Cyclic Peptide Natural Products Research Articles

Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products.

Cyclic peptide natural products contain a variety of conserved, nonproteinogenic structural elements such as d-amino acids and amide N-methylation. In addition, many cyclic peptides incorporate γ-amino acids and other elements derived from polyketide synthases. We hypothesized that the position and orientation of these extended backbone elements impact the ADME properties of these hybrid molecules, especially their ability to cross cell membranes and avoid metabolic degradation. Here we report the synthesis of cyclic hexapeptide diastereomers containing γ-amino acids (e.g., statines) and systematically investigate their structure-permeability relationships. These compounds were much more water-soluble and, in many cases, were both more membrane permeable and more stable to liver microsomes than a similar non-statine-containing derivative. Permeability correlated well with the extent of intramolecular hydrogen bonding observed in the solution structures determined in the low-dielectric solvent CDCl3, and one compound showed an oral bioavailability of 21% in rat. Thus, the incorporation of γ-amino acids offers a route to increase backbone diversity and improve ADME properties in cyclic peptide scaffolds.

Serine/threonine ligation for natural cyclic peptide syntheses.

Covering: 2000 to 2014Cyclic peptides are a class of abundant natural products, often exhibiting attractive biological activities. The challenges in the total synthesis of cyclic peptides lie in the preparation of unnatural amino acids if present and the peptide cyclization. Cyclization is an entropy-disfavoured process, with competition between intermolecular and intramolecular reactions. Biological methods can utilize the pre-organized conformation of the side chain unprotected peptide, which brings the reacting termini into proximity, while chemical synthesis requires protecting groups, often large-size and hydrophobic in nature. In this regard, performing peptide cyclization can be an arbitrary and trial-and-error practice. In this highlight, we discuss the application of chemoselective ligation-mediated peptide cyclization in the total synthesis of natural cyclic peptides.

The structure of the cyanobactin domain of unknown function from PatG in the patellamide gene cluster.

Patellamides are members of the cyanobactin family of ribosomally synthesized and post-translationally modified cyclic peptide natural products, many of which, including some patellamides, are biologically active. A detailed mechanistic understanding of the biosynthetic pathway would enable the construction of a biotechnological `toolkit' to make novel analogues of patellamides that are not found in nature. All but two of the protein domains involved in patellamide biosynthesis have been characterized. The two domains of unknown function (DUFs) are homologous to each other and are found at the C-termini of the multi-domain proteins PatA and PatG. The domain sequence is found in all cyanobactin-biosynthetic pathways characterized to date, implying a functional role in cyanobactin biosynthesis. Here, the crystal structure of the PatG DUF domain is reported and its binding interactions with plausible substrates are investigated.

Antibiotic May Sidestep Resistance

Researchers finally know exactly how the promising antibiotic GE23077 (GE) inhibits an essential bacterial enzyme. They predict that GE’s ability to hit this enzyme in its active site could make it difficult for bacteria to develop resistance to the agent. The study also shows how GE might be conjugated with another antibiotic to make a combination drug the scientists believe might be unusually resistance-proof. Some bacterial infections are difficult or impossible to treat effectively because bacteria evolve to eliminate antibiotic efficacy, and too few new antibacterial agents have been developed in recent years. The tendency of GE and GE conjugates to evade resistance has yet to be confirmed, but the study points to one possible way to sidestep antibiotic resistance. In 2001, an Italian screening study found that the cyclic peptide natural product GE expressed antibiotic activity by inhibiting the essential bacterial enzyme RNA polymerase (RNAP). A 2004 patent covering ...

Conformational Diversity in Contryphans from Conus Venom: cis–trans Isomerisation and Aromatic/Proline Interactions in the 23‐Membered Ring of a 7‐Residue Peptide Disulfide Loop

Conformational diversity or "shapeshifting" in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCV(D)LYPWC* (In936) and Conus loroisii, GCP(D)WDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis↔trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds.

Form and Function in Cyclic Peptide Natural Products: A Pharmacokinetic Perspective

The structural complexity of many natural products sets them apart from common synthetic drugs, allowing them to access a biological target space that lies beyond the enzyme active sites and receptors targeted by conventional small molecule drugs. Naturally occurring cyclic peptides, in particular, exhibit a wide variety of unusual and potent biological activities. Many of these compounds penetrate cells by passive diffusion and some, like the clinically important drug cyclosporine A, are orally bioavailable. These natural products tend to have molecular weights and polar group counts that put them outside the norm based on classic predictors of "drug-likeness". Because of their size and complexity, cyclic peptides occupy a chemical "middle space" in drug discovery that may provide useful scaffolds for modulating more challenging biological targets such as protein-protein interactions and allosteric binding sites. However, the relationship between structure and pharmacokinetic (PK) behavior, especially cell permeability and metabolic clearance, in cyclic peptides has not been studied systematically, and the generality of cyclic peptides as orally bioavailable scaffolds remains an open question. This review focuses on cyclic peptide natural products from a "structure-PK" perspective, outlining what we know and don't know about their properties in the hope of uncovering trends that might be useful in the design of novel "rule-breaking" molecules.

Form and Function in Cyclic Peptide Natural Products: A Pharmacokinetic Perspective

Form and Function in Cyclic Peptide Natural Products: A Pharmacokinetic Perspective

Total Synthesis of Cyclocitropside A and Its Conversion to Cyclocitropsides B and C via Asparagine Deamidation

The total syntheses of three closely related cyclic peptide natural products, cyclocitropsides A-C, are described. Cyclocitropside A could be readily converted into cyclocitropsides B and C through an asparagine deamidation pathway, indicating that this is a plausible biosynthetic route to these compounds.

Chemoselective cyclization of unprotected linear peptides by α-ketoacid–hydroxylamine amide-ligation

Cyclic peptides are important synthetic targets due to their constrained conformation, enhanced metabolic stability and improved bioavailability, which combine to make them promising lead compounds for drug candidates. They are typically synthesized by a multi-step sequence of carefully orchestrated protecting group manipulations and cyclization of side-chain protected linear precursors. In the present manuscript we disclose an alternative approach to the synthesis of peptide macrocycles by the α-ketoacid-hydroxylamine (KAHA) ligation. This reaction allows readily prepared linear peptides to be cyclized without reagents or side-chain protecting groups and delivers a native backbone amide bond at the ligation site. The precursors are prepared with Fmoc-based solid phase peptide synthesis using reagents that we have previously disclosed. No post-cyclization manipulations or deprotections other than purification are required. This protocol was applied to five different cyclic peptide natural products of varying ring sizes and side chain functionalities.

Synthesis of the Leu - Trp Component of the Celogentin Family of Cyclic Peptides Through a C - H Activation - Cross-Coupling Strategy

A bioinspired approach to the central leucine(C3)–tryptophan(C6) cross-linked moiety present in the celogentin family of cyclic peptide natural products was achieved. The key transformation was enabled through a palladium-catalyzed C–H activation–cross-coupling of leucine quinoline amide and 6-iodotryptophan derivatives. X-Ray crystallographic analysis of a β-(indol-6-yl)-leucine derivative confirms the stereochemistry of the cross-linked adduct matches that of the natural products. The method enables the preparation of the Leu–Trp adduct as a single stereoisomer from l-leucine and l-tryptophan.

Peptide Fragment Ion Analyser (PFIA): a simple and versatile tool for the interpretation of tandem mass spectrometric data and de novo sequencing of peptides

The software Peptide Fragment Ion Analyser (PFIA) aids in the analysis and interpretation of tandem mass spectrometric data of peptides. The software package has been designed to facilitate the analysis of product ions derived from acyclic and cyclic peptide natural products that possess unusual amino acid residues and are heavily post-translationally modified. The software consists of two programmes: (a) PFIA-I lists the amino acid compositions and their corresponding product ion types for 'a queried m/z value' (z = +1) and (b) PFIA-II displays fragmentation pattern diagram(s) and lists all sequence-specific product ion types for the protonated adduct of 'a queried sequence'. The unique feature of PFIA-II is its ability to handle cyclic peptides. The two programmes used in combination can prove helpful for deriving peak assignments in the de novo sequencing of novel peptides.

High-Throughput Synthesis and Screening of Cyclic Peptide Antibiotics

Cyclic peptides are a rich source of biologically active compounds and are produced in nature by plants, bacteria, fungi, and lower sea animals. A high-throughput methodology has been developed for the combinatorial synthesis, screening, and identification of cyclic peptide natural product analogues with improved biological activities or useful new activities. The methodology was applied to generate a library of 1716 tyrocidine A analogues, which were screened for antibacterial activity in 96-well plates. The identity of the active peptides was determined by partial Edman degradation/mass spectrometry. This has resulted in the discovery of a series of tyrocidine analogues that have significantly improved therapeutic indices compared to the natural product. The availability of tyrocidine analogues with varying antibacterial activities has provided important insights into the structure-function relationship of tyrocidine A, which should help reveal its mechanism of action.

Organoboron Reagents in the Preparation of Functionalized ?-Amino Acids

Over the past decade, major advances in the preparation and utilization of organoboron reagents have been applied to virtually all areas of organic synthesis. The present review collates recent examples of the use of organoboron reagents in the synthesis of α-amino acids and their derivatives. Aryl- and alkenylboronic acids have been used in the asymmetric synthesis of α-amino acids through conjugate addition to unsaturated amino acids and the Petasis three-component coupling reaction. Additionally, α-amino acid derivatives with organoboron functionality on the side-chain have been prepared and used in metal-catalyzed cross-coupling reactions to prepare cross-linked amino acids and complex cyclic peptide natural products.

First Synthesis of Argadin: A Nanomolar Inhibitor of Family‐18 Chitinases

AbstractThe first synthesis of the cyclic peptide natural product, argadin is reported. Use of a solid‐phase approach featuring side‐chain resin attachment through histidine and a novel protecting group strategy allows rapid and efficient access to the argadin backbone, whereupon the unusual 3‐amino‐5‐hydroxy‐2‐pyrrolidone moiety of the peptide is introduced by oxidative cyclisation of a homoserine residue. Argadin is shown to exist as a 5:1 mixture of diastereoisomers at the 5‐hydroxy centre of the pyrrolidone ring, and inhibits a representative family‐18 chitinase (ChiB1 from Aspergillus fumigatus) with Ki = 33 nM. The high‐resolution X‐ray crystal structure of synthetic argadin in complex with the same enzyme shows the binding of a single diastereoisomer as previously observed with the authentic natural product. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)

Preparation of Cyclic Peptide Alkaloids Containing Functionalized Tryptophan Residues

This review covers the synthesis of various cyclic peptide natural products possessing highly functionalized tryptophan residues, focusing on the examples of diazonamide A, the TMC-95 compounds, the celogentin/moroidin family and the complestatin/chloropeptin system. Recent efforts toward the preparation of these modified-tryptophan-containing peptides will be outlined, focusing primarily on the novel methods for the assembly of the highly functionalized indole/tryptophan moieties at the core of these structures.

Chemoenzymatic Approach to Enantiopure Streptogramin B Variants: Characterization of Stereoselective Pristinamycin I Cyclase fromStreptomyces pristinaespiralis

Streptogramin B antibiotics are cyclic peptide natural products produced by Streptomyces species. In combination with the synergistic group A component, they are "last line of defense" antimicrobial agents against multiresistant cocci. The racemization sensitivity of the phenylglycine (Phg(7)) ester is a complex challenge in total chemical synthesis of streptogramin B molecules. To provide fast and easy access to novel streptogramin antibiotics, we introduce a novel chemoenzymatic strategy in which diversity is generated by standard solid phase protocols and stereoselectivity by subsequent enzymatic cyclization. For this approach, we cloned, overproduced, and biochemically characterized the recombinant thioesterase domain SnbDE TE of the pristinamycin I nonribosomal peptide synthetase from Streptomyces pristinaespiralis. SnbDE TE catalyzes regioselective ring closure of linear peptide thioester analogues of pristinamycin I as well as stereoselective cyclization out of complex in situ racemizing substrate mixtures, enabling synthesis of Streptogramin B variants via a dynamic kinetic resolution assay. A remarkable substrate tolerance was detected for the enzymatic cyclization including all the seven positions of the peptide backbone. Interestingly, SnbDE TE was observed to be the first cyclase from a macrolactone forming NRPS which is additionally able to catalyze macrolactamization of peptide thioester substrates. An N-methylated peptide bond between positions 4 and 5 is mandatory for a high substrate turnover. The presented strategy is potent to screen for analogues with improved activity and guides our understanding of structure--activity relationships in the important class of streptogramin antibiotics.

Organic reactions in frozen water: Michael addition of amines and thiols to the dehydroalanine side chain of nocathiacins

Nocathiacins are densely functionalized cyclic thiazolyl peptide natural products with potent in vitro and in vivo antibacterial activity against a variety of gram-positive bacteria, including a number of multiple drug-resistant strains. Attempts to prepare Michael adducts using known conditions resulted in the formation of complex mixture of products. In order to overcome this problem, we developed unique conditions in which Michael addition of amine and thiol nucleophiles to the dehydroalanine moiety of nocathiacins was successfully achieved in frozen water. Under these conditions, the Michael addition was highly chemoselective, very efficient and provided good isolated yields of the desired products.

Kinetic Control of Proline Amide Rotamers: Total Synthesis of trans,trans- and cis,cis-Ceratospongamide

Ceratospongamide is a cyclic peptide natural product that is biosynthesized as a mixture of two proline rotamers. Remarkably, these rotamers do not detectably interconvert at temperatures up to 100 degress C. Here we report high-yielding syntheses of each rotamer and demonstrate that the threonine-derived oxazoline plays a critical role in determining the kinetic distribution of conformational isomers.

Molecular cloning and sequence analysis of the complestatin biosynthetic gene cluster.

Streptomyces lavendulae produces complestatin, a cyclic peptide natural product that antagonizes pharmacologically relevant protein-protein interactions including formation of the C4b,2b complex in the complement cascade and gp120-CD4 binding in the HIV life cycle. Complestatin, a member of the vancomycin group of natural products, consists of an alpha-ketoacyl hexapeptide backbone modified by oxidative phenolic couplings and halogenations. The entire complestatin biosynthetic and regulatory gene cluster spanning ca. 50 kb was cloned and sequenced. It consisted of 16 ORFs, encoding proteins homologous to nonribosomal peptide synthetases, cytochrome P450-related oxidases, ferredoxins, nonheme halogenases, four enzymes involved in 4-hydroxyphenylglycine (Hpg) biosynthesis, transcriptional regulators, and ABC transporters. The nonribosomal peptide synthetase consisted of a priming module, six extending modules, and a terminal thioesterase; their arrangement and domain content was entirely consistent with functions required for the biosynthesis of a heptapeptide or alpha-ketoacyl hexapeptide backbone. Two oxidase genes were proposed to be responsible for the construction of the unique aryl-ether-aryl-aryl linkage on the linear heptapeptide intermediate. Hpg, 3,5-dichloro-Hpg, and 3,5-dichloro-hydroxybenzoylformate are unusual building blocks that repesent five of the seven requisite monomers in the complestatin peptide. Heterologous expression and biochemical analysis of 4-hydroxyphenylglycine transaminon confirmed its role as an aminotransferase responsible for formation of all three precursors. The close similarity but functional divergence between complestatin and chloroeremomycin biosynthetic genes also presents a unique opportunity for the construction of hybrid vancomycin-type antibiotics.

ChemInform Abstract: Conformationally Constrained Biologically Active Peptides: Tentative Identification of the Antimitogenic Bioactive Conformer of the Naturally Occurring Cyclic Tetrapeptides.

AbstractConcerning the objective denoted in the title, the structure‐activity and conformational aspects of a class of cyclic peptide natural products such as (I) are described.