Antioxidant activities of major tryptophyllin L peptides: A joint investigation of Gaussian-based 3D-QSAR and radical scavenging experiments

New Insights into Antioxidant Peptides: An Overview of Efficient Screening, Evaluation Models, Molecular Mechanisms, and Applications

Antioxidant peptides are currently a hotspot in food science, pharmaceuticals, and cosmetics. In different fields, the screening, activity evaluation, mechanisms, and applications of antioxidant peptides are the pivotal areas of research. Among these topics, the efficient screening of antioxidant peptides stands at the forefront of cutting-edge research. To this end, efficient screening with novel technologies has significantly accelerated the research process, gradually replacing the traditional approach. After the novel antioxidant peptides are screened and identified, a time-consuming activity evaluation is another indispensable procedure, especially in in vivo models. Cellular and rodent models have been widely used for activity evaluation, whilst non-rodent models provide an efficient solution, even with the potential for high-throughput screening. Meanwhile, further research of molecular mechanisms can elucidate the essence underlying the activity, which is related to several signaling pathways, including Keap1-Nrf2/ARE, mitochondria-dependent apoptosis, TGF-β/SMAD, AMPK/SIRT1/PGC-1α, PI3K/Akt/mTOR, and NF-κB. Last but not least, antioxidant peptides have broad applications in food manufacture, therapy, and the cosmetics industry, which requires a systematic review. This review introduces novel technologies for the efficient screening of antioxidant peptides, categorized with a new vision. A wide range of activity evaluation assays, encompassing cellular models, as well as rodent and non-rodent models, are provided in a comprehensive manner. In addition, recent advances in molecular mechanisms are analyzed with specific cases. Finally, the applications of antioxidant peptides in food production, therapy, and cosmetics are systematically reviewed.

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.

Purification, Conformational Analysis and Cytotoxic Activities of Host-Defense Peptides from the Giant Gladiator Treefrog Boana boans (Hylidae: Hylinae)

Frogs from the extensive amphibian family Hylidae are a rich source of peptides with therapeutic potential. Peptidomic analysis of norepinephrine-stimulated skin secretions from the Giant Gladiator Treefrog Boana boans (Hylidae: Hylinae) collected in Trinidad led to the isolation and structural characterization of five host-defense peptides with limited structural similarity to figainin 2 and picturin peptides from other frog species belonging to the genus Boana. In addition, the skin secretions contained high concentrations of tryptophyllin-BN (WRPFPFL) in both C-terminally α-amidated and non-amidated forms. Figainin 2BN (FLGVALKLGKVLG KALLPLASSLLHSQ) and picturin 1BN (GIFKDTLKKVVAAVLTTVADNIHPK) adopt α-helical conformations in trifluroethanol-water mixtures and in the presence of cell membrane models (sodium dodecylsulfate and dodecylphosphocholine micelles). The CD data also indicate contributions from turn structures. Both peptides and picturin 2BN (GLMDMLKKVGKVALT VAKSALLP) inhibited the growth of clinically relevant Gram-negative and Gram-positive bacteria with MIC values in the range 7.8-62.5 µM. Figainin 2BN was potently cytotoxic to A549, MDA-MB-231 and HT-29 human tumor-derived cells (LC₅₀ = 7-14 µM) but displayed comparable potency against non-neoplastic HUVEC cells (LC₅₀ = 15 µM) indicative of lack of selectivity for cancer cells.

Antimicrobial, cytotoxic, and insulin-releasing activities of the amphibian host-defense peptide ocellatin-3N and its L-lysine-substituted analogs

The host-defense peptide ocellatin-3N (GIFDVLKNLAKGVITSLAS.NH₂ ), first isolated from the Caribbean frog Leptodactylus nesiotus, inhibited growth of clinically relevant Gram-positive and Gram-negative bacteria as well as a strain of the major emerging yeast pathogen Candida parapsilosis. Increasing cationicity while maintaining amphipathicity by the substitution Asp⁴ →Lys increased potency against the microorganisms by between 4- and 16-fold (MIC ≤3 μM) compared with the naturally occurring peptide. The substitution Ala¹⁸ →Lys and the double substitution Asp⁴ →Lys and Ala¹⁸ →Lys had less effects on potency. The [D4K] analog also showed 2.5- to 4-fold greater cytotoxic potency against non-small-cell lung adenocarcinoma A549 cells, breast adenocarcinoma MDA-MB-231 cells, and colorectal adenocarcinoma HT-29 cells (LC₅₀ values in the range of 12-20 μM) compared with ocellatin-3N but was less hemolytic to mouse erythrocytes. However, the peptide showed no selectivity for tumor-derived cells [LC₅₀  = 20 μM for human umbilical vein endothelial cells (HUVECs)]. Ocellatin-3N and [D4K]ocellatin-3N stimulated the release of insulin from BRIN-BD11 clonal β-cells at concentrations ≥1 nM, and [A18K]ocellatin-3N, at concentrations ≥0.1 nM. No peptide stimulated the release of lactate dehydrogenase at concentrations up to 3 μM, indicating that plasma membrane integrity had been preserved. The three peptides produced an increase in intracellular [Ca²⁺ ] in BRIN-BD11 cells when incubated at a concentration of 1 μM. In view of its high insulinotropic potency and relatively low hemolytic activity, the [A18K] ocellatin analog may represent a template for the design of agents with therapeutic potential for the treatment of patients with type 2 diabetes.

Antioxidant and Neuroprotective Effects of the First Tryptophyllin Found in Snake Venom (Bothrops moojeni)

In this study, we report the isolation, characterization, and synthesis of the peptide BmT-2 belonging to the tryptophyllins family, isolated from the venom of the snake Bothrops moojeni. This is the first time a tryptophyllin is identified in snake venom. We tested whether BmT-2 had cytotoxic effects and antioxidant activity in a set of experiments that included both in vitro and cell-based assays. BmT-2 presented a radical scavenging activity toward ABTS^• and AAPH-derived radicals. BmT-2 protected fluorescein, DNA molecules, and human red blood cells (RBCs) from free radicals generated by the thermal decomposition of AAPH. The novel tryptophyllin was not toxic in cell viability tests, where it (up to 0.4 mg/mL) did not cause hemolysis of human RBCs and did not cause significant loss of cell viability, showing a CC₅₀ > 1.5 mM for cytotoxic effects against SK-N-BE(2) neuroblastoma cells. BmT-2 prevented the arsenite-induced upregulation of Nrf2 in Neuro-2a neuroblasts and the phorbol myristate acetate-induced overgeneration of reactive oxygen species and reactive nitrogen species in SK-N-BE(2) neuroblastoma cells. Electronic structure calculations and full atomistic reactive molecular dynamics simulations revealed the relevant contribution of aromatic residues in BmT-2 to its antioxidant properties. Our study presents a novel peptide classified into the family of the tryptophyllins, which has been reported exclusively in amphibians. Despite the promising results on its antioxidant activity and low cytotoxicity, the mechanisms of action of BmT-2 still need to be further elucidated.

Antioxidant Activity of Pharmaceuticals: Predictive QSAR Modeling for Potential Therapeutic Strategy

Since oxidative stress has been linked to several pathological conditions and diseases, drugs with additional antioxidant activity can be beneficial in the treatment of these diseases. Therefore, this study takes a new look at the antioxidant activity of frequently prescribed drugs using the HPLC-DPPH method. The antioxidative activity expressed as the TEAC value of 82 drugs was successfully determined and is discussed in this work. Using the obtained values, the QSAR model was developed to predict the TEAC based on the selected molecular descriptors. The results of QSAR modeling showed that four- and seven-variable models had the best potential for TEAC prediction. Looking at the statistical parameters of each model, the four-variable model was superior to seven-variable. The final model showed good predicting power (r = 0.927) considering the selected descriptors, implying that it can be used as a fast and economically acceptable evaluation of antioxidative activity. The advantage of such model is its ability to predict the antioxidative activity of a drug regardless of its structural diversity or therapeutic classification.

Neuroprotective effects on microglia and insights into the structure-activity relationship of an antioxidant peptide isolated from Pelophylax perezi

Tryptophyllins constitute a heterogeneous group of peptides that are one of the first classes of peptides identified from amphibian’s skin secretions. Here, we report the structural characterization and antioxidant properties of a novel tryptophyllin‐like peptide, named PpT‐2, isolated from the Iberian green frog Pelophylax perezi. The skin secretion of P. perezi was obtained by electrical stimulation and fractionated using RP‐HPLC. De novo peptide sequencing was conducted using MALDI MS/MS. The primary structure of PpT‐2 (FPWLLS‐NH₂) was confirmed by Edman degradation and subsequently investigated using in silico tools. PpT‐2 shared physicochemical properties with other well‐known antioxidants. To test PpT‐2 for antioxidant activity in vitro, the peptide was synthesized by solid phase and assessed in the chemical‐based ABTS and DPPH scavenging assays. Then, a flow cytometry experiment was conducted to assess PpT‐2 antioxidant activity in oxidatively challenged murine microglial cells. As predicted by the in silico analyses, PpT‐2 scavenged free radicals in vitro and suppressed the generation of reactive species in PMA‐stimulated BV‐2 microglia cells. We further explored possible bioactivities of PpT‐2 against prostate cancer cells and bacteria, against which the peptide exerted a moderate antiproliferative effect and negligible antimicrobial activity. The biocompatibility of PpT‐2 was evaluated in cytotoxicity assays and in vivo toxicity with Galleria mellonella. No toxicity was detected in cells treated with up to 512 µg/ml and in G. mellonella treated with up to 40 mg/kg PpT‐2. This novel peptide, PpT‐2, stands as a promising peptide with potential therapeutic and biotechnological applications, mainly for the treatment/prevention of neurodegenerative disorders.

Controlling the diversity of ion-induced fragmentation pathways by N-methylation of amino acids

We present a combined experimental and theoretical study of the fragmentation of singly and doubly N-methylated glycine (sarcosine and N,N-dimethyl glycine, respectively) induced by low-energy (keV) O⁶⁺ ions. Multicoincidence mass spectrometry techniques and quantum chemistry simulations (ab initio molecular dynamics and density functional theory) allow us to characterise different fragmentation pathways as well as the associated mechanisms. We focus on the fragmentation of doubly ionised species, for which coincidence measurements provide unambiguous information on the origin of the various charged fragments. We have found that single N-methylation leads to a larger variety of fragmentation channels than in no methylation of glycine, while double N-methylation effectively closes many of these fragmentation channels, including some of those appearing in pristine glycine. Importantly, the closure of fragmentation channels in the latter case does not imply a protective effect by the methyl group.

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.