Novel peptidomimetics of the antifungal cyclic peptide Rhodopeptin: design of mimetics utilizing scaffolding methodology

Marine Cyclic Peptides: Antimicrobial Activity and Synthetic Strategies

Oceans are a rich source of structurally unique bioactive compounds from the perspective of potential therapeutic agents. Marine peptides are a particularly interesting group of secondary metabolites because of their chemistry and wide range of biological activities. Among them, cyclic peptides exhibit a broad spectrum of antimicrobial activities, including against bacteria, protozoa, fungi, and viruses. Moreover, there are several examples of marine cyclic peptides revealing interesting antimicrobial activities against numerous drug-resistant bacteria and fungi, making these compounds a very promising resource in the search for novel antimicrobial agents to revert multidrug-resistance. This review summarizes 174 marine cyclic peptides with antibacterial, antifungal, antiparasitic, or antiviral properties. These natural products were categorized according to their sources—sponges, mollusks, crustaceans, crabs, marine bacteria, and fungi—and chemical structure—cyclic peptides and depsipeptides. The antimicrobial activities, including against drug-resistant microorganisms, unusual structural characteristics, and hits more advanced in (pre)clinical studies, are highlighted. Nocathiacins I–III (91–93), unnarmicins A (114) and C (115), sclerotides A (160) and B (161), and plitidepsin (174) can be highlighted considering not only their high antimicrobial potency in vitro, but also for their promising in vivo results. Marine cyclic peptides are also interesting models for molecular modifications and/or total synthesis to obtain more potent compounds, with improved properties and in higher quantity. Solid-phase Fmoc- and Boc-protection chemistry is the major synthetic strategy to obtain marine cyclic peptides with antimicrobial properties, and key examples are presented guiding microbiologist and medicinal chemists to the discovery of new antimicrobial drug candidates from marine sources.

Cyclic Tetrapeptides from Nature and Design: A Review of Synthetic Methodologies, Structure, and Function

Small cyclic peptides possess a wide range of biological properties and unique structures that make them attractive to scientists working in a range of areas from medicinal to materials chemistry. However, cyclic tetrapeptides (CTPs), which are important members of this family, are notoriously difficult to synthesize. Various synthetic methodologies have been developed that enable access to natural product CTPs and their rationally designed synthetic analogues having novel molecular structures. These methodologies include the use of reversible protecting groups such as pseudoprolines that restrict conformational freedom, ring contraction strategies, on-resin cyclization approaches, and optimization of coupling reagents and reaction conditions such as temperature and dilution factors. Several fundamental studies have documented the impacts of amino acid configurations, N-alkylation, and steric bulk on both synthetic success and ensuing conformations. Carefully executed retrosynthetic ring dissection and the unique structural features of the linear precursor sequences that result from the ring dissection are crucial for the success of the cyclization step. Other factors that influence the outcome of the cyclization step include reaction temperature, solvent, reagents used as well as dilution levels. The purpose of this review is to highlight the current state of affairs on naturally occurring and rationally designed cyclic tetrapeptides, including strategies investigated for their syntheses in the literature, the conformations adopted by these molecules, and specific examples of their function. Using selected examples from the literature, an in-depth discussion of the synthetic techniques and reaction parameters applied for the successful syntheses of 12-, 13-, and 14-membered natural product CTPs and their novel analogues are presented, with particular focus on the cyclization step. Selected examples of the three-dimensional structures of cyclic tetrapeptides studied by NMR, and X-ray crystallography are also included.

Chiral β3-isocyanopropionates for multicomponent synthesis of peptides and depsipeptides containing a β-amino acid fragment

An efficient three-step synthesis of a novel family of enantiomerically pure isocyanides derived from β3-isocyanopropionic acids was elaborated. Easily available N-formylated α-amino acids were used as starting materials towards this aim. The 3-step sequence (Arndt-Eistert reaction-Wolff rearrangement-dehydration) resulted in target isonitriles in good yields (up to 97%). As a result a new family of isocyanides bearing a fragment of β3-amino acids with different functional groups (amides, esters and short peptides) was obtained. It was demonstrated that these new isonitriles can be used in the Ugi and Passerini reactions to prepare short peptides and depsipeptides having a β-amino acid fragment incorporated.

Identification of a novel bacteriocin-like protein and structural gene from Rhodococcus erythropolis JCM 2895, using suppression-subtractive hybridization

A novel bacteriocin-like protein and its structural gene (rap) were identified from Rhodococcus erythropolis JCM 2895. The rapA and B genes are located on a 5.4-kb circular plasmid, and were obtained using a modified suppression-subtractive hybridization method. The rapA and B genes were heterologously expressed in Rhodococcus sp. or Escherichia coli, and then characterized. The results indicated that RapA is a small, water-soluble, heat-stable antimicrobial protein, and that RapB is an immunity protein against RapA, estimated to be located on the cell membrane. RapA showed antimicrobial activity particularly against R. erythropolis, and the activity persisted even after SDS-PAGE analysis. For the heterologous expressed RapA protein, N-terminal amino acid sequence was also confirmed. This is the first report of a bacteriocin-like substance obtained from the genus Rhodococcus.

Identification of novel non-peptide CXCR4 antagonists by ligand-based design approach

The design and synthesis of novel non-peptide CXCR4 antagonists is described. The peptide backbone of highly potent cyclic peptide-based CXCR4 antagonists was entirely replaced by an indole framework, which was expected to reproduce the disposition of the key pharmacophores consistent with those of potential bioactive conformations of the original peptides. A structure-activity relationship study on a series of modified indoles identified novel small-molecule antagonists having three pharmacophore functional groups through the appropriate linkers.

Rapid Approach to 3,5-Disubstituted 1,4-Benzodiazepines via the Photo-Fries Rearrangement of Anilides

Different anilides derived from carboxylic acids and substituted anilines have been submitted to the photochemically induced Fries rearrangement giving the corresponding o-amino phenones under conditions that are compatible with the presence of acid-labile groups (such as N-Boc or TBDMSO) on R1 and R3. These compounds, not easily obtained in other ways, are useful building blocks for the preparation of benzocondensated heterocycles. After coupling with N-Boc amino acids and TFA-mediated deprotection, the products cyclized to the corresponding 3,5-disubstituted 1,4-benzodiazepin-2-ones, privileged structures predominantly active in the central nervous system. The same results were obtained by coupling with N-Cbz-protected alpha-amino acids followed by microwave assisted hydrogenolysis. When the Fries rearrangement was carried out on the anilide derived from N-Boc-Ala-OH and the further coupling done with N-Cbz-(OMe)Asp-OH, the formed benzodiazepines could be inserted in a peptide chain for the preparation of conformationally constrained peptidomimetics.

Synthesis of Structurally Defined Scaffolds for Bivalent Ligand Display Based on Glucuronic Acid Anilides. The Degree of Tertiary Amide Isomerism and Folding Depends on the Configuration of a Glycosyl Azide

[structures: see text] Syntheses and structural analyses of bivalent carbohydrates based on anilides of glucuronic acid are described. Secondary anilides predominantly adopted the Z-anti structure; there is also evidence for population of the Z-syn isomer. Bivalent tertiary anilides displayed two signal sets in their NMR spectra, consistent with the presence of (i) a major isomer where both amides have E configurations (EE) and (ii) a minor isomer where one amide is E and the other Z (EZ). Qualitative NOE/ROE spectroscopic studies in solution support the proposal that the anti conformation is preferred for E amides. The crystal structure of one bivalent tertiary anilide showed E-anti and E-syn structural isomers; intramolecular carbohydrate-carbohydrate stacking was observed and mediated by carbonyl-pyranose, azide-azide, and pyranose-aromatic interactions. The EE to EZ isomer ratio, or the degree of folding, for tertiary amides, was greatest for a bivalent compound containing two alpha-glycosyl azide groups; this was enhanced in water, suggesting that hydrophobic interactions are partially but not wholly responsible. Computational methods predicted azide-aromatic (N...H-C interaction) and azide-azide interactions for folded isomers. The close contact of the azide and aromatic protons (N...H-C interaction) was observed upon examination of the close packing in the crystal structure of a related monomer. It is proposed that the alpha-azide group is more optimally aligned, compared to the beta-azide, to facilitate interaction and minimize the surface area of the hydrophobic groups exposed to water, and this leads to the increased folding. The alkylation of bivalent secondary anilides induces a switch from Z to E amide that alters the scaffold orientation. The synthesis of a bivalent mannoside, based on a secondary anilide scaffold, for investigation of mannose-binding receptor cross-linking and lattice formation is described.

Synthesis and Structural Analysis of the Anilides of Glucuronic Acid and Orientation of the Groups on the Carbohydrate Scaffolding

[structures: see text] The synthesis of anilides derived from glucuronic acid is described. Secondary anilides had a Z configuration in the solid state and showed intramolecular and intermolecular hydrogen bonding. However, on the basis of NMR and IR studies, there was generally no evidence for the same hydrogen bonding in solution. Tertiary anilides showed a strong preference for the E configuration on the basis of NOE studies and molecular mechanics calculations. The alkylation of the secondary anilides induces a configurational switch that alters the orientation of the aromatic group with respect to the pyranose, which has relevance for presentation or orientation of pharmacophoric groups on carbohydrate scaffolds.

Synthesis and Binding Affinities of Novel SRIF-Mimicking β-d-Glucosides Satisfying the Requirement for a π-Cloud at C1

[reaction: see text] The synthesis of four bioactive analogues of the somatostatin (SRIF-14) mimetic, beta-d-glucoside (+)-2, in which the C1 indole side chain is replaced with indole surrogates, has been achieved. These congeners, possessing the naphthyl, benzothiophene, benzyl, and benzofuran substituents, were predicted to satisfy the electrostatic requirements of the tryptophan binding pocket of SRIF. Unlike the previously described C4 picolyl and pyrazinyl congeners, these ligands bind the hSST4 receptor.

MexAB-OprM specific efflux pump inhibitors in Pseudomonas aeruginosa. Part 2: achieving activity in vivo through the use of alternative scaffolds

Problems of low solubility, high serum protein binding, and lack of efficacy in vivo in first generation MexAB-OprM specific efflux pump inhibitors were addressed. Through the use of pharmacophore modelling, the key structural elements for pump inhibition were defined. Use of alternative scaffolds upon which the key elements were arrayed gave second generation leads with greatly improved physical properties and activity in the potentiation of antibacterial quinolones (levofloxacin and sitafloxacin) versus Pseudomonas aeruginosa in vivo.

A combinatorial scaffold approach based upon a multicomponent reaction

A combinatorial scaffolding procedure for the synthesis and spatial arrangement of tripartite structures was developed. [reaction: see text]

An enantioselective synthesis of differentially protected erythro-alpha,beta-diamino acids and its application to the synthesis of an analogue of rhodopeptin B5

Methodology for the enantioselective synthesis of differentially protected erythro-alpha,beta-diamino acids from N-tosyloxy beta-lactams is reported. The requisite N-tosyloxy beta-lactams are readily available from simple beta-keto esters. The reported approach is flexible and compatible with a variety of functional groups. The synthetic utility of the method is demonstrated through its application to the preparation of an analogue of the antifungal cyclic peptide rhodopeptin B5.

Structure-based design and synthesis of HIV-1 protease inhibitors employing beta-D-mannopyranoside scaffolds

A preliminary account on the structure-based design, synthesis and evaluation of peptidomimetic inhibitors of HIV-1 protease containing beta-D-mannopyranoside scaffolds is given. The compounds prepared had IC(50) values in the micromolar range. The results provide a platform for the development of more potent carbohydrate-based inhibitors of HIV-1 and other aspartic proteases.

Novel peptidomimetics of the antifungal cyclic peptide Rhodopeptin: design of mimetics utilizing scaffolding methodology

[reaction: see text]. Novel nonpeptide peptidomimetics of the antifungal cyclic peptide Rhodopeptin were designed utilizing hydantoin, benzimidazole, D-glucosamine, quinolone, and benzodiazepine units as scaffolds. The scaffolds were chosen on the basis of their potential to improve the physiochemical properties of the peptidomimetics as well as their ability to bear the requisite Rhodopeptin side-chain moieties with the proper three-dimensional orientation.