Cyclic Tetrapeptide Research Articles

Computational and Experimental Investigations into the Conformations of Cyclic Tetra-α/β-peptides

We present a combined computational and experimental study of the energy landscapes of cyclic tetra-α/β-peptides. We have performed discrete path sampling calculations on a series of cyclic tetra-α/β-peptides to obtain the relative free energies and barriers to interconversion of their conformers. The most stable conformers of cyclo-[(β-Ala-Gly)2] contain all-trans peptide groups. The relative energies of the cis isomers and the cis-trans barriers are lower than in acyclic peptides but not as low as in the highly strained cyclic α-peptides. For cyclic tetra-α/β-peptides containing a single proline residue, of the type cyclo-[β-Ala-Xaa-β-Ala-Pro], the energy landscapes show that the most stable isomers containing cis and trans β-Ala-Pro have similar free energies and are separated by barriers of approximately 15 kcal mol(-1). We show that the underlying energy landscapes of cyclo-[β-Ala-Lys-β-Ala-Pro] and cyclo-[β-Ala-Ala-β-Ala-Pro] are similar, allowing the substitution of the flexible side chain of Lys with Ala to reduce the computational demand of our calculations. However, the steric bulk of the Val side chain in cyclo-[β-Ala-Val-β-Ala-Pro] affects the conformations of the ring, leading to significant differences between its energy landscape and that of cyclo-[β-Ala-Ala-β-Ala-Pro]. We have synthesized the cyclic peptide cyclo-[β-Ala-Lys-β-Ala-Pro], and NMR spectroscopy shows the presence of conformers that interconvert slowly on the NMR time scale at temperatures up to 80 °C. Calculated circular dichroism (CD) spectra for the proposed major isomer of cyclo-[β-Ala-Ala-β-Ala-Pro] are in good agreement with the experimental spectra of cyclo-[β-Ala-Lys-β-Ala-Pro], suggesting that the Ala cyclic tetrapeptide is a viable model for the Lys analogue.

Cyclic α,β-Tetrapeptoids: Sequence-Dependent Cyclization and Conformational Preference

The presence of at least one N-Cα branched side chain is crucial for successful cyclization of α,β-tetrapeptoids. The ctct amide sequence revealed in the crystal structure of the 14-membered cyclotetrapeptoid 8 is also the most populated conformation in solution and is reminiscent of the predominant amide arrangement of the 12-membered cyclic tetrapeptides (CTPs).

Asperterrestide A, a Cytotoxic Cyclic Tetrapeptide from the Marine-Derived Fungus Aspergillus terreus SCSGAF0162

A new cytotoxic and antiviral cyclic tetrapeptide, asperterrestide A (1), a new alkaloid, terremide C (2), and a new aromatic butenolide, aspernolide E (3), together with 10 known compounds were isolated from the fermentation broth of the marine-derived fungus Aspergillus terreus SCSGAF0162. Their structures were elucidated by spectroscopic analysis, and the absolute configuration of 1 was determined by the Mosher ester technique and analysis of the acid hydrolysates using a chiral-phase HPLC column. Compound 1 contains a rare 3-OH-N-CH3-Phe residue and showed cytotoxicity against U937 and MOLT4 human carcinoma cell lines and inhibitory effects on influenza virus strains H1N1 and H3N2.

Cyclic tetrapeptides with –SS– bridging between amino acid side chains for potent histone deacetylases’ inhibition

Cyclic depsipeptide FK228 with an intramolecular disulfide bond is a potent inhibitor of histone deacetylases (HDAC). FK228 is stable in blood because of its prodrug function, whose -SS- bond is reduced within the cell. Here, cyclic peptides with -SS- bridges between a variety of amino acids were synthesized and assayed for HDAC inhibition. Cyclic peptide 3, cyclo(-L-amino acid-L-amino acid-L-Val-D-Pro-), with an -SS- bridge between the first and second amino acids, was found to be a potent HDAC inhibitor. Cyclic peptide 7, cyclo(-L-amino acid-D-amino acid-L-Val-D-Pro-), with an -SS- bridge between the first and second amino acids, was also a potent HDAC inhibitor.

ChemInform Abstract: New Cyclic Tetrapeptides and Asteltoxins from Gorgonian‐Derived Fungus Aspergillus sp. SCSGAF 0076.

AbstractAspergillipeptides A‐C (Ia‐c) and asteltoxin B (II) are isolated and characterized.

A lead (II) 3D coordination polymer based on a marine cyclic peptide motif.

The crystal structure of a naturally occurring cyclic tetrapeptide cyclo(Gly-l-Ser-l-Pro-l-Glu) [cyclo(GSPE)] was obtained. The conformation of synthesized cyclo(GSPE) fixes the coordination to lead ion in a 1:1 ratio. This cyclo(GSPE)-Pb complex was constructed as an asymmetric 3D network in the crystalline state. The polymerization of a heavy metal ion with a rigid asymmetric cyclic tetrapeptide represents the first example of a new class of macrocyclic complexes.

Flexible Synthesis and Evaluation of Diverse Anti-Apicomplexa Cyclic Peptides

A modular approach to synthesize anti-Apicomplexa parasite inhibitors was developed that takes advantage of a pluripotent cyclic tetrapeptide scaffold capable of adjusting appendage and skeletal diversities in only a few steps (one to three steps). The diversification processes make use of selective radical coupling reactions and involve a new example of a reductive carbon-nitrogen cleavage reaction with SmI2. The resulting bioactive cyclic peptides have revealed new insights into structural factors that govern selectivity between Apicomplexa parasites such as Toxoplasma and Plasmodium and human cells.

ChemInform Abstract: A New Cyclic Tetrapeptide from the Jellyfish‐Derived Fungus Phoma sp.

AbstractNew tentoxin B (I) is isolated together with two known congeners, dihydrotentoxin and tentoxin.

Conformation and Dynamics of a Cyclic Disulfide-Bridged Peptide: Effects of Temperature and Solvent

The cyclic disulfide-bridged tetrapeptide cyclo(Boc-Cys-Pro-Gly-Cys-OMe) (1) was designed as a model for the study of solvent-driven conformational changes in peptides. The three-dimensional structure and dynamics of 1 were studied using a variety of experimental and computational techniques. The crystal structure of 1 reveals a β-turn stabilized by a hydrogen bond between the two cysteine residues. In solution, the UV-CD and NMR analysis of 1 suggest a β-turn II conformation, stable up to 60 °C. The characteristic NMR (13)C shifts of the Cβ and Cγ atoms of proline show that the peptide adopts exclusively the energetically favored trans conformation of the peptidyl-prolyl bond. The combination of IR spectroscopy with Car-Parrinello MD simulations and DFT calculations allowed us to assign the absorptions in the amide I region to the individual amino acids. The NH group of Gly, which as hydrogen bond donor competes with the NH group of Cys4 for the carbonyl oxygen atom of Cys1 as hydrogen bond acceptor, plays a relevant role for the structure and spectroscopic properties of the peptide. Since Gly is more exposed to the solvent, its hydrogen-bonding capability can be partially blocked by external solvent molecules in solution or by a second peptide molecule in the crystal. Furthermore, the presence of only one molecule of acetonitrile is sufficient to change the preferred conformation of 1, and even in acetonitrile solution the simulations suggest that on average only one solvent molecule strongly interacts with the cyclic core of the peptide.

Efficient Construction of Proline-Containing β-Turn Mimetic Cyclic Tetrapeptides via CuAAC Macrocyclization

A range of macrocyclic β-turn mimetic tetrapeptides was prepared by efficient copper-tris(triazole) ligand complex catalyzed azide-alkyne "click" macrocyclizations in good to high yields. Preliminary conformational studies using X-ray crystallography and NMR spectroscopy demonstrated the presence of intramolecular H-bonds characteristic of β-turns in these cyclic tetrapeptides.

Opioid Peptidomimetics: Leads for the Design of Bioavailable Mixed Efficacy μ Opioid Receptor (MOR) Agonist/δ Opioid Receptor (DOR) Antagonist Ligands

We have previously described opioid peptidomimetic, 1, employing a tetrahydroquinoline scaffold and modeled on a series of cyclic tetrapeptide opioid agonists. We have recently described modifications to these peptides that confer a μ opioid receptor (MOR) agonist, δ opioid receptor (DOR) antagonist profile, which has been shown to reduce the development of tolerance to the analgesic actions of MOR agonists. Several such bifunctional ligands have been reported, but none has been demonstrated to cross the blood-brain barrier. Here we describe the transfer of structural features that evoked MOR agonist/DOR antagonist behavior in the cyclic peptides to the tetrahydroquinoline scaffold and show that the resulting peptidomimetics maintain the desired pharmacological profile. Further, the 4R diastereomer of 1 was fully efficacious and approximately equipotent to morphine in the mouse warm water tail withdrawal assay following intraperitoneal administration and thus a promising lead for the development of opioid analgesics with reduced tolerance.

Preparation, chromatographic evaluation and comparison between linear peptide- and cyclopeptide-bonded stationary phases

In this paper, linear and cyclic tetrapeptide bonded stationary phases, were synthesized by the solid-phase synthesis method. Each amino acid coupling step was monitored by the ninhydrin test using UV/visible spectrophotometry. The proposed materials were characterized by UV spectroscopy, Fourier transform infrared spectroscopy, elemental analysis and thermogravimetric analysis, which proved the successful immobilization of tetrapeptide on the silica support. The cyclopeptide stationary phase displayed mixed-mode behavior and had the size selectivity for polycyclic aromatic hydrocarbon such as anthracene, while the linear peptide stationary phase only exhibited typical hydrophilic interaction chromatography (HILIC) characteristics and was more hydrophilic under the same mobile phase condition. Retention behaviors of polar compounds on the two stationary phases were studied through varying column temperature, the water content, pH and ionic strength in mobile phase. Applications in the separation of the mixture of nucleosides, sulfa compounds, organic acids and isomers of substituted benzoic acid compounds were demonstrated.

Interactions of disulfide-constrained cyclic tetrapeptides with Cu(2+).

The purpose of this work is to characterize the interactions of two disulfide-constrained cyclic tetrapeptides [c(Ac-Cys-Pro-Phe-Cys-NH(2)), SS1; c(Ac-Cys-Pro-Gly-Cys-NH(2)), SS2] with Cu(2+) ions in order to facilitate the design of cyclic peptides as sensors for metal ions. The Cu(2+)-peptide complex cations at m/z 569.1315 for Cu(2+)-SS1 and m/z 479.0815 for Cu(2+)-SS2 were detected by mass spectrometry. The gas-phase fragmentation of the Cu(2+)-peptide complexes was studied by collision-induced dissociation and suggests the atoms involved in the coordination. Cu(2+) ion binds to a single SS1 or SS2 with K (d(app)) of 0.57 ± 0.02 and 0.55 ± 0.01 μM, respectively. Isothermal titration calorimetry data indicate both enthalpic and entropic contributions for the binding of Cu(2+) ion to SS1 and SS2. The characteristic wavenumber of 947 cm(-1) and the changes at 1,664 and 1,530 cm(-1) in the infrared spectrum suggest that the sulfydryl of cysteine, the carbonyl group, and amide II are involved in the coordination of Cu(2+). The X-ray absorption near-edge structure signal from the Cu(2+)-peptide complex corresponds to the four-coordination structure. The extended X-ray absorption fine structure and electron paramagnetic resonance results demonstrate the Cu(2+) ion is in an S/N/2O coordination environment, and is a distinct type II copper center. Theoretical calculations further demonstrate that Cu(2+) ion binds to SS1 or SS2 in a slightly distorted tetragonal geometry with an S/N/2O environment and the minimum potential energy.

New cyclic tetrapeptides and asteltoxins from gorgonian-derived fungus Aspergillus sp. SCSGAF 0076

Three new cyclic tetrapeptides, aspergillipeptides A–C (1–3), and one new asteltoxin B (4) were isolated from a culture broth of gorgonian-derived fungal strain Aspergillus sp. SCSGAF 0076. Their structures were elucidated by spectroscopic analysis, and the absolute configurations of aspergillipeptides A–C were determined by Marfey's method. Aspergillide C (3) showed strong antifouling activity against Bugula neritina larvae settlement with LC50/EC50>25.

Exploring the Energy Landscapes of Cyclic Tetrapeptides with Discrete Path Sampling.

Cyclic tetrapeptides are an important class of biologically active molecules that exhibit interesting conformational dynamics, with slow interconversion of several different structures. We present calculations on their energy landscapes using discrete path sampling. In acyclic peptides and large cyclic peptides, isomers containing cis-peptide groups are much less stable than the all-trans isomers and separated from them by large barriers. Strain in small cyclic peptides causes the cis and trans isomers to be closer in energy and separated by much lower barriers. If d-amino acids or proline residues are introduced, isomers containing cis-peptides become more stable than the all-trans structures. We also show that changing the polarity of the solvent has a significant effect on the energy landscapes of cyclic tetrapeptides, causing changes in the orientations of the peptide groups and in the degree of intramolecular hydrogen bonding.

Exploring Solution-Phase Cyclization and Sulfamyl Safety-Catch Resin Strategies for the Total Synthesis of the Marine Antimicrobial Cyclic Tetrapeptide Cyclo(GSPE)

Head-to-tail cyclization of 12-membered tetrapeptides has been reported to be synthetically challenging due to their highly strained ring systems. Previously, we reported the total synthesis of the marine antimicrobial cyclic tetrapeptide cyclo(GSPE) using the glutamic acid side-chain Wang resin tethering strategy with a 5 % yield under microwave irradiation (Lim et al., Int J Pept Res Ther 16:145–152, 2010). Besides the low yield, this strategy was also constrained to glutamic acid-containing peptides. In this communication, we report the outcomes of two alternate strategies to synthesize cyclo(GSPE): (A) solution-phase cyclization and (B) solid-phase synthesis using the sulfamylbutyryl safety-catch resin. Experimental results using all four possible linear precursors revealed that the former strategy failed to produce the target cyclic peptide while the latter approach afforded an improved overall yield of 8–9 % using the linear precursor H-Ser(tBu)-Pro-Glu(OtBu)-Gly-resin. Interestingly, we discovered that the placement of proline at the N- or C-termini of the linear peptide precursors failed to produce the target cyclic peptide. We also concluded that strategy B could provide the versatility needed to make a cyclic tetrapeptide library for bioactivity screening.

Synthesis and Reactions of New Chiral Linear and Macrocyclic Tetraand Penta-peptide Candidates

9a A series of linear and macrocyclic pentapeptide derivatives have been prepared via the coupling of pyridine-2,6-dicarboxylic acid (1) or pyridine-2,6-dicarbonyl dichloride (2) with appropriate amino acid methyl esters. The coupling of 1or 2with aminoacid methyl esters gave the corresponding pyridine dipeptide methyl esters 3, which were hydrolyzed with sodium hydroxide to the corresponding acids 4. The latter compounds 4were coupled with other amino acid methyl esters to afford the corresponding tetrapeptide esters 5, which were hydrolyzed with sodium hydroxide to the corresponding acids 6. Cyclization of tetrapeptide acids with L-lysine methyl ester or with aliphatic diamide derivatives afforded the corresponding cyclic pentapeptide methyl ester derivatives 7and cyclic tetrapeptide diamines 8, respectively. Finally, hydrolysis with 1 N sodium hydroxide or hydrazinolysis with hydrazine hydrate of methyl esters 7afforded the corresponding acids - e and hydrazides 10a - e, respectively

Dioxygen Oxidation Cu(II) → Cu(III) in the Copper Complex of cyclo(Lys-dHis-βAla-His): A Case Study by EXAFS and XANES Approach

A former spectroscopic study of Cu(II) coordination by the 13-membered ring cyclic tetrapeptide c(Lys-dHis-βAla-His) (DK13), revealed the presence, at alkaline pH, of a stable peptide/Cu(III) complex formed in solution by atmospheric dioxygen oxidation. To understand the nature of this coordination compound and to investigate the role of the His residues in the Cu(III) species formation, Cu K-edge XANES, and EXAFS spectra have been collected for DK13 and two other 13-membered cyclo-peptides: the diastereoisomer c(Lys-His-βAla-His) (LK13), and c(Gly-βAla-Gly-Lys) (GK13), devoid of His residues. Comparison of pre-edge peak features with those of Cu model compounds, allowed us to get information on copper oxidation state in two of the three peptides, DK13 and GK13: DK13 contains only Cu(III) ions in the experimental conditions, while GK13 binds only with Cu(II). For LK13/Cu complex, EXAFS spectrum suggested and UV-vis analysis confirmed the presence of a mixture of Cu(II) and Cu(III) coordinated species. Theoretical XANES spectra have been calculated by means of the MXAN code. The good agreement between theoretical and experimental XANES data collected for DK13, suggests that the refined structure, at least in the first coordination shell around Cu, is a good approximation of the DK13/Cu(III) coordination species present at strongly alkaline pH. All the data are consistent with a slightly distorted pyramidal CuN(4) unit, coming from the peptide bonds. Surprisingly, the His side-chains seemed not involved in the final, stable, Cu(III) scaffold.

Cloning and characterization of histone deacetylase from Babesia bovis

The effect of inhibitors of histone deacetylase (HDAC) on Apicomplexa has been previously reported with the discovery of apicidin, a cyclic tetrapeptide having broad-spectrum antiparasitic activity. In the current study, we expressed Babesia bovis (B. bovis) recombinant-HDAC 3 (rBbHDAC3) as a GST-fusion protein in Escherichia coli (E. coli) and found that it was antigenic. An antiserum against the recombinant protein was generated in mice. The mice serum demonstrated the presence of HDAC in B. bovis by a Western blot assay. The murine anti-rBbHDAC3 reacted with B. bovis, Babesia bigemina (B. bigemina), Theileria equi (T. equi), and Babeisa caballi (B. caballi) merozoites in the indirect fluorescent antibody test (IFAT). Furthermore, the HDAC-enzymatic activity of the rBbHDAC3 protein was evaluated by a colorimetric assay. The enzymatic activity of rBbHDAC3 was inhibited by 100ng/ml of apicidin, and the inhibitory effect of apicidin was dose-dependent. The inhibition of BbHDAC3 by apicidin was confirmed by Western blot, IFAT, and reverse transcription-polymerase chain reaction (RT-PCR). Finally, apicidin potentially inhibited the in vitro growth of Babesia parasites. The lower IC50 values of apicidin against apicomplexan parasites than those of mammalian cells point to HDAC as an excellent drug target. The findings of the present study indicate that BbHDAC3 is a potential target for apicidin and might be a promising target for the development of novel anti-babesial drugs.

Isolation and Structural Elucidation of Cyclic Tetrapeptides from Onychocola sclerotica

Three new cyclic tetrapeptides (1-3) have been isolated from the crude fermentation extract of Onychocola sclerotica. The planar structures of 1-3 were elucidated by detailed spectroscopic analyses using one- and two-dimensional NMR experiments and high-resolution mass spectrometry. The absolute configuration of the amino acid residues in each cyclotetrapeptide was established by Marfey's method. Compounds 1-3 displayed activity as cardiac calcium channel blockers (Cav1.2) but did not inhibit the hERG potassium channel and were not cytotoxic. These peptides are the first secondary metabolites ever reported from fungi of the order Arachnomycetales.