Linear Dipeptides Research Articles

Cyclization of alanyl-valine dipeptides in the solid state. The effects of molecular radiator and heat capacity.

Heating of linear dipeptides above a critical temperature initiates their cyclization even in the solid state. This method of obtaining cyclic dipeptides meets the requirements of "green chemistry", provides a high yield of the main product and releases only water as a by-product of the reaction, and does not require solvents. However, to date, the cyclization of only a small number of dipeptides in the solid state has been studied, and some correlations of the process were discovered. The influence of the structure of dipeptide molecules and their crystal packing on the kinetics of solid-state cyclization is still not fully understood. In this work, the cyclization of L-alanyl-L-valine in the solid state upon heating was studied. Using non-isothermal kinetic approaches, the kinetic parameters of this reaction and the optimal kinetic model describing this process were determined. The effect of the features of the crystal packing of dipeptides and their heat capacity on the temperature of the cyclization in the solid state was analyzed. This study expands our knowledge about solid-state reactions involving dipeptides and the ability to control such reactions.

Cyclization of l-leucyl-l-valine dipeptide in the crystal phase under non-isоthermal conditions

Thermal treatment of linear dipeptides in the solid phase makes it possible to obtain their cyclic analogues in high yield and without additional costs. At the same time, such reactions occurring under the constraints of a crystal lattice with the participation of molecules in the zwitterionic form have not been sufficiently studied. In this work, the cyclization reaction of the dipeptide L-leucyl-L-valine in the crystalline phase upon heating was studied. Using isoconversion kinetics approaches, a kinetic model describing this process is determined, and kinetic parameters are calculated, including activation energy, Arrhenius multiplier, and reaction order. The enantiomeric purity of the resulting cyclic product was assessed. The self-assembly of linear and cyclic dipeptides on a solid support was studied. The results of the study will be useful for establishing the mechanism of the cyclization reaction of dipeptides in the solid phase, and can also be used in the development of effective and cost-effective methods for the production of cyclic dipeptides.

A new insight into the mechanism of solid-state cyclization of dipeptides: The effect of the sequence of amino acid residues in phenylalanyl-leucine and leucyl-phenylalanine

Heat treatment of linear dipeptides in the solid state is a good strategy for obtaining their cyclic analogs with a high yield and minimal costs. However, the cyclization of dipeptides under the crystal lattice constraints is still poorly understood. In this work, the thermally induced cyclization of l-phenylalanyl-l-leucine and l-leucyl-l-phenylalanine in the solid state was studied. Kinetic parameters of these reactions were estimated using the approaches of nonisothermal kinetics. For the first time, a possible mechanism of the reaction and rate-determining step is discussed. The effect of the sequence of amino acid residues in the dipeptide molecules on temperature and activation energy of solid-state cyclization was observed. The optical purity of the reaction products was estimated. The effect of temperature on the state of dipeptides films was visualized using atomic force microscopy. The results obtained contribute to the understanding of the mechanisms of solid-state cyclization of dipeptides and can be useful in the development of methods for the synthesis of diketopiperazine derivatives.

Chiral analysis of linear protonated dipeptides by complexing with Cyclodextrins using Ion-Mobility Mass-Spectrometry and DFT structural calculations

The functions and applications of dipeptides have been reported to possess unique characteristics compared to that of proteins or amino acids. Naturally occurring amino acids, except for glycine, are chiral molecules; thus, for each type of dipeptide there are four possible isomers. Isomeric structural analysis of dipeptides is important for measuring the quality of dipeptide products, as well as understanding their chemical and biological functions in humans. In the present study, a rapid and simple method for isomeric recognition of protonated dipeptides H-D/l-Phe-D/L-X-OH, where X = hydrophobic amino acids, including alanine (Ala), isoleucine (Ile), leucine (Leu), proline (Pro), tryptophan (Trp), valine (Val), phenylalanine (Phe), and methionine (Met), was developed and investigated. Mixed solutions of dipeptides and cyclodextrins (CDs) were prepared for the production of gas phase, non-covalent complex ions by electrospray ionization (ESI). Trapped ion-mobility mass spectrometry (TIMS-MS) was subsequently used to investigate the corresponding ion mobilities (IM). The TIMS and density functional theory (DFT) results showed that the chiral structure of different dipeptides can be distinguished by β-CD, which indicates that different isomeric complexes have different collision cross sections (CCSs) and spatial conformations. The relative content of isomeric dipeptides mixtures was also obtained in the ratio range from 10:1 to 1:10 to measure the detection limits. Our work provides a direct analytical method for determining isomeric dipeptides, which could potentially have wide applications in the field of chiral recognition.

Cyclodipeptides: From Their Green Synthesis to Anti-Age Activity.

Cyclodipeptides (CDPs) or diketopiperazines (DKPs) are often found in nature and in foodstuff and beverages and have attracted great interest for their bioactivities, biocompatibility, and biodegradability. In the laboratory, they can be prepared by green procedures, such as microwave-assisted cyclization of linear dipeptides in water, as performed in this study. In particular, five CDPs were prepared and characterized by a variety of methods, including NMR and ESI-MS spectroscopies and single-crystal X-ray diffraction (XRD), and their cytocompatibility and anti-aging activity was tested in vitro, as well as their ability to penetrate the different layers of the skin. Although their mechanism of action remains to be elucidated, this proof-of-concept study lays the basis for their future use in anti-age cosmetic applications.

Deletion of COM donor and acceptor domains and the interaction between modules in bacillomycin D produced by Bacillus amyloliquefaciens

Bacillomycin D is a cyclic lipopeptide produced by Bacillus amyloliquefaciens fmbJ. At present, no relevant report has described the combinatorial biosynthesis of bacillomycin D. Due to the strong biosynthetic potential of the communication-mediating (COM) domains, its crosstalk between NRPS subunits has been studied to some extent, but the interaction of COM domain between modules is rarely reported. Therefore, in this study, we conducted the combinatorial biosynthesis of bacillomycin D through the deletion of the COM donor and acceptor domains between the modules and elucidated the interaction between the NRPS modules. The results showed that the deletion of the donor domain between modules 2 and 3 did not affect catalysis by upstream modules, but prevented downstream modules from catalysing the extension of the lipopeptide product, ultimately resulting in mutant complexes that could form linear dipeptides with the sequence β-NH2FA-Asn-Tyr. However, the engineered hybrid bacillomycin D NRPSs lacking the donor domains between modules 3 and 4 and modules 6 and 7 could form multiple assembly lines that produced bacillomycin D and its analogs (linear tripeptides, cyclic hexapeptides and linear hexapeptides). In addition, all the acceptor domain deletion strains failed to produce bacillomycin D, only truncated peptides produced by module interruption (except for the acceptor domain deletion strains between modules 3 and 4, which also produced cyclic hexapeptides). In conclusion, deletion of the inter-module donor domains led to a more flexible hybrid biosynthetic system for the production of diverse peptide products; compared with the inter-subunit donor domain deletion strains that could only produce truncated peptides, the former had a greater biosynthetic capacity. Meanwhile, the acceptor domains between modules were an important part of module-module interactions and efficient communication within bacillomycin D synthetase.

Comprehensive Metabolomic Comparison of Five Cereal Vinegars Using Non-Targeted and Chemical Isotope Labeling LC-MS Analysis.

Vinegar is used as an acidic condiment and preservative worldwide. In Asia, various black vinegars are made from different combinations of grains, such as Sichuan bran vinegar (SBV), Shanxi aged vinegar (SAV), Zhenjiang aromatic vinegar (ZAV), and Fujian Monascus vinegar (FMV) in China and Ehime black vinegar in Japan (JBV). Understanding the chemical compositions of different vinegars can provide information about nutritional values and the quality of the taste. This study investigated the vinegar metabolome using a combination of GC-MS, conventional LC-MS, and chemical isotope labeling LC-MS. Different types of vinegar contained different metabolites and concentrations. Amino acids and organic acids were found to be the main components. Tetrahydroharman-3-carboxylic acid and harmalan were identified first in vinegar. Various diketopiperazines and linear dipeptides contributing to different taste effects were also detected first in vinegar. Dipeptides, 3-phenyllactic acid, and tyrosine were found to be potential metabolic markers for differentiating vinegars. The differently expressed pathway between Chinese and Japanese vinegar was tryptophan metabolism, while the main difference within Chinese vinegars was aminoacyl-tRNA biosynthesis metabolism. These results not only give insights into the metabolites in famous types of cereal vinegar but also provide valuable knowledge for making vinegar with desirable health characteristics.

Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide.

Dipeptides, the prototype peptides, exist in both linear (l-) and cyclo (c-) structures. Since the first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.

Modulation of Naturally Occurring Linear Dipeptide Chirality to Reduce the Affinity for Oligopeptide Transporter 1 and Increase Intestinal Stability for an Enhanced Colon-Targeting Effect in the Treatment of Inflammatory Bowel Disease: An Application of trans-4-l-Hydroxyprolyl-l-serine.

The naturally occurring linear dipeptide JBP923 (trans-4-l-Hyp-l-Ser, HS-tLL) with anti-inflammatory effects showed potential for the treatment of inflammatory bowel disease (IBD). However, colon-specific delivery after oral administration is still a challenge because its absorption is mediated by oligopeptide transporter 1 (PEPT1) in the upper small intestine and because of its instability in the gastrointestinal tract. Therefore, we aimed to enhance the colon-targeting efficiency by modulating HS-tLL chirality to synthesize eight enantiomers. Among these enantiomers, trans-4-d-Hyp-d-Ser, cis-4-l-Hyp-d-Ser, cis-4-d-Hyp-l-Ser, and cis-4-d-Hyp-d-Ser did not work as substrates of PEPT1 and were stable in the gastrointestinal tract, resulting in enhanced colonic accumulation through the paracellular pathway due to the loose tight junctions in IBD. Interestingly, cis-4-d-Hyp-d-Ser exerted the most potent therapeutic effect on IBD. Our findings revealed the impact of chirality on the colonic accumulation of the linear dipeptide, providing strategies for the colon-targeted delivery of the linear dipeptide for the treatment of IBD.

Stackable Aromatic Dipeptide Ring Structures toward Nanotube Formation: Thermodynamics and Interactions in Gas‐Phase and Solution

AbstractIncreasing attention has been drawn towards self‐assembling dipeptide nanotube materials (NT) for their tunable properties. Despite recent advances, a fundamental understanding of the conditions that drive the self‐assembly process is still lacking. Here, we report the structures, thermodynamics, and underlying interactions of the nanotube forming potential of cyclic and linear aromatic dipeptides phenylalanine‐tyrosine, tryptophan‐tyrosine, and dityrosine via the piecewise self‐assembly mechanism. The cyclic dipeptides have better favorability of oligomerization in the gas phase than the linear dipeptides, largely due to the enthalpic gain of forming more hydrogen bonds, suggesting that the piecewise mechanism is plausible for vapor deposition methods. Oligomerization in solution, which would require desolvation of free monomers, was shown to be thermodynamically unfavorable, especially in polar solvents, demonstrating the need for an external stimulus for the crystallization of NTs. The generated oligomeric rings show structural robustness and symmetry, allowing excellent stacking potential in both lateral and axial directions. The nature of the sidechains significantly affects the stabilizations within the oligomeric structure. The insights generated can be used as a basis for dipeptide modifications that could enhance targeted NT properties for different applications.

Self-Assembly Dipeptide Hydrogel: The Structures and Properties.

Self-assembly peptide-based hydrogels are well known and popular in biomedical applications due to the fact that they are readily controllable and have biocompatibility properties. A dipeptide is the shortest self-assembling motif of peptides. Due to its small size and simple synthesis method, dipeptide can provide a simple and easy-to-use method to study the mechanism of peptides’ self-assembly. This review describes the design and structures of self-assembly linear dipeptide hydrogels. The strategies for preparing the new generation of linear dipeptide hydrogels can be divided into three categories based on the modification site of dipeptide: 1) COOH-terminal and N-terminal modified dipeptide, 2) C-terminal modified dipeptide, and 3) uncapped dipeptide. With a deeper understanding of the relationship between the structures and properties of dipeptides, we believe that dipeptide hydrogels have great potential application in preparing minimal biocompatible materials.

Cyclic Dipeptides Formation From Linear Dipeptides Under Potentially Prebiotic Earth Conditions

Cyclic dipeptides (DKPs) are peptide precursors and chiral catalysts in the prebiotic process. This study reports proline-containing DKPs that were spontaneously obtained from linear dipeptides under an aqueous solution. Significantly, the yields of DKPs were affected by the sequence of linear dipeptides and whether the reaction contains trimetaphosphate. These findings provide the possibility that DKPs might play a key role in the origin of life.

Using fast scanning calorimetry to study solid-state cyclization of dipeptide L-leucyl-L-leucine

The possibility of using fast scanning calorimetry (FSC) to study the kinetics of the solid-state cyclization of dipeptide was demonstrated in the present work for the first time. The activation energy and Arrhenius constant of the cyclization of L-leucyl-L-leucine (Leu-Leu) were estimated. FSC data obtained at heating rates from 18,000 to 54,000 K min−1 were evaluated by non-isothermal kinetics. The dependence of the specific heat capacity cp on temperature was determined for linear and cyclic Leu-Leu dipeptides using differential scanning calorimetry (DSC) and FSC. The application of FSC allows studies of solid-state reactions for expensive substances and compounds synthesized in very small amounts.

Quantum-chemical ab initio study of side chain pKa of linear and cyclic lysine dipeptides

Cyclic dipeptides show interesting biological activities such as antitumor, antiviral and so on. In biological systems, the bioavailability of drugs is determined by several parameters such as pKa values. In this study, we used DFT and thermodynamics cycle to determine pKa value of side chain of lysine in linear and cyclic dipeptides. All considered dipeptides were optimized using B3LYP and RMSD tool was used to compare the optimized structures. The calculated pKa values were compared with the available experimental data. Our results show that pKa of side chain of lysine increases for cyclic dipeptides compared to the linear ones. To justify the reason of increasing of pKa of cyclic dipeptides, we used NBO and AIM analyses. The analyses showed that a hydrogen bond in cyclic lysine dipeptides is responsible for increasing of pKa.

Quantum-Chemical ab initio Study of Side Chain pKa of Linear and Cyclic Lysine Dipeptides

Cyclic dipeptides show interesting biological activities such as antitumor, antiviral and so on. In biological systems, the bioavailability of drugs is determined by several parameters such as pKa values. In this study, we used DFT and thermodynamics cycle to determine pKa value of side chain of lysine in linear and cyclic dipeptides. All considered dipeptides were optimized using B3LYP and RMSD tool was used to compare the optimized structures. The calculated pKa values were compared with the available experimental data. Our results show that pKa of side chain of lysine increases for cyclic dipeptides compared to the linear ones. To justify the reason of increasing of pKa of cyclic dipeptides, we used NBO and AIM analyses. The analyses showed that a hydrogen bond in cyclic lysine dipeptides is responsible for increasing of pKa.

Cyclization Effect on pKa of the Side Chain of Aspartic Acid in Dipeptides: A DFT Study

Cyclic dipeptides are very important compounds that have a wide range of applications in pharmaceutical chemistry and life sciences. In the current work, the acidity of the side chain of aspartic acid was calculated for various linear and a cyclic dipeptide. pKa values were derived using the thermodynamics cycle and DFT/B3LYP approach. The obtained pKa values show strong acidity for cyclic with respect to linear dipeptides. We found an intramolecular hydrogen bond in cyclic dipeptide structure, which can be used to justify the increasing acidity of the side chain of Asp as compared to linear structures.

Bioactivatable Pseudotripeptidization of Cyclic Dipeptides To Increase the Affinity toward Oligopeptide Transporter 1 for Enhanced Oral Absorption: An Application to Cyclo(l-Hyp-l-Ser) (JBP485).

The cyclic dipeptides generally present lower affinity toward intestinal oligopeptide transporter 1 (PEPT1) than the linear dipeptides. JBP485 (cyclo(l-Hyp-l-Ser)) is a low-affinity substrate of PEPT1 with poor oral bioavailability. However, JBP923 (l-Hyp-l-Ser) is a high-affinity substrate of PEPT1 with high oral absorption. We hypothesize that the bioactivatable pseudo-tripeptidization prodrug strategy is promising to increase the affinity of cyclic dipeptides toward PEPT1. To test our hypothesis, we design five amino acid ester prodrugs of JBP485. Compared with JBP485, the optimal prodrug (JBP485-3-CH2-O-valine, J3V) demonstrates improved affinity of PEPT1, oral bioavailability in rats and beagle dogs. Moreover, J3V can dose-dependently protect against liver injury. Additionally, J3V is stable in the gastrointestinal tract, beneficial to the PEPT1-mediated membrane transport, and is bioactivated in the enterocytes and hepatic cells, essential to elicit its bioactivity. In summary, the bioactivatable pseudo-tripeptidization strategy shows potential in increasing affinity of PEPT1 to enhance oral bioavailability of cyclic dipeptides.

Thermally induced cyclization of L‐isoleucyl‐L‐alanine in solid state: Effect of dipeptide structure on reaction temperature and self‐assembly

Thermal treatment of short-chain oligopeptides is able to initiate the process of their self-assembly with the formation of organic nanostructures with unique properties. On the other hand, heating can lead to a chemical reaction with the formation of new substances with specific properties and ability to form structures with different morphology. Therefore, in order to have a desired process, researcher needs to find its temperature range. In the present work, cyclization of L -isoleucyl-L -alanine dipeptide in the solid state upon heating was studied. Kinetic parameters of this reaction were estimated within the approaches of the nonisothermal kinetics. The correlation between side chain structure of dipeptides and temperature of their cyclization in the solid state was found for the first time. This correlation may be used to predict the temperature, at which dipeptide self-assembly changes to chemical reaction. The differences in self-assembly of linear and cyclic dipeptides were demonstrated using atomic force microscopy. The effect of dipeptide concentration in a source solution and an organic solvent used on self-assembly of dipeptides was shown. The new information obtained on the thermal properties and self-assembly of linear and cyclic forms of L -isoleucyl-L -alanine may be useful for the design of new nanomaterials based on oligopeptides, as well as for the synthesis of cyclic oligopeptides.

Probing the Nature of Noncovalent Interactions in Dimers of Linear Tyrosine-Based Dipeptides.

Tyrosine-based dipeptides self-assemble to form higher order structures. To gain insights into the nature of intermolecular interactions contributing to the early stages of the self-assembly of aromatic dipeptides, we study the dimers of linear dityrosine (YY) and tryptophan–tyrosine (WY) using quantum-chemical methods with dispersion corrections and universal solvation model based on density in combination with energy decomposition and natural bond orbital (NBO) analyses. We find that hydrogen bonding is a dominant stabilizing force. The lowest energy structure for the linear YY dimer is characterized by Ocarboxyl···H(O)tyr. In contrast, the lowest energy dimer of linear WY is stabilized by Ocarboxyl···H(N)trp and πtyr···πtyr. The solvent plays a critical role as it can change the strength and nature of interactions. The lowest energy for linear WY dimer in acetone is stabilized by Ocarboxyl···H(O)tyr, πtrp···H(C), and πtrp···H(N). The ΔG of dimerization and stabilization energies of solvated dipeptides reveal that the dipeptide systems are more stable in the solvent phase than in gas phase. NBO confirms increased magnitudes for donor–acceptor interaction for the solvated dipeptides.

Molecular Mechanisms of Tryptophan-Tyrosine Nanostructures Formation and their Influence on PC-12 Cells.

The discovery of self-assembling peptides, which can form well-ordered structures, has opened a realm of opportunity for the design of tailored short peptide-based nanostructures. In this study, a combined experimental and computational approach was utilized to understand the intramolecular and intermolecular interactions contributing to the self-assembly of linear and cyclic tryptophan-tyrosine (WY) dipeptides. The density functional tight binding (DFTB) calculations with empirical dispersive corrections assisted the identification of the lowest energy conformers. Conformer analysis and the prediction of the electronic structure for the monomeric, dimeric, and hexameric forms of the cyclic and linear WY confirmed the contributions of hydrogen bonding, π-π stacking, and CH-π interactions in the stability of the self-assembled nanotubes. The influence of the processing conditions on the morphological and thermal characteristics, as well as the secondary structures of the synthesized nanostructures, were analyzed. Preliminary studies of the influence of the nanotubes on the fate of neuronalcell lines such as, PC-12cells indicate that the nanotubes promote cellular proliferation, and differentiation in the absence of growth factors. The aspect ratio of the nanotubes played an essential role in cellular interactions where a higher cellular uptake was observed in nanotubes of lower aspect ratios. These results provide insight for future applications of such nanotubes as scaffolds for tissue engineering and nerve regeneration and in drug delivery.