Synthons

We have developed a new approach for the synthesis of “improbable” rotaxanes by using malonate-centered rotaxanes as interlocked surrogate precursors. Here, the desired dumbbell-shaped structure can be assembled from two different, completely separate, portions, with the only residual structure introduced from the malonate surrogate being a methylene group. We have synthesized improbable [2]- and [3]rotaxanes with all-hydrocarbon dumbbell-shaped components to demonstrate the potential structural flexibility and scope of the guest species that can be interlocked when using this approach.     

Synthesis of cyclic peptides by ring-closing metathesis

The synthesis of a series of "amide to amide" cyclized peptides by ring-closing metathesis (RCM) as well as a convenient synthesis for the linear precursors is described. In addition, the influence of the length of the alkene substituents and the influence of the peptide sequence is investigated, leading to a set of general rules to obtain "amide to amide" cyclized peptides by RCM.     

Rotaxanes via Michael addition

[reaction: see text] The application of a template effect to the classical Michael addition of heteronucleophiles to various Michael acceptor systems leads in good yields to a new trapping synthesis of [2]rotaxanes with conjugated functional groups in their axles.     

Understanding lipid recognition by protein-mimicking cyclic peptides

This paper describes our investigation of the structural determinants of a designed cyclic peptide (cLac, cyclic peptide mimicking lactadherin) (Zheng, H.; Wang, F.; Wang, Q.; Gao, J. J. Am. Chem. Soc.2011, 133, 15280–15283) for phosphatidylserine (PS) recognition. A highly efficient strategy that takes advantage of the native chemical ligation (NCL) chemistry has been developed for the synthesis and labeling of cyclic peptides in general. Ala scanning of the cLac peptide revealed a sophisticated model for PS binding, in which the peptide scaffold assembles multiple polar residues to balance the desolvation and electrostatic interactions (salt bridge and hydrogen bonding) to achieve lipid selectivity. The results suggest that cLac effectively mimics the membrane binding mechanism of the parent protein lactadherin.     

N-methylated cyclic pentaalanine peptides as template structures

The N-methylation of cyclic peptides can be used to modify the activity and/or selectivity of biologically active peptides. As N-methylation introduces different flexibility and lipophilicity, it can also improve the bioavailability (the ADMET profile). To search for conformationally constrained cyclic peptides, a library of 30 different N-methylated peptides with the basic sequence cyclo(-D-Ala-L-Ala4-) was synthesized. Based on the NMR analysis, seven of these peptides exhibited single conformations (>98%). The structural features of these peptides were determined by a combination of NMR and distance geometry and then further refined by molecular dynamics simulations in an explicit DMSO solvent box. The structures provided from these efforts can now serve as templates for the rational design of cyclic pentapeptides with a distinct backbone conformation or for "spatial screening" to explore the bioactive conformation of medically important peptide systems.     

Synthesis of cyclic peptides by solid phase methodology

Four carba analogues of oxytocin and a cyclic analogue of melanocyte stimulating hormone were synthesized using solid phase methodology. Purified compounds were shown to be highly biologically active.     

Solid-phase synthesis of homodetic cyclic peptides from Fmoc-MeDbz-resin

Cyclic homodetic peptides are very appealing for medicinal chemistry programs. In addition to the high efficiency and selectivity inherently associated with peptides, a cyclic structure totally formed by amide bonds increases their stability under physiological conditions. Here Fmoc-MeDbz-resin was studied for the preparation of these peptides. Our results demonstrate the usefulness of this strategy for the preparation of cyclic “head-to-side chain” peptides through cyclative cleavage (simultaneous cyclization and release from the resin). In contrast, for the synthesis of the “head-to-tail” counterparts, the cyclization-cleavage should be carried out in the presence of thiophenol.     

beta-turn mimetic: synthesis of cyclic thioenamino peptides

[reaction: see text] Following the discovery of callynormine A, a marine metabolite of a new class, the cyclic endiamino peptides, and the synthesis of compounds of this group, we have now prepared an analogue group of compounds, i.e., cyclic thioenamine peptides. The latter peptides contain the alpha-amino-beta-thioacrylamide functionality, a potential new type of beta-turn mimic. The superiority of the SH group over the NH(2) group in the reaction with enol-tosylates was demonstrated.     

Synthesis of cyclic peptides through hydroxyl side-chain anchoring

A general method was developed for the synthesis of serine or threonine containing cyclic peptides utilizing the β-hydroxyl side-chain of these residues as an anchor point to Wang resin. The peptide chain was assembled by conventional Fmoc/tBu solid-phase chemistry followed by palladium catalyzed exposure of the allyl protected C-terminus group and on-resin cyclization. The cyclic heptapeptide stylostatin 1 was prepared to demonstrate the utility of this technique.     

Synthesis of cyclic proline-containing peptides via ring-closing metathesis

[reaction: see text] Several dienes embedded in di- and tripeptides which incorporate proline have been prepared and subjected to ring-closing metathesis. Bicyclic peptides of well-defined amide geometry and of varying ring sizes were prepared. Several limitations of the cyclization step were revealed.