Tripeptide Fragment Research Articles

On the Variativity of Cell Adhesive Response under the Action of Related Short Peptides

Analysis of the participation of short peptides GER and FGER containing common tripeptide fragment in the regulation of adhesive response of CHO-K1 cells was conducted. Both peptides stimulated cell adhesion both to untreated plastic and to gelatin-coated plastic, but did not change cell attachment to poly-L-lysine-coated plastic. Tripeptide GER had larger stimulation effect on cell adhesion to untreated plastic. Peptide FGER increased the rate of cell attachment to gelatin in a wider range of concentrations as compared to adhesion to untreated plastic. Variativity of cell spreading to different substrates under peptide action was demonstrated. On untreated plastic both investigated peptides practically in equal extent stimulated cell spreading. On gelatin peptide FGER kept the stimulation effect on cell spreading, but peptide GER partly inhibited cell spreading as compared to cell spreading on untreated plastic. It was established that insertion of additional N-terminal hydrophobic amino acid residue Phe to tripeptide fragment GER changes the regulatory activity of peptide at the cell adhesion model depending on the stage of cell connection with substrate and/or on substrate properties. The structural-functional activity of investigated short peptides on the instance of different structural components of adhesive structures is discussed.

Integration of machine learning in 3D-QSAR CoMSIA models for the identification of lipid antioxidant peptides.

The comparative molecular similarity indices analysis (CoMSIA) method is a widely used 3D-quantitative structure-activity relationship (QSAR) approach in the field of medicinal chemistry and drug design. However, relying solely on the Partial Least Square algorithm to build models using numerous CoMSIA indices has, in some cases, led to statistically underperforming models. This issue has also affected 3D-CoMSIA models constructed for the ferric thiocyanate (FTC) dataset from linoleic antioxidant measurements. In this study, a novel modeling routine has been developed incorporating various machine learning (ML) techniques to explore different options for feature selection, model fitting, and tuning algorithms with the ultimate goal of arriving at optimal 3D-CoMSIA models with high predictivity for the FTC activity. Recursive Feature Selection and SelectFromModel techniques were applied for feature selection, resulting in a significant improvement in model fitting and predictivity (R2, RCV2, and R2_test) of 24 estimators. However, these selection methods did not fully address the problem of overfitting and, in some instances, even exacerbated it. On the other hand, hyperparameter tuning for tree-based models resulted in dissimilar levels of model generalization for four tree-based models. GB-RFE coupled with GBR (hyperparameters: learning_rate = 0.01, max_depth = 2, n_estimators = 500, subsample = 0.5) was the only combination that effectively mitigated overfitting and demonstrated superior performance (RCV2 of 0.690, R2_test of 0.759, and R2 of 0.872) compared to the best linear model, PLS (with RCV2 of 0.653, R2_test of 0.575, and R2 of 0.755). Therefore, it was subsequently utilized to screen potential antioxidants among a range of Tryptophyllin L tripeptide fragments, leading to the synthesis and testing of three peptides: F-P-5Htp, F-P-W, and P-5Htp-L. These peptides exhibited promising activity levels, with FTC values of 4.2 ± 0.12, 4.4 ± 0.11, and 1.72 ± 0.15, respectively.

Antimicrobial Activity of Silver Nanoparticles Loaded Biomimetic Isomeric Short Lipopeptide Nanostructures

AbstractLipopeptide‐inspired lipidation of two short tripeptides, Phe‐Tyr‐β‐Ala and Tyr‐Phe‐β‐Ala leads to a pair of constitutional isomers of short peptide amphiphile (sPA). These two molecules were able to mimic lipopeptides properties and therefore could be used as potential drug delivery vehicles up to target sites. Further, these isomeric peptide amphiphiles were able to synthesize stable silver nanoparticles (AgNPs) in presence of sunlight without using any reducing agents. Interestingly, the presence of AgNPs significantly controls the secondary structures of these two isomeric sPAs and hence their self‐assembly. Therefore, such AgNPs‐sPA nanostructures are further used to develop antibacterial materials. Various microscopy and spectroscopy techniques were used to characterize these nanostructures. The antibacterial analysis demonstrated that owing to high biocompatibility and less cytotoxicity, designed sPA exhibited great potential in locally addressing bacterial infections. Thus, such a strategic design of lipidated tripeptide fragments can be tuned for potential therapeutic value for future applications.

Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome.

Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.

Virtual screening and rational design of antioxidant peptides based on tryptophyllin L structures isolated from the Litoria rubella frog.

Discovery of natural antioxidants has been carried out for decades relying mainly on experimental approaches that are commonly associated with time and cost demanding biochemical assays. The maturation of quantitative structure activity relationship (QSAR) modelling has provided an alternative approach for searching and designing antioxidant compounds with alleviated costs. As a contribution to this approach, this work aimed to establish a fragment-based 3D-QSAR procedure to discover and design potential antioxidants based on tryptophyllin L structures isolated from the red tree frog Litoria rubella. A force field and a Gaussian 3D-QSAR model were built to screen for potential antioxidants from tripeptide fragments covering all sequences of tryptophyllin L database. Among those, PWY(NH2 ) corresponding tryptophyllin L 4.1 was predicted to have the highest 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical cation (ABTS+ ·) scavenging capability. Two newly designed peptides PYW and PYW(NH2 ) together with PWY(NH2 ), tryptophyllin L 4.1, and the reference peptide PWY were synthesized and subjected to two antioxidant assays including ABTS scavenging and ferric reducing antioxidant power assays. Although the experimental TEAC values of the five peptides were roughly similar to those from predictions, the activity order was not in agreement with the predictions. The dissimilarities were accounted by the difference in the experimental procedures, the deviation of modelling regression, and the synergetic effect of structural and experimental features. The ABTS radical scavenging assays revealed that all the tested peptides were strong ABTS+ · scavengers with the antioxidant capabilities approximately twice as high as trolox and higher than glutathione. The ferric reducing activities of the peptides were, on the other hand, much weaker than that of trolox suggesting different antioxidant mechanisms inserted by trolox and the peptides. This work was a demonstration that 3D-QSAR methods can be employed in conjunction with experimental methods to effectively detect and design antioxidant peptides.

γ-Glutamyl transpeptidase–activated indole-quinolinium based cyanine as a fluorescence turn-on nucleolus-targeting probe for cancer cell detection and inhibition

A nucleolus as a prominent sub-nuclear, membraneless organelle plays a crucial role in ribosome biogenesis, which is in the major metabolic demand in a proliferating cell, especially in aggressive malignancies. We develop a γ-glutamyltranspeptidase (GGT)-activatable indole-quinolinium (QI) based cyanine consisting of a novel tripeptide fragment (Pro-Gly-Glu), namely QI-PG-Glu as a turn-on red fluorescent probe for the rapid detection of GGT-overexpressed A549 cancer cells in vivo. QI-PG-Glu can be triggered by GGT to rapidly release an activated fluorophore, namely HQI, in two steps including the cleavage of the γ-glutamyl group recognized by GGT and the rapid self-driven cyclization of the Pro-Gly linker. HQI exhibits dramatically red fluorescence upon binding to rRNA for imaging of nucleolus in live A549 cells. HQI also intervenes in rRNA biogenesis by declining the RNA Polymerase I transcription, thus resulting in cell apoptosis via a p53 dependent signaling pathway. Our findings may provide an alternative avenue to develop multifunctional cancer cell-specific nucleolus-targeting fluorescent probes with potential anti-cancer effects.

QSSR Modeling of Bacillus Subtilis Lipase A Peptide Collision Cross-Sections in Ion Mobility Spectrometry: Local Descriptor Versus Global Descriptor.

To investigate the structure-dependent peptide mobility behavior in ion mobility spectrometry (IMS), quantitative structure-spectrum relationship (QSSR) is systematically modeled and predicted for the collision cross section Ω values of totally 162 single-protonated tripeptide fragments extracted from the Bacillus subtilis lipase A. Two different types of structure characterization methods, namely, local and global descriptor as well as three machine learning methods, namely, partial least squares (PLS), support vector machine (SVM) and Gaussian process (GP), are employed to parameterize and correlate the structures and Ω values of these peptide samples. In this procedure, the local descriptor is derived from the principal component analysis (PCA) of 516 physicochemical properties for 20 standard amino acids, which can be used to sequentially characterize the three amino acid residues composing a tripeptide. The global descriptor is calculated using CODESSA method, which can generate > 200 statistically significant variables to characterize the whole molecular structure of a tripeptide. The obtained QSSR models are evaluated rigorously via tenfold cross-validation and Monte Carlo cross-validation (MCCV). A comprehensive comparison is performed on the resulting statistics arising from the systematic combination of different descriptor types and machine learning methods. It is revealed that the local descriptor-based QSSR models have a better fitting ability and predictive power, but worse interpretability, than those based on the global descriptor. In addition, since the QSSR modeling using local descriptor does not consider the three-dimensional conformation of tripeptide samples, the method would be largely efficient as compared to the global descriptor.

Synthesis of New Cyclopeptide Analogues of the Miuraenamides.

Miuraenamides belong to natural marine compounds with interesting biological properties. Miuraenamides initiate polymerization of monomeric actin and therefore show high cytotoxicity by influencing the cytoskeleton. New derivatives of the miuraenamides have been synthesized containing an N-methylated amide bond instead of the more easily hydrolysable ester in the natural products. Incorporation of an aromatic side chain onto the C-terminal amino acid of the tripeptide fragment also led to highly active new miuraenamides. In this study, we showed that the ester bond of the natural product miuraenamide can be replaced by an N-methyl amide. The yields in the cyclization step were high and generally much better than with the corresponding esters. On the other hand, the biological activity of the new amide analogs was lower compared to the natural products, but the activity could significantly be increased by incorporation of a p-nitrophenyl group at the C-terminus of the peptide fragment.

Mapping Conformational Space of All 8000 Tripeptides by Quantum Chemical Methods: What Strain Is Affordable within Folded Protein Chains?

To gain more insight into the physicochemical aspects of a protein structure from the first principles, conformational space of all 8000 "capped" tripeptides (i.e., N-Ac-X1X2X3-NH-CH3, where Xi is one of the 20 natural amino acids) was investigated computationally. An enormous dataset (denoted P-CONF_1.6M and containing close to 1 600 000 conformers in total) has been obtained by employing a composite protocol combining density functional theory, semiempirical quantum mechanics (SQM), and state-of-the-art solvation methods with 1000 K molecular dynamics (MD) used to generate initial structures (200 snapshots for each tripeptide). This allowed us to present the first rigorous QM-based glimpse at the vast conformational space spanned by small protein fragments. The same computational procedure was repeated for tripeptide fragments taken from the SCOPe database of three-dimensional protein folds, by restraining them to their geometry in a protein. Such complementary data allowed us to compare the distribution of conformational strain energies of unrestrained tripeptidic fragments "in solvent" with those in existing protein chains. Besides providing a rigorous (ab initio) proof of a few well-known concepts and hypotheses concerning protein structures, such as the distribution of (φ, ψ) angles in Ramachandran plots, we have made several observations that came as a certain surprise: (1) distribution of conformational energies does not significantly differ between the "unbiased/unrestrained" conformers obtained from MD sampling in solvent and the biased conformers, i.e., those of a given tripeptide obtained from protein structures; (2) conformational (strain) energy window up to ∼20 to 25 kcal·mol-1 is readily available to tripeptide fragments within the context of a protein chain; (3) overpopulation in certain regions of Ramachandran plot was observed for the unbiased conformers. Last but not least, the massive dataset of accurate (DFT-D3//COSMO-RS) conformational (free) energies of ∼1.6 M peptide conformers, P-CONF_1.6M, obtained throughout this work may serve as excellent dataset for calibrating and benchmarking of popular force fields.

Spatial Structure of the Acth-(6-9)-PGP Molecule

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

Spatial Structure of the Acth-(6-9)-PGP Molecule

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

The journey of total synthesis toward nannocystin Ax

Herein we describe the detail on our full investigations that led to the achievement of the total synthesis of nannocystin Ax, a 21-membered macrocyclic natural product composing of a tripeptide fragment and a polyketide fragment, which featured in 8 longest linear steps in with 13.9% total overall yield. The key synthetic strategy relied on the late-stage stille coupling for the macrolactonization to construct the 21-membered ring, while direct connection between the tripeptide fragment and the polyketide fragment failed. 1H NMR experiments reveal that nannocystin Ax should exist as conformational mixtures in deuterated solvents.

Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database

Intrinsically disordered proteins (IDPs) play fundamental roles in signaling, regulation, and cell homeostasis by specifically interacting with their partners. The structural characterization of these interacting regions remains challenging and requires the integration of extensive experimental information. Here we present an approach that exploits the structural information encoded in tripeptide fragments from coil regions of high-resolution structures. Our results indicate that a simple building approach that disregards the sequence context provides a good structural representation of fully disordered regions. Conversely, the description of partially structured motifs calls for the consideration of sequence-dependent structural preferences. By using nuclear magnetic resonance residual dipolar couplings and small-angle X-ray scattering data for multiple IDPs we demonstrate that the appropriate combination of these two building strategies produces ensemble models that correctly describe the secondary structural classes and the population of partially structured regions. This study paves the way for the extension of structure prediction and protein design to disordered proteins.

Opioid Tripeptides Hybridized with trans-1-Cinnamylpiperazine as Proliferation Inhibitors of Pancreatic Cancer Cells in Two- and Three-Dimensional in vitro Models.

According to the World Health Organization, the mortality rate among patients with pancreatic cancer will increase in the upcoming years. Gemcitabine is the first choice for treatment of pancreatic malignancy, but increasing resistance to this drug is decreasing its overall efficacy. Studies on new therapies that target metabolic pathways, growth factor inhibitors, and tumor stroma or tumor stem cells are currently underway in many research groups. Herein we report the bioactive properties (cytotoxicity and hemolytic activity) of synthetic peptidomimetics containing an opioid tripeptide fragment (Tyr-R1 -R2 -; where R1 is d-Ala or d-Thr, and R2 is Phe or Trp) hybridized with trans-1-cinnamylpiperazine. These compounds are stable in plasma up to 96 h and exhibit low hemotoxicity and good inhibitory effects on cancer cell growth in two- and three-dimensional in vitro models of pancreatic cancer.

Total Synthesis and Pharmacological Investigation of Cordyheptapeptide A.

The present investigation reports the synthesis of a phenylalanine-rich N-methylated cyclopeptide, cordyheptapeptide A (8), previously isolated from the insect pathogenic fungus Cordyceps sp. BCC 1788, accomplished through the coupling of N-methylated tetrapeptide and tripeptide fragments followed by cyclization of the linear heptapeptide unit. Structure elucidation of the newly synthesized cyclopolypeptide was performed by means of FT-IR, 1H-NMR, 13C-NMR, and fast atom bombardment mass spectrometry (FABMS), and screened for its antibacterial, antidermatophytic, and cytotoxic potential. According to the antimicrobial activity results, the newly synthesized N-Methylated cyclopeptide exhibited potent antibacterial activity against Gram-negative bacteria Pseudomonas aeruginosa and Klebsiella pneumoniae and antifungal activity against dermatophytes Trichophyton mentagrophytes and Microsporum audouinii at a concentration of 6 μg/mL, in comparison to the reference drugs, gatifloxacin and griseofulvin. In addition, cyclopolypeptide 8 displayed suitable levels of cytotoxicity against Dalton’s lymphoma ascites (DLA) and Ehrlich’s ascites carcinoma (EAC) cell lines.

Interaction of Chloramphenicol Tripeptide Analogs with Ribosomes.

Chloramphenicol amine peptide derivatives containing tripeptide fragments of regulatory "stop peptides" - MRL, IRA, IWP - were synthesized. The ability of the compounds to form ribosomal complexes was studied by displacement of the fluorescent erythromycin analog from its complex with E. coli ribosomes. It was found that peptide chloramphenicol analogs are able to bind to bacterial ribosomes. The dissociation constants were 4.3-10µM, which is 100-fold lower than the corresponding values for chloramphenicol amine-ribosome complex. Interaction of the chloramphenicol peptide analogs with ribosomes was simulated by molecular docking, and the most probable contacts of "stop peptide" motifs with the elements of nascent peptide exit tunnel were identified.

Kilogram-Scale Synthesis of Osteogenic Growth Peptide (10–14) Using a Fragment Coupling Approach

Kilogram-scale synthesis of a bioactive pentapeptide in solution by “3 + 2” fragment coupling strategy has been successively accomplished in the development of OGP (10–14), a minimal OGP-derived sequence that retains the full proliferative activity of the osteogenic growth peptide. The synthetic scheme, coupling conditions, and scaling-up of the process are systematically studied; the epimerization of the tripeptide fragment and pentapeptide are also evaluated.

Hydrophilic bioconjugatable trans-AB-porphyrins and peptide conjugates

Porphyrins bearing a single bioconjugatable group and a single water-solubilization motif in a trans-AB-architecture (with no other substituents) provide a compact design of value for studies in diverse disciplines. Established synthetic methods have been employed to prepare four new free base porphyrins and one Mn ( III ) chelate. The hydrophilic motif includes 4-N-methylpyridinium, 2,4,6-tris(carboxymethoxy)phenyl, 2,6-bis(phosphonomethoxy)phenyl, and carboxy; the bioconjugatable unit includes carboxy, maleimido, and N-hydroxysuccinimido (NHS) ester. Bioconjugation experiments with a protected porphyrin-diphosphate or unprotected porphyrin-diphosphonate were examined in organic solution or water, respectively. Both approaches were employed to conjugate to the ε-amino group of Lys11 in AcKPV- NH 2, a tripeptide fragment [ Ac -α-MSH(11-13)- NH 2] of melanocyte stimulating hormone, yielding porphyrin-peptide conjugates.

The synthesis of a glucoconjugate of the peptidic fragment of cryptophycin-24

A novel glucoconjugate of the peptidic fragment of cryptophycin-24 was prepared through the replacement of the leucic acid residue with L-leucine and the functionalisation of tyrosine residue with glucose.Those modifications lead to a novel protected tripeptide fragment of cryptophycin-24.

Vascular effects of a tripeptide fragment of novokinine in hypertensive rats: Mechanism of the hypotensive action

BackgroundActivation of angiotensin AT2 receptors (AT2R) counteracts vasoconstrictor effects of AT1R stimulation and contributes to blood pressure control. We examined effects on mean arterial pressure (MAP) and renal hemodynamics of LKP, a tripeptide fragment of novokinine, an established AT2R agonist. MethodsEffects of intravenous LKP infusion and then superimposed losartan (AT1R antagonist) on MAP, total renal (RBF, Transonic probe) and renal medullary blood flows (laser-Doppler), and on renal excretion, were examined in anesthetized (1) Wistar rats with acute norepinephrine-induced hypertension, untreated or pretreated with AT2R antagonist (PD 123319) and (2) spontaneously hypertensive rats (SHR) maintained on standard or high-sodium (HS) diet. ResultsIn Wistar rats LKP decreased MAP (−4%, p<0.01) and increased renal medullary perfusion, these effects were abolished in rats pretreated with PD 123319 in which a post-LKP increase in MAP (+6%, p<0.02) occurred. LKP did not alter MAP in SHR; in those on HS diet RBF decreased (−14%, p<0.02), the response that was reverted by losartan. Addition of losartan always decreased or tended to decrease MAP. ConclusionsLKP lowered MAP in norepinephrine-induced hypertension, probably via activation of AT2R. At reduced availability of AT2R, as in SHR, LKP appeared to bind to different receptors, possibly AT1, and induced systemic or renal vasoconstriction. Compared to the parent novokinine, a smaller LKP molecule might be easier absorbed after oral application and more useful in therapy.