A Dicopper(II)-Based Carbonic Anhydrase Model-Quantum-Chemical Evaluation of the Mechanistic Pathway

The cyanobacterium Prochloron didemni, an obligate symbiont of different species of colonial ascidians, occurring in the Pacific and Indian Oceans, produces a variety of cyclic peptides. These patellamide-type macrocycles lead to relatively stable dicopper(II) complexes that are extremely efficient carbonic anhydrase mimics, the most active model systems known so far. Importantly, it recently was shown that copper(II) is coordinated to patellamide derivatives in Prochloron cells. An interesting question therefore is, whether the biological function of patellamide-type macrocycles is related to the catalytic activity in CO2 hydration or its reverse. Here, we present a computational study to evaluate the energetics of the catalytic cycle in search of a possible answer to these questions and compare the computed energy barriers with the experimental kinetic data. It emerges that release of the bridging carbonate is a critical step and that the catalysis product inhibits catalysis at pH values above approx. 7. Therefore, carbonate transport rather than CO2 hydrolysis is proposed as the biological function of copper(II)-patellamide complexes in the Prochloron-Ascidian symbiosis.

Synthetic Receptors Based on Abiotic Cyclo(pseudo)peptides

Work on the use of cyclic peptides or pseudopeptides as synthetic receptors started even before the field of supramolecular chemistry was firmly established. Research initially focused on the development of synthetic ionophores and involved the use of macrocycles with a repeating sequence of subunits along the ring to facilitate the correlation between structure, conformation, and binding properties. Later, nonnatural amino acids as building blocks were also considered. With growing research in this area, cyclopeptides and related macrocycles developed into an important and structurally diverse receptor family. This review provides an overview of these developments, starting from the early years. The presented systems are classified according to characteristic structural elements present along the ring. Wherever possible, structural aspects are correlated with binding properties to illustrate how natural or nonnatural amino acids affect binding properties.

Possible Functional Roles of Patellamides in the Ascidian-Prochloron Symbiosis

Patellamides are highly bioactive compounds found along with other cyanobactins in the symbiosis between didemnid ascidians and the enigmatic cyanobacterium Prochloron. The biosynthetic pathway of patellamide synthesis is well understood, the relevant operons have been identified in the Prochloron genome and genes involved in patellamide synthesis are among the most highly transcribed cyanobacterial genes in hospite. However, a more detailed study of the in vivo dynamics of patellamides and their function in the ascidian-Prochloron symbiosis is complicated by the fact that Prochloron remains uncultivated despite numerous attempts since its discovery in 1975. A major challenge is to account for the highly dynamic microenvironmental conditions experienced by Prochloron in hospite, where light-dark cycles drive rapid shifts between hyperoxia and anoxia as well as pH variations from pH ~6 to ~10. Recently, work on patellamide analogues has pointed out a range of different catalytic functions of patellamide that could prove essential for the ascidian-Prochloron symbiosis and could be modulated by the strong microenvironmental dynamics. Here, we review fundamental properties of patellamides and their occurrence and dynamics in vitro and in vivo. We discuss possible functions of patellamides in the ascidian-Prochloron symbiosis and identify important knowledge gaps and needs for further experimental studies.

Origins and Bioactivities of Natural Compounds Derived from Marine Ascidians and Their Symbionts

Marine ascidians are becoming important drug sources that provide abundant secondary metabolites with novel structures and high bioactivities. As one of the most chemically prolific marine animals, more than 1200 inspirational natural products, such as alkaloids, peptides, and polyketides, with intricate and novel chemical structures have been identified from ascidians. Some of them have been successfully developed as lead compounds or highly efficient drugs. Although numerous compounds that exist in ascidians have been structurally and functionally identified, their origins are not clear. Interestingly, growing evidence has shown that these natural products not only come from ascidians, but they also originate from symbiotic microbes. This review classifies the identified natural products from ascidians and the associated symbionts. Then, we discuss the diversity of ascidian symbiotic microbe communities, which synthesize diverse natural products that are beneficial for the hosts. Identification of the complex interactions between the symbiont and the host is a useful approach to discovering ways that direct the biosynthesis of novel bioactive compounds with pharmaceutical potentials.

Contemplating 1,2,4-Thiadiazole-Inspired Cyclic Peptide Mimics: A Computational Investigation

Marine derived cyclic peptides have inspired chemists for decades as the cavitand architecture can be compared with macrocyclic ligands, and hence easily conceived as mediators of metal-ion transport. Lissoclinamide 5 and ascidiacyclamide are two such cyclic peptides that have received much attention both for their metal ion complexation properties and biological activity; the metal ion binding properties of mimics of these two systems have been reported. Reported herein is a computational study aimed at evaluating the stability, and potential for copper(ii) ion binding by lissoclinamide 5 mimics that substitute the naturally occurring 4-carboxy-1,3-thiazole units for novel valine- and phenylalanine-derived 1,2,4-thiadiazole units. Our results suggest that one lissoclinamide 5 mimic, 1,2,4-thiadiazole (TDA)-lissoclinamide 9, may be capable of forming a complex with one CuII ion, [Cu(9-H)(H2O)]+. A complex with two CuII ions, [Cu2(9-H)(μ-OH)]2+, was also considered. These results set the stage for synthetic and experimental metal binding studies.

Ascidian Toxins with Potential for Drug Development

Ascidians (tunicates) are invertebrate chordates, and prolific producers of a wide variety of biologically active secondary metabolites from cyclic peptides to aromatic alkaloids. Several of these compounds have properties which make them candidates for potential new drugs to treat diseases such as cancer. Many of these natural products are not produced by the ascidians themselves, rather by their associated symbionts. This review will focus mainly on the mechanism of action of important classes of cytotoxic molecules isolated from ascidians. These toxins affect DNA transcription, protein translation, drug efflux pumps, signaling pathways and the cytoskeleton. Two ascidian compounds have already found applications in the treatment of cancer and others are being investigated for their potential in cancer, neurodegenerative and other diseases.

Bistratamides M and N, Oxazole-Thiazole Containing Cyclic Hexapeptides Isolated from Lissoclinum bistratum Interaction of Zinc (II) with Bistratamide K

Two novel oxazole-thiazole containing cyclic hexapeptides, bistratamides M (1) and N (2) have been isolated from the marine ascidian Lissoclinum bistratum (L. bistratum) collected in Raja Ampat (Papua Bar, Indonesia). The planar structure of 1 and 2 was assigned on the basis of extensive 1D and 2D NMR spectroscopy and mass spectrometry. The absolute configuration of the amino acid residues in 1 and 2 was determined by the application of the Marfey’s and advanced Marfey’s methods after ozonolysis followed by acid-catalyzed hydrolysis. The interaction between zinc (II) and the naturally known bistratamide K (3), a cyclic hexapeptide isolated from a different specimen of Lissoclinum bistratum, was monitored by ¹H and ¹³C NMR. The results obtained are consistent with the proposal that these peptides are biosynthesized for binding to metal ions. Compounds 1 and 2 display moderate cytotoxicity against four human tumor cell lines with GI₅₀ values in the micromolar range.

Bio-inspired Herringbone Foldamers: Strategy for Changing the Structure of Helices

Cyclic oligomers of azole peptides were isolated from a multitude of marine organisms and were used for a large number of molecular machines. As shown previously, oligomers derived from achiral imidazole amino acids fold into canonical helices. Here we show that a minor change, the introduction of a methyl group in the δ position, results in a significant change in the secondary structure of the corresponding oligomers. Instead of a canonical helix, a noncanonical herringbone helix is formed. In the latter, the slope along the helix changes its sign at least twice per turn. This strategy allows a remarkable change of the secondary structure via a small modification. By means of enantiomerically pure amino acids, we were able to control, for the first time, both the helicity of the helix and the form of the herringbone. The investigation of the underlying herringbone basic element and its folding to a noncanonical helix were conducted by NMR and CD spectroscopy, as well as by X-ray crystallography and quantum chemical calculations.

Dinuclear ZnII and mixed CuII-ZnII complexes of artificial patellamides as phosphatase models

The patellamides (cyclic pseudo-octapeptides) are produced by Prochloron, a symbiont of the ascidians, marine invertebrate filter feeders. These pseudo-octapeptides are present in the cytoplasm and a possible natural function of putative metal complexes of these compounds is hydrolase activity, however the true biological role is still unknown. The dinuclear Cu^II complexes of synthetic patellamide derivatives have been shown in in vitro experiments to be efficient hydrolase model catalysts. Many hydrolase enzymes, specifically phosphatases and carboanhydrases, are Zn^II-based enzymes and therefore, we have studied the Zn^II and mixed Zn^II/Cu^II solution chemistry of a series of synthetic patellamide derivatives, including solution structural and computational work, with the special focus on model phosphatase chemistry with bis-(2,4-dinitrophenyl)phosphate (BDNPP) as the substrate. The Zn^II complexes of a series of ligands are shown to form complexes of similar structure and stability compared to the well-studied Cu^II analogues and the phosphatase reactivities are also similar. Since the complex stabilities and phosphatase activities are generally a little lower compared to those of Cu^II and since the concentration of Zn^II in Prochloron cells is slightly smaller, we conclude that the Cu^II complexes of the patellamides are more likely to be of biological importance.

Ctr-1 Mets7 motif inspiring new peptide ligands for Cu(i)-catalyzed asymmetric Henry reactions under green conditions

Hybrid catalysts were developed from the Cu(i) binding domain of Ctr1 protein and their activity was evaluated in an asymmetric Henry reaction.

Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge

Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.

Imidazole-peptide foldamers: parabolic dependence of the folding process on the water content of the solvent

Oligomers of azole peptides have been isolated from a multitude of marine organisms. Up to now, these azole-containing dipeptide-analogue oligomers have only been found as cyclic n-mers (mostly tri- and tetramers) in nature. Herein, we show that imidazole-containing pseudopeptides form helixlike secondary structures in different solvents. The screw sense of the helix can be determined by attaching a single chiral imidazole unit to the N terminus of the oligomer. Investigation by means of circular dichroism (CD) spectroscopy showed that the folding process of the helix depends on the water content of the solvent in a parabolic way. In a pure organic medium, the helix is stabilized by hydrogen bonds between the hydrogen atoms of the amide groups and the nitrogen atoms of the azole ring. In aqueous solution, the formation of the helix is driven by dispersion interactions. The formation of the helix is more pronounced in aqueous solution than in organic solvents.

Iodine catalysed intramolecular C(sp3)–H functionalization: synthesis of 2,5-disubstituted oxazoles from N-arylethylamides

Iodine catalyzed synthesis of 2,5-substituted oxazoles from N-arylethylamides through intramolecular C(sp³)–H functionalization under metal-free conditions is described.

Copper(ii) complexes of macrocyclic and open-chain pseudopeptidic ligands: synthesis, characterization and interaction with dicarboxylates

Cu(ii) complexes of pseudopeptides interact with very similar dicarboxylates of biological interest (malate and aspartate) affording strikingly different outcomes.

Ferro- and antiferromagnetic coupling in a chlorido-bridged, tetranuclear Cu(ii) complex

A binuclear complex of copper(ii) chloride with a heptadentate bispidine-like ligand undergoes dimerisation in the solid state involving chloride bridging and leading to both ferro- and antiferromagnetic coupling of the Cu(ii) centres.