Cyclic Tetrapeptide Research Articles

Impact of ring size on the copper(II) coordination abilities of cyclic tetrapeptides

A new, 14-membered, tetraza cyclic tetrapeptide containing histidine and lysine side-chains, c(beta(3)homoLysdHisbeta-AlaHis), was designed, synthesized and characterized; its copper(II) binding properties were investigated in dependence of pH by potentiometric and spectroscopic methods. In line with previous studies of similar systems, the progressive involvement of amide nitrogens in copper(II) coordination was evidenced for pH values greater than 6. At physiological pH the dominant species consists of a copper(II) center coordinated by two amide nitrogens, an imidazole nitrogen and a water molecule. In contrast, at pH values higher than 8.7, a copper(II) coordination environment consisting of four amide nitrogens in the equatorial plane and the axial imidazole ligands is formed as clearly indicated by spectroscopic data and theoretical calculations. The behavior of this 14-membered cyclic tetrapeptide is compared to that of its 12-membered cyclic analog, particular attention being paid to the effects of ring size on the respective copper(II) binding abilities.

Design, synthesis, biological evaluation, and structural characterization of potent histone deacetylase inhibitors based on cyclic alpha/beta-tetrapeptide architectures.

Histone deacetylases (HDACs) are a family of enzymes found in bacteria, fungi, plants, and animals that profoundly affect cellular function by catalyzing the removal of acetyl groups from -N-acetylated lysine residues of various protein substrates including histones, transcription factors, alpha-tubulin, and nuclear importers. Although the precise roles of HDAC isoforms in cellular function are not yet completely understood, inhibition of HDAC activity has emerged as a promising approach for reversing the aberrant epigenetic states associated with cancer and other chronic diseases. Potent new isoform-selective HDAC inhibitors would therefore help expand our understanding of the HDAC enzymes and represent attractive lead compounds for drug design, especially if combined with high-resolution structural analyses of such inhibitors to shed light on the three-dimensional pharmacophoric features necessary for the future design of more potent and selective compounds. Here we present structural and functional analyses of a series of beta-amino-acid-containing HDAC inhibitors inspired by cyclic tetrapeptide natural products. To survey a diverse ensemble of pharmacophoric configurations, we systematically varied the position of the beta-amino acid, amino acid chirality, functionalization of the Zn(2+)-coordinating amino acid side chain, and alkylation of the backbone amide nitrogen atoms around the macrocycle. In many cases, the compounds were a single conformation in solution and exhibited potent activities against a number of HDAC isoforms as well as effective antiproliferative and cytotoxic activities against human tumor cells. High-resolution NMR solution structures were determined for a selection of the inhibitors, providing a useful means of correlating detailed structural information with potency. The structure-based approach described here is expected to furnish valuable insights toward the future design of more selective HDAC inhibitors.

On‐Surface Cyclization of Tetrapeptides Using Molecularly Imprinted Polymers as Non‐Covalent Auxiliaries

AbstractBased on the fabrication of molecularly imprinted polymeric film on cellulose paper (MIFC), we have developed a robotic system for homodetic tetrapeptide cyclization. We constructed molecularly imprinted polymeric film (MIPF) on cellulose paper as the non‐covalent auxiliary to assist cyclic tetrapeptide (CTP) formation. Tetrapeptides were bound by their hydrophobic interaction with MIFC. With the help of MIFC and a coupling reagent, quantitative synthesis of CTPs was achieved conveniently for various tetrapeptides. The syntheses of cyclic tetrapeptide (CTP) could also be facilitated using the MIFC induced from CTP or other tetrapeptides with partially matched sequences.

Synthesis, conformational studies, and molecular dynamics calculations of two cyclic tetrapeptides with 17- and 18-membered rings

Two cyclic tetrapeptides [Boc-cyclo(-Xxx-Pro-Asn-Lys-)OMe (Xxx = Asp or Glu)] were synthesized and investigated by NMR spectroscopy. They were designed in order to mimic the salt bridge found in physalaemin. Isomers of the urethane bond were observed in DMSO solution. The ROESY spectrum allowed the assignment of many signals of the minor isomer of both compounds. Conformational studies based on the temperature gradients of the NH chemical shifts, coupling constants, and ROEs revealed a similar conformation for the Asp analogue as proposed for physalaemin. A beta I turn with Pro and Asn in the corner positions was found for the major isomer. No hydrogen bonds were detected for the major isomer of the cyclic Glu analogue. Molecular dynamics calculations, using the NMR based initial structures, yielded sets of conformations in agreement with the experimental data. It is concluded that the salt bridge in physalaemin is best approximated by a lactam formed from the original amino acids.

Purification and Phytotoxicity of Apicidins Produced by the Fusarium semitectum KCTC16676

Apicidin is a cyclic tetrapeptide produced by some Fusarium species and is known to inhibit Apicomplexan histone deacetylase. The goals of this study were to determine species identity of Fusarium isolate KCTC16676, an apicidin producer, to improve a method for apicidin extraction, and to test phytotoxicity of apicidin and its analogs. We compared sequences of the translation elongation factor 1-alpha (TEF) gene in KCTC16676 with those from isolates representing diverse Fusarium species, which showed that KCTC16676 belongs to the F. semitectum-F. equiseti species complex. To enhance apicidin production, after culturing isolate KCTC16676 on a wheat medium for 3 weeks at 25oC, the culture was extracted with chloroform. Apicidins were purified through a reverse phase C18 silica gel column, resulting in 5 g of apicidin, 200 mg of apicidin A, and 300 mg of apicidin D2 from 4 kg of wheat cultures; this represents a significant yield improvement from a previous method, offers more materials to study the modes of its action, and facilitates the elucidation of the apicidin biosynthesis pathway. Apicidin and apicidin D2 showed phytotoxicity on both seedlings and 2-week-old plants of diverse species, and weeds were more sensitive to apicidins than vegetables

Total Synthesis of Azumamide E and Sugar Amino Acid-Containing Analogue

An efficient and practical total synthesis of marine cyclic tetrapeptide, natural product azumamide E (1) is achieved via high-yielding reactions. The strategy also allowed us to synthesize the azumamide E-SAA (sugar amino acid) analogue (2), whose solution-phase NMR and biological activity studies were also carried out.

New cyclic tetrapeptides from Nonomuraea sp. TA-0426 that inhibit glycine transporter type 1 (GlyT1)

In the course of our search for natural antipsychotic agents, we isolated five new cyclic tetrapeptides from the fermentation broth of Nonomuraea sp. TA-0426. These compounds turned out to be analogues of WSS2220, which had been produced by the same actinomycete and showed strong inhibitory activity against GlyT1. Four of the present peptides exhibit more potent GlyT1 inhibitory activities than WSS2220.

A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank

Reverse turns are often recognition sites for protein/protein interactions and, therefore, valuable potential targets for determining recognition motifs in development of potential therapeutics. A virtual combinatorial library of cyclic tetrapeptides (CTPs) was generated and the bonds in the low-energy structures were overlapped with canonical reverse-turn Calpha-Cbeta bonds (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005) to determine the utility of CTPs as reverse-turn peptidomimetics. All reverse turns in the Protein Data Bank (PDB) with a crystal structures resolution < or = 3.0 A were classified into the same known canonical reverse-turn Calpha-Cbeta bond clusters (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005). CTP reverse-turn mimics were compiled that mimicked both the relative orientations of three of the four as well as all four Calpha-Cbeta bonds in the reverse turns of the PDB. 54% of reverse turns represented in the PDB had eight or more CTPs structures that mimicked the orientation of all four of the Calpha-Cbeta bonds in the reverse turn.

New Open‐Chain and Cyclic Tetrapeptides, Consisting of α‐, β2‐, and β3‐Amino‐Acid Residues, as Somatostatin Mimics – A Survey

AbstractCyclo‐β‐tetrapeptides are known to adopt a conformation with an intramolecular transannular hydrogen bond in solution. Analysis of this structure reveals that incorporation of a β2‐amino‐acid residue should lead to mimics of ‘α‐peptidic β‐turns’ (cf. A, B, C). It is also known that short‐chain mixed β/α‐peptides with appropriate side chains can be used to mimic interactions between α‐peptidic hairpin turns and G protein‐coupled receptors. Based on these facts, we have now prepared a number of cyclic and open‐chain tetrapeptides, 7–20, consisting of α‐, β2‐, and β3‐amino‐acid residues, which bear the side chains of Trp and Lys, and possess backbone configurations such that they should be capable of mimicking somatostatin in its affinity for the human SRIF receptors (hsst1–5). All peptides were prepared by solid‐phase coupling by the Fmoc strategy. For the cyclic peptides, the three‐dimensional orthogonal methodology (Scheme 3) was employed with best success. The new compounds were characterized by high‐resolution mass spectrometry, NMR and CD spectroscopy, and, in five cases, by a full NMR‐solution‐structure determination (in MeOH or H2O; Fig. 4). The affinities of the new compounds for the receptors hsst1–5 were determined by competition with [125I]LTT‐SRIF28 or [125I] [Tyr10]‐CST14. In Table 1, the data are listed, together with corresponding values of all β‐ and γ‐peptidic somatostatin/Sandostatin® mimics measured previously by our groups. Submicromolar affinities have been achieved for most of the human SRIF receptors hsst1–5. Especially high, specific binding affinities for receptor hsst4 (which is highly expressed in lung and brain tissue, although still of unknown function!) was observed with some of the β‐peptidic mimics. In view of the fact that numerous peptide‐activated G protein‐coupled receptors (GPCRs) recognize ligands with turn structure (Table 2), the results reported herein are relevant far beyond the realm of somatostatin: many other peptide GPCRs should be ‘reached’ with β‐ and γ‐peptidic mimics as well, and these compounds are proteolytically and metabolically stable, and do not need to be cell‐penetrating for this purpose (Fig. 5).

ChemInform Abstract: WSS2220, a Novel Cyclic Tetrapeptide with a New Sulfonoamino Acid, Exhibits Potent and Selective Inhibitory Activity Against GlyT1.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform Abstract: Natural Cyclopeptaibiotics and Related Cyclic Tetrapeptides: Structural Diversity and Future Prospects

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Synthesis and Conformational Studies of a Hybrid Cyclic Peptide Based on cis‐β‐Furanoid Sugar Amino Acid (FSAA) and Ornithine

AbstractThe conformational control of a 14‐helix nucleating template, cis‐β‐furanoid sugar amino acid (FSAA), over a flexible δ‐amino acid, ornithine is studied in a FSAA‐ornithine cyclic tetrapeptide. Extensive NMR and MD studies reveal that the cyclic peptide adopts a three‐dimentional bowl‐shape cavity, which promotes six‐ and seven‐membered intra‐ and inter‐residue H‐bonding, in polar and non‐polar solvents, respectively.

Characterisation of the novel apoptotic and therapeutic activities of the histone deacetylase inhibitor romidepsin

Histone deacetylase inhibitors (HDACi) are compounds that target the epigenome and cause tumor cell-selective apoptosis. A large number of these agents that have different chemical structures and can target multiple HDACs are being testing in clinical trials and vorinostat is now an approved drug for the treatment of cutaneous T-cell lymphoma. Although these agents are showing promise for the treatment of hematologic malignancies, it is possible that different drugs may have different mechanistic, biological, and therapeutic activities. When comparing an HDACi belonging to the hydroxamic acid class of compounds (vorinostat) with a cyclic tetrapeptide (romidepsin), we showed that these agents regulate the expression of a common set of cellular genes, but certain genes specifically responded to each agent. Using the Emu-myc mouse model of B-cell lymphoma, we showed previously that overexpression of the prosurvival proteins Bcl-2 and Bcl-XL inhibited the apoptotic and therapeutic activities of the vorinostat. Herein, we compared and contrasted the apoptotic-inducing activities of the hydroxamic acid oxamflatin with romidepsin. Like vorinostat, oxamflatin was unable to kill lymphomas overexpressing Bcl-2 and Bcl-XL, indicating that these proteins can generally protect cells against this class of HDACi. In contrast, romidepsin was able to induce apoptosis in lymphomas overexpressing Bcl-2 with delayed kinetics of cell death and could mediate therapeutic responses against these lymphomas. However, romidepsin was inactive when Bcl-XL was overexpressed. These data provide strong support that HDACi of different chemical classes may have subtle yet potentially important differences in their molecular and biological activities.

Natural Cyclopeptaibiotics and Related Cyclic Tetrapeptides: Structural Diversity and Future Prospects

Linearity is not considered a prerequisite anymore, and extension of the current definition of 'peptaibiotics' to cyclic, Aib-containing peptides is proposed. Sequences and bioactivities, together with ecophysiological importance of cyclopeptaibiotics and related cyclic tetrapeptides, and their fungal-taxonomic relationships, are discussed.

Backbone Amide Linker Strategy for the Synthesis of 1,4‐Triazole‐Containing Cyclic Tetra‐ and Pentapeptides

AbstractA backbone amide linker strategy was chosen for the solid‐phase synthesis of triazole‐containing cyclic tetra‐ and pentapeptides. An alkyne‐substituted linker derived from 4‐hydroxy‐2‐methoxybenzaldehyde was elongated by using standard “Fmoc‐based” solid phase chemistry and terminated by coupling of an azido acid. In solution, the peptides were cyclized by a CuI‐catalyzed azide‐alkyne cycloaddition reaction. The solid‐supported synthesized linear peptides had to be cleaved prior to cyclization. As an example of cyclic tetrapeptides, a triazole analog of cyclo‐[Pro‐Val‐Pro‐Tyr] (2) was prepared by the solid‐phase/solution‐phase method. For the cyclic pentapeptides, segetalin B (3) was chosen as a model compound to show the applicability of this method.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)

A Novel Series of Potent and Selective Ketone Histone Deacetylase Inhibitors with Antitumor Activity in Vivo

Histone deacetylase (HDAC) inhibitors offer a promising strategy for cancer therapy, and the first generation HDAC inhibitors are currently in the clinic. Entirely novel ketone HDAC inhibitors have been developed from the cyclic tetrapeptide apicidin. These compounds show class I subtype selectivity and levels of cellular activity comparable to clinical candidates. A representative example has demonstrated tumor growth inhibition in a human colon HCT-116 carcinoma xenograft model comparable to known inhibitors.

Synthesis and biological evaluation of histone deacetylase inhibitors that are based on FR235222: A cyclic tetrapeptide scaffold

We outline the synthesis of six novel derivatives that are based on a recently discovered HDAC inhibitor FR235222. Our work is the first report utilizing a novel binding element, guanidine, as metal coordinators in HDAC inhibitors. Further, we demonstrate that these compounds show cytotoxicity that parallels their ability to inhibit deacetylase activity, and that the most potent compounds maintain an L-Phe at position 1, and a D-Pro at position 4. Both inhibition of HDAC activity and cytotoxicity against the pancreatic cancer cell line BxPC3 are exhibited by these compounds, establishing that a guanidine unit can be utilized successfully to inhibit HDAC activity.

WSS2220, a novel cyclic tetrapeptide with a new sulfonoamino acid, exhibits potent and selective inhibitory activity against GlyT1

In the course of our screening program for novel glycine transporter inhibitors, we obtained a novel cyclic tetrapeptide (WSS2220) from the culture broth of Nonomuraea sp. The structure of WSS2220 was elucidated based on physicochemical data. WSS2220 contained a novel amino acid (4-oxo-3′-sulfoisoleucine), the absolute stereochemistry of which was determined by chemical modifications and the modified Mosher’s method. WSS2220 selectively inhibited glycine transporter type1 with an IC 50 of 20 nM.

Sponge-associated fungi and their bioactive compounds: the Suberites case

Abstract Specimens of Suberites domuncula that had been cultured in aquaria for 4 weeks were analyzed for their associated fungi. A total of 81 fungal strains belonging to 20 different genera was isolated and identified by morphological and molecular methods. The most frequently isolated taxa were Cladosporium spp., Penicillium spp., Petriella sp., Phialophora spp. and Engyodontium album. Based on chromatographic and mass spectrometric analysis of fungal extracts, as well as on bioassay results, Aspergillus ustus, Penicillium sp., Petriella sp. and Scopulariopsis sp. were selected for in-depth analysis of their natural products. A total of 19 different fungal metabolites, including three new natural products, was isolated and structurally identified. A. ustus yielded two sesquiterpenes, a drimane derivative and deoxyuvidin, as well as a sesterterpene ophiobolin H. The drimane derivative had an ED50 value against L5178Y cells of 1.9 μg ml-1 in vitro. The crude extract of Petriella sp. was also strongly cytotoxic against the L5178Y cell line. The cyclic tetrapeptide WF-3161 was primarily responsible for the activity; the ED50 value was &lt;0.1 μg ml-1. It was identical to the known compound WF-3161 and had been previously isolated from Petriella guttulata. In addition to WF-3161, three further natural products were obtained and unequivocally identified as new derivatives of infectopyrone by one- and two-dimensional NMR spectroscopy and by mass spectroscopy. Of the new compounds, only dihydroinfectopyrone was active against L5178Y cells; the ED50 value was 0.2 μg ml-1. Penicillium sp. yielded the largest number of metabolites. Viridicatin, viridicatol, cyclopenin and cyclopenol suppressed larval growth of the polyphagous pest insect Spodoptera littoralis when incorporated into an artificial diet at an arbitrarily chosen concentration of 237 ppm. Viridicatol was the most active compound and had an ED50 value of ca. 50 ppm. Scopulariopsis sp. yielded three metabolites, including the known acetylcholinesterase inhibitors quinolactacin A1 and A2.

A guardian of grasses: Specific origin and conservation of a unique disease-resistance gene in the grass lineage

The maize Hm1 gene provides protection against a lethal leaf blight and ear mold disease caused by Cochliobolus carbonum race 1 (CCR1). Although it was the first disease-resistance (DR) gene to be cloned, it remains a novelty because, instead of participating in the plant recognition and response system as most DR genes do, Hm1 disarms the pathogen directly. It does so by encoding an NADPH-dependent reductase, whose function is to inactivate Helminthosporium carbonum (HC) toxin, an epoxide-containing cyclic tetrapeptide, which the pathogen produces as a key virulence factor to colonize maize. Although CCR1 is strictly a pathogen of maize, orthologs of Hm1 and the HC-toxin reductase activity are present in the grass family, suggesting an ancient and evolutionarily conserved role of this DR trait in plants. Here, we provide proof for such a role by demonstrating its involvement in nonhost resistance of barley to CCR1. Barley leaves in which expression of the Hm1 homologue was silenced became susceptible to infection by CCR1, but only if the pathogen was able to produce HC toxin. Phylogenetic analysis indicated that Hm1 evolved exclusively and early in the grass lineage. Given the devastating ability of CCR1 to kill maize, these findings imply that the evolution and/or geographical distribution of grasses may have been constrained if Hm1 did not emerge.