Structure of the Keap1:Nrf2 interface provides mechanistic insight into Nrf2 signaling

Fluorinated sulfonamide-flavonoid derivatives as novel Keap1-Nrf2 inhibitors: Potent induction of cytoprotective gene HO-1 in vivo

Nuclear factor-erythroid 2 related factor 2 (Nrf2) is a key regulator in cellular defense against oxidative stress. While flavonoids have been identified as Nrf2 activators by inhibiting Keap1-Nrf2 protein-protein interaction (PPI), their limited bioactivity presents significant challenges for therapeutic applications. To compensate for this shortcoming, 28 sulfonamide-flavonoid analogues targeting the Keap1-Nrf2 PPI were synthesized by a fragment-based approach. Among these, SG16, which incorporates a fluorine atom, exhibited potent Nrf2-activated capacity and notable anti-inflammatory properties. In AML12 hepatocytes, SG16 significantly enhanced the expression of antioxidant genes by promoting Nrf2 nuclear translocation. In an acute liver injury (ALI) mouse model, SG16 treatment led to a substantial, hundredfold upregulation of the cytoprotective gene HO-1 mRNA. Meanwhile, a dose-dependent decline in ALT, AST, and inflammatory cytokine levels was observed, reflecting improved liver function. Histopathological evaluations, including hematoxylin and eosin (HE) staining, TUNEL, myeloperoxidase (MPO) activity assessment, and F4/80 macrophage marker analysis, consistently demonstrated substantial attenuation of liver tissue damage following SG16 treatment. Moreover, Co-IP assays combined with experiments in Nrf2 knockout mice suggested that the novel sulfonamide-containing flavonoids are a promising class of Nrf2-targeted therapeutic candidates, warranting further exploration for oxidative stress-related disorders.

Activation, interaction and intimation of Nrf2 pathway and their mutational studies causing Nrf2 associated cancer

Responses against infection trigger several signaling pathways that lead to the production of cytokines, these cytokines release ROS and RNS, damaging DNA and proteins turn into various diseases including cancer. To combat these harmful cytokines, the Nrf2 pathway is activated. The gene NFE2L2 encodes Nrf2, which is divided into seven conserved domains (Neh1-7). The DLG and ETGE motifs, conserved sequences of amino acid in the Neh2 domain of Nrf2, bind to the BTB domain of Keap1. BTB domain promotes Keap1's homodimerization resulting in Cul3 recruitment providing scaffold formation to E2 ubiquitin ligase to form ubiquitin complex. Under normal conditions, this complex regularly degrades Nrf2. However, once the cell is exposed to oxidative stress by ROS interaction with Keap1 resulting in conformational changes that stabilize the Nrf2. Nrf2 further concentrates on the nucleus where it binds with the transcriptional factor to perform the desired genes transcription for synthesizing SOD, GSH, CAT, and various other proteins which reduce the ROS levels preventing certain diseases. To prevent cells from oxidative stress, molecular hydrogen activates the Nrf2 pathway. To activate the Nrf2 pathway, molecular hydrogen oxidizes the iron porphyrin which acts as an electrophile and interacts with Keap1's cysteine residue.

Exploring the links between polyphenols, Nrf2, and diabetes: A review

Diabetes mellitus, a complex metabolic disorder, is marked by chronic hyperglycemia that drives oxidative stress and inflammation, leading to complications such as neuropathy, retinopathy, and cardiovascular disease. The Nrf2 pathway, a key regulator of cellular antioxidant defenses, plays a vital role in mitigating oxidative damage and maintaining glucose homeostasis. Dysfunction of Nrf2 has been implicated in the progression of diabetes and its related complications. Polyphenols, a class of plant-derived bioactive compounds, have shown potential in modulating the Nrf2 pathway. Numerous compounds have been found to activate Nrf2 through mechanisms including Keap1 interaction, transcriptional regulation, and epigenetic modification. Preclinical studies indicate their ability to reduce reactive oxygen species (ROS), improve insulin sensitivity, and attenuate inflammation in diabetic models. Clinical trials with certain polyphenols, such as resveratrol, have demonstrated improvements in glycemic parameters, though results remain inconsistent. While polyphenols show promise as a component of non-pharmacological approaches to diabetes management, challenges such as bioavailability, individual variability in response, and limited clinical evidence highlight the need for further investigation. Continued research could enhance understanding of their mechanisms and improve their practical application in mitigating diabetes-related complications.

In vivo functional screens reveal KEAP1 loss as a driver of chemoresistance in small cell lung cancer

Exquisitely chemosensitive initially, small cell lung cancer (SCLC) exhibits dismal outcomes owing to rapid transition to chemoresistance. Elucidating the genetic underpinnings has been challenging owing to limitations with cellular models. As SCLC patient-derived xenograft (PDX) models mimic therapeutic responses, we perform genetic screens in chemosensitive PDX models to identify drivers of chemoresistance. cDNA overexpression screens identify MYC, MYCN, and MYCL, while CRISPR deletion screens identify KEAP1 loss as driving chemoresistance. Deletion of KEAP1 switched a chemosensitive SCLC PDX model to become chemoresistant and resulted in sensitivity to inhibition of glutamine metabolism. Data from the IMpower133 clinical trial revealed ~6% of patients with extensive-stage SCLC exhibit KEAP1 genetic alterations, with activation of a KEAP1/NRF2 transcriptional signature associated with reduced survival upon chemotherapy treatment. While roles for KEAP1/NRF2 have been unappreciated in SCLC, our genetic screens revealed KEAP1 loss as a driver of chemoresistance, while patient genomic analyses demonstrate clinical importance.

Two Antihypertensive and Antioxidant Peptides Derived from Alaska Pollack (Theragra chalcograma) Skin: In Silico, In Vitro, and In Vivo Investigation

This study aimed to identify and characterize two novel dual-functional peptides with antihypertensive and antioxidant activities from byproducts of Alaska pollock skin (APS). Results showed that fifty-nine peptides were identified from APS, of which two peptides, GP1 (GSAGPAGPSGPRGP) and GP2 (LGDARNSPAPP), were predicted to exhibit the highest angiotensin-converting enzyme (ACE) inhibitory and antioxidant activities. GP1 and GP2 demonstrated favorable ACE inhibitory activities (IC50 values of 0.166 and 0.177 mmol/L, respectively) and significantly reduced blood pressure in hypertensive rats. Additionally, both peptides effectively scavenged 2,2'-casino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radicals, with EC50 values of 0.273 and 0.629 mg/mL and protected HepG2 cells against H2O2-induced damage. Molecular docking revealed that the peptides interacted with amino acid residues within the active pocket and at the entrance channel of ACE, displaying mixed-competitive inhibition patterns. These peptides could also bind to the Kelch domain of Kelch-like ECH associating protein (Keap1), thereby promoting nuclear factor erythroid 2-related factor 2 (Nrf2)-mediated transcriptional activation of antioxidant enzymes through the Keap1-Nrf2 pathway. The dual ACE inhibitory and antioxidant properties of APS peptides, coupled with high gastrointestinal stability, validated their utilization as multifunctional ingredients in antihypertensive functional foods, nutraceuticals, and peptide-based hydrogel development.

EGF-Upregulated lncRNA ESSENCE Promotes Colorectal Cancer Growth through Stabilizing CAD and Ferroptosis Defense

Epidermal growth factor receptor/mitogen-activated protein kinase (EGFR/MAPK) signaling is highly activated in various types of cancer. The long noncoding RNAs induced by this pathway and their roles in colorectal cancer (CRC) have not been fully elucidated. In this study, based on the profiling of long noncoding RNAs triggered by EGFR/MAPK signaling, we identified that ESSENCE (EGF [epidermal growth factor] Signal Sensing CAD's Effect; ENST00000415336), which is mediated by the transcription factor early growth response factor 1, functions as a potent oncogenic molecule that predicts poor prognosis in CRC. Mechanistically, ESSENCE directly interacts with carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD) and competitively attenuates CAD degradation mediated by its newly discovered E3 ligase KEAP1, thereby suppressing ferroptosis and promoting CRC progression. Importantly, combinational treatment of the mitogen-activated extracellular signal-regulated kinase inhibitor selumetinib and ferroptosis inducer sulfasalazine synergistically suppresses ESSENCE-high CRC in a patient-derived xenograft mouse model. Taken together, these findings demonstrate the crucial role of ESSENCE in mediating CRC progression by regulating CAD stabilization and suggest a therapeutic strategy of targeting the ESSENCE-CAD axis in CRC.

Structural mimicry of UM171 and neomorphic cancer mutants co-opts E3 ligase KBTBD4 for HDAC1/2 recruitment

Neomorphic mutations and drugs can elicit unanticipated effects that require mechanistic understanding to inform clinical practice. Recurrent indel mutations in the Kelch domain of the KBTBD4 E3 ligase rewire epigenetic programs for stemness in medulloblastoma by recruiting LSD1-CoREST-HDAC1/2 complexes as neo-substrates for ubiquitination and degradation. UM171, an investigational drug for haematopoietic stem cell transplantation, was found to degrade LSD1-CoREST-HDAC1/2 complexes in a wild-type KBTBD4-dependent manner, suggesting a potential common mode of action. Here, we identify that these neomorphic interactions are mediated by the HDAC deacetylase domain. Cryo-EM studies of both wild-type and mutant KBTBD4 capture 2:1 and 2:2 KBTBD4-HDAC2 complexes, as well as a 2:1:1 KBTBD4-HDAC2-CoREST1 complex, at resolutions spanning 2.7 to 3.3 Å. The mutant and drug-induced complexes adopt similar structural assemblies requiring both Kelch domains in the KBTBD4 dimer for each HDAC2 interaction. UM171 is identified as a bona fide molecular glue binding across the ternary interface. Most strikingly, the indel mutation reshapes the same surface of KBTBD4 providing an example of a natural mimic of a molecular glue. Together, the structures provide mechanistic understanding of neomorphic KBTBD4, while structure-activity relationship (SAR) analysis of UM171 reveals analog S234984 as a more potent molecular glue for future studies.

Patenting perspective on Keap1 inhibitors (2019-2024)

INTRODUCTION

Kelch-like ECH-associated protein 1 (Keap1), an E3 ligase negatively regulating the nuclear factor erythroid 2-related factor 2 (Nrf2), has emerged as an auspicious drug target for treating ailments associated with oxidative stress and inflammation. Discovery of Keap1 inhibitors have attracted significant interest.

AREAS COVERED

This review covers patents on Keap1 inhibitors from 2019 to 2024, providing a comprehensive analysis of their structural characteristics, optimization strategies, pharmacological properties and clinical progress.

EXPERT OPINION

Extensive efforts have been devoted to enhance potency and drug-like properties of Keap1 inhibitors. Strategies such as ROS-cleavable prodrug design, bivalent inhibition and PROTACs are emerging. As the range of drug types and applications expands, Keap1 inhibitors are becoming a sagacious option for disease treating.

Germination affects structural and techno-functional properties of proteins from quinoa seeds with increased realease of antioxidant peptides by gastrointestinal digestion

This study investigated the impact of germination on quinoa protein (QP) composition, techno-functional properties, and the release of antioxidant peptides during gastrointestinal digestion. Germinated QP (GQP) at 36 and 48 h showed significant degradation of storage proteins. GQP12 and GQP24 exhibited increased surface hydrophobicity but decreased solubility, foaming, and emulsifying properties, while that of GQP60 and GQP72 were improved. Both QP and GQP demonstrated good digestibility, with over 90 % of their gastrointestinal digests smaller than 1 kDa. Gastrointestinal digests of GQP12 (QPGI12) exhibited excellent antioxidant activity, attributed to higher hydrophobic amino acid content of GQP12 and peptides of QPGI12 digests. Eight antioxidant peptides with strong binding affinity to Keap1 were identified, with peptides FGDL, FGGL, and FDGL interacting through hydrogen bonding and hydrophobic interactions. Findings gained in this study indicated that germination might serve as an efficient strategy for improving techno-functionality and bioactivity of QP for antioxidant peptides production.

Running a genetic stop sign accelerates oxygen metabolism and energy production in horses

Horses are among nature's greatest athletes, yet the ancestral molecular adaptations fueling their energy demands are poorly understood. Within a clinically important pathway regulating redox and metabolic homeostasis (NRF2/KEAP1), we discovered an ancient mutation-conserved in all extant equids-that increases mitochondrial respiration while decreasing tissue-damaging oxidative stress. This mutation is a de novo premature opal stop codon in KEAP1 that is translationally recoded into a cysteine through previously unknown mechanisms, producing an R15C mutation in KEAP1 that is more sensitive to electrophiles and reactive oxygen species. This recoding enables increased NRF2 activity, which enhances mitochondrial adenosine 5'-triphosphate production and cellular resistance to oxidative damage. Our study illustrates how recoding of a de novo stop codon, a strategy thought restricted to viruses, can facilitate adaptation in vertebrates.

Exploring the separation, characterization and antioxidant activity of proteins and peptides from selected seagrasses in Palk Bay region of Tamil Nadu in India

In this study, five seagrass species Halodule uninervis, Thalassia hemprichii, Enhalus acoroides, Cymodocea serrulata, and Syringodium isoetifolium collected from the Mandapam coastal region of Rameswaram (Palk Bay region), Tamil Nadu, India, were selected to identify the antioxidant-rich proteins/peptides. The primary objective was to identify the proteins/peptides present in these seagrass filtrates extracted by using four different pH-based buffer extracts and to assess their antioxidant activity. Among the various buffer extracts, 0.1 M Citrate buffer (pH 5.5) exhibited the highest proteins/peptides recovery in all species. Of these, S. isoetifolium showed the highest recovery percentage (20.18 %) in the 10 kDa filtrate. Notably, the 3 kDa filtrate of S. isoetifolium demonstrated the highest antioxidant activity (83 %). The peptides sequences in all five seagrass samples were identified by MALDI - TOF MS analysis, Furthermore, in silico protein-peptide docking studies were conducted to assess the interaction of the identified peptides with key antioxidant-related targets, including superoxide dismutase, xanthine oxidase, inducible nitric oxide synthase, keap 1 protein, and myeloperoxidase. With all these targets, the peptide derived from S. isoetifolium exhibited better binding affinity. This study emphasized that the potential peptides identified from seagrass are the natural antioxidant sources that can be used to treat disorders linked to oxidative stress.

RoseTTAFold diffusion-guided short peptide design: a case study of binders against Keap1/Nrf2

In this study, we proposed a novel comprehensive computational framework that combines deep generative modeling with in silico peptide optimization to expedite the discovery of bioactive compounds. Our methodology utilizes RFdiffusion, a variation of the RoseTTAFold model for protein design, in tandem with ProteinMPNN, a deep neural network for protein sequence optimization, to provide short candidate peptides for targeted binding interactions. As a proof-of-concept, we focused on Keap1 (Kelch-like ECH-associated protein 1), a key regulator in the Keap1/Nrf2 antioxidant pathway. To achieve this, we designed peptide sequences that would interact with specific binding subpockets within its Kelch domain. We integrated machine learning models to forecast essential peptide properties, including toxicity, stability, and allergenicity, thus enhancing the selection of prospective candidates. Our in silico screening identified eight top candidates that exhibited strong binding affinity and good biophysical characteristics. The candidates underwent additional validation via comprehensive molecular dynamics simulations, which confirmed their strong binding contacts and structural stability over time. This integrated framework offers a scalable and adaptable platform for the rapid design of therapeutic peptides, merging breakthrough computational techniques with focused case studies. Furthermore, our modular methodology facilitates its straightforward adaptation to alternative protein targets, hence considerably enhancing its potential influence in drug development and discovery.

Timosaponin B II as a novel KEAP1-NRF2 inhibitor to alleviate alcoholic liver disease:Receptor structure-based virtual screening and biological evaluation

Oxidative stress induced by excess ethanol is an important factor in the progression of alcoholic liver disease (ALD). In recent years, inhibiting Kelch-like ECH-associated protein 1 (KEAP1) to activate the antioxidant regulator Nuclear factor erythroid 2-related factor 2 (NRF2) has been considered an effective strategy for treating oxidative stress-related diseases, but its application in ALD remains insufficiently explored. This study aims to discover high-affinity inhibitors targeting the KEAP1 receptor. We conducted virtual screening of a compound library based on a structure-based pharmacophore model, ultimately identifying the candidate compound Timosaponin B II (TBII). Subsequently, we established ALD models in AML-12 cells and C57BL/6 mice, and evaluated the therapeutic effects and mechanisms of TBII on ALD using methods including Immunofluorescence, Western blotting, RT-qPCR, Biochemical assays, and histological staining. Results indicate that TBII significantly improved ethanol-induced liver injury, inhibited the elevation of serum Alanine Aminotransferase (ALT), Aspartate Aminotransferase (AST), Total Cholesterol (T-CHO), and Triglycerides (TG) levels, and reduced lipid droplet accumulation in liver tissues. Furthermore, TBII treatment enhanced the antioxidant capacity of AML-12 cells and mouse liver, increasing Glutathione (GSH) and Superoxide Dismutase (SOD) levels while reducing Malondialdehyde (MDA) and Reactive Oxygen Species (ROS) levels. Mechanistic studies indicated that TBII inhibited the ethanol-induced increase in KEAP1 and reversed the ethanol-induced changes in NRF2 and its downstream targets. In conclusion, this study suggests that TBII may become a potential therapeutic agent for ALD by modulating the KEAP1-NRF2 pathway to alleviate oxidative stress and lipid metabolism abnormalities.

Peptide design to control protein-protein interactions

Targeting of protein-protein interactions has become of huge interest in every aspect of medicinal and biological sciences. The control of protein interactions selectively offers the opportunity to control biological processes while limiting off target effects. This interest has massively increased with the development of cryo-EM and protein structure prediction with tools such as RosettaFold and AlphaFold. When designing molecules to control protein interactions, either inhibition or stabilisation, a starting point is commonly peptide design. This tutorial review describes that process, highlighting the selection of an initial sequence with and without structural information. Subsequently, methods for how the sequence can be analysed for key residues and how this information can be used to optimise the ligand efficiency are highlighted. Finally a discussion on how peptides can be further modified to increase their affinity and cell permeability, improving their drug-like properties, is presented.

Extract of Nanhaia speciosa J. Compton & Schrire alleviates LPS-induced acute lung injury via the NF-κB/Nrf2/AQPs pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Nanhaia speciosas J. Compton & Schrire (the name Nanhaia speciosas J. Compton & Schrire has been accepted by the World Checklist of Vascular Plants https://www.worldfloraonline.org/taxon/wfo-0001444004) is a traditional Zhuang medicine that have been widely used for centuries. It has been used in the treatment of lung inflammation, tuberculosis, rheumatic pain, lumbar muscle strain, and various other ailments, such as chronic hepatitis, menoxenia, leukorrhea, and injuries. In addition, N. speciosa has also been used to treat acute lung injury (ALI).

AIM OF THE STUDY

The objective of this study was to conduct a comparative analysis of the effects of various constituents present in N. speciosas extract (NSE) on ALI and the related mechanisms while also elucidating the potential active monomeric components.

MATERIALS AND METHODS

NSE was extracted using an AB-8 macroporous resin column, and five fractions (Fr. 0%, 25%, 50%, 75% and 95%) were obtained. The anti-inflammatory and antioxidant capacities of the five fractions were evaluated in an A549 cell-based in vitro model, with the aim of evaluating their potential therapeutic effects. The anti-inflammatory and antioxidant capacities of NSE were assessed in a murine model of ALI induced by intratracheal injection of LPS. We utilized an in vitro model to analyse the critical molecular mechanisms through which NSE ameliorates ALI. The chemical composition of the optimal fraction was analysed and confirmed using UHPLC/MS.

RESULTS

Different fractions (especially Fr. 75%) significantly reduced inflammation and oxidative stress in A549 cells. Fr.75% abrogated LPS-induced pathological alterations and decreased the lung W/D ratio, total protein concentration in BALF, and the levels of the proinflammatory factors TNF-α, IL-6, and IL-1β. Moreover, Fr.75% reduced MPO and MDA concentrations and elevated SOD and GSH concentrations in pulmonary tissues. Additionally, it decreased the pulmonary tissue inflammation caused by LPS by downregulating the expression of p-NF-κB p65 and upregulating the expression of Nrf2, AQP1 and AQP5. Fr. 75% decreased p-NF-κB p65 protein levels; increased Keap1, Nrf2, HO-1, NQO1, AQP1 and AQP5 protein levels; and promoted the entry of Nrf2 into the nucleus. After UHPLC/MS analysis was conducted, the flavonoid Maackiain was determined to potentially play a pivotal role in this process.

CONCLUSION

Fr.75% alleviates ALI by regulating the NF-κB/Nrf2/AQPs signalling pathway. The flavonoid Maackiain may also play an important role in this process. Overall, N. speciosas may be a potential therapeutic agent for the prevention and treatment of ALI.

Targeting the Interplay Between Autophagy and the Nrf2 Pathway in Parkinson's Disease with Potential Therapeutic Implications

Parkinson's disease (PD) is a prevalent neurodegenerative disorder marked by the progressive degeneration of midbrain dopaminergic neurons and resultant locomotor dysfunction. Despite over two centuries of recognition as a chronic disease, the exact pathogenesis of PD remains elusive. The onset and progression of PD involve multiple complex pathological processes, with dysfunctional autophagy and elevated oxidative stress serving as critical contributors. Notably, emerging research has underscored the interplay between autophagy and oxidative stress in PD pathogenesis. Given the limited efficacy of therapies targeting either autophagy dysfunction or oxidative stress, it is crucial to elucidate the intricate mechanisms governing their interplay in PD to develop more effective therapeutics. This review overviews the role of autophagy and nuclear factor erythroid 2-related factor 2 (Nrf2), a pivotal transcriptional regulator orchestrating cellular defense mechanisms against oxidative stress, and the complex interplay between these processes. By elucidating the intricate interplay between these key pathological processes in PD, this review will deepen our comprehensive understanding of the multifaceted pathological processes underlying PD and may uncover potential strategies for its prevention and treatment.

Structural characterization, HepG2 cell cytoprotective ability, and antioxidant mechanism of novel antioxidant peptides identified from black soldier fly larvae (Hermetia illucens L.)

This study isolated a novel antioxidant peptide from black soldier fly larvae (BSFL) using enzymatic hydrolysis. Firstly, the BSFL enzymatic hydrolysate was fractionated through ultrafiltration, with the <3 kDa fraction exhibiting the strongest DPPH and ABTS radical scavenging activity. Subsequently, this fraction was further fractionated through gel filtration chromatography and RP-HPLC. Totally, 153 peptides were identified through LC-MS/MS analysis, from which a novel peptide EDEGTYKCVLS (Pep6) was screened according to activity prediction and verification. Pep6 exhibited high radical scavenging capacity and cytoprotective effect on HepG2 cells against H2O2 damage, meanwhile significantly increasing the intracellular antioxidant enzymes activity. Molecular docking analysis indicated that Pep6 competitively bound to Keap1, thereby inhibiting the formation of Keap1-Nrf2 complex, ultimately protecting cells from oxidative stress damage. In this study, a novel antioxidant peptide Pep6 was identified from BSFL, and its antioxidant mechanism was elucidated, providing a theoretical basis for its use as a natural antioxidant.

Screening and preparation of highly active antioxidant peptides of apricot and their inhibitory effect on ultraviolet radiation

In today's social environment, the objective reality of people's increasing life pressure, environmental deterioration, and enhanced ultraviolet rays caused by the destruction of the ozone layer has led to the aggravation of people's oxidative stress. Therefore, exogenous antioxidant peptides have become a hot topic in research. In the context of insufficient protein supply and resource recycling, almond meal was used as raw material in this study. As a by-product of oil processing, it has a protein content of 68 % and antioxidant-related amino acids accounted for 84.62 %, which can be used as a high-quality natural source of antioxidant peptides. Taking antioxidant activity as the only indicator, papain was screened as a hydrolase, and 7 antioxidant peptides such as YLSF, LPSYVN and SPHWNVN were separated and purified. The affinity energy of docking with Keap1-Nrf2-ARE protein molecules was -7.5--8.9 kal/mol, and hydrophobic stacking, hydrogen bonding and intermolecular forces were maintained. Seven antioxidant peptides were synthesized in solid phase, and the IC50 values of in vitro ABTS+ scavenging rates were 3.59 μg/mL-6.73 μg/mL, and the antioxidant capacity was stronger than that of glutathione and ascorbic acid. In the in vitro cellular ROS scavenging capacity, all seven peptides had the effect of scavenging intracellular ROS, among which YLSF and ESWNPRDPQF had stronger scavenging capacity than glutathione. Finally, the mouse skin staining method determined that apricot antioxidant peptides had a significant inhibitory effect on UV damage to mouse skin, and targeted proteomics was used to clarify that apricot antioxidant peptides inhibited UV damage by mainly affecting three pathways, including the base excision repair pathway. This study not only improved the economic value of processing by-products, but also obtained 7 highly active almond antioxidant peptides, tapping the potential ability of apricot antioxidant peptides to be incorporated into functional food or cosmetic formulations.

Covalent Inhibitors of KEAP1 with Exquisite Selectivity

The NRF2-KEAP1 interaction is central for cytoprotection against stresses, giving it high clinical significance. Covalent modification of KEAP1 is an efficient approach, but the covalent inhibitors used in the clinic carry undesired side effects originating in their moderate selectivity. Starting with a phenotypic screen, we identified a new covalent inhibitor chemotype that was optimized to deliver a series of potent and highly selective KEAP1 binders. While the developed compounds showed both cellular and in vivo activity, upregulating antioxidant response element-dependent target genes, they showed no genotoxicity in vitro. The lead compound exhibited broad selectivity in activity-based protein profiling and showed no significant interaction with a panel of commonly studied receptors nor with a broad panel of kinases. The nature of its interaction with KEAP1 and the origin of its selectivity were revealed by X-ray crystallography.

Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics

The development of potent, specific, and pharmacologically viable chemical probes and therapeutics is a central focus of chemical biology and therapeutic development. However, a significant portion of predicted disease-causal proteins have proven resistant to targeting by traditional small molecule and biologic modalities. Many of these so-called "undruggable" targets feature extended, dynamic protein-protein and protein-nucleic acid interfaces that are central to their roles in normal and diseased signaling pathways. Here, we discuss the development of synthetically stabilized peptide and protein mimetics as an ever-expanding and powerful region of chemical space to tackle undruggable targets. These molecules aim to combine the synthetic tunability and pharmacologic properties typically associated with small molecules with the binding footprints, affinities and specificities of biologics. In this review, we discuss the historical and emerging platforms and approaches to design, screen, select and optimize synthetic "designer" peptidomimetics and synthetic biologics. We examine the inspiration and design of different classes of designer peptidomimetics: (i) macrocyclic peptides, (ii) side chain stabilized peptides, (iii) non-natural peptidomimetics, and (iv) synthetic proteomimetics, and notable examples of their application to challenging biomolecules. Finally, we summarize key learnings and remaining challenges for these molecules to become useful chemical probes and therapeutics for historically undruggable targets.

Rosmarinic Acid Ameliorates Dermatophagoides farinae Extract-Induced Atopic Dermatitis-like Skin Inflammation by Activating the Nrf2/HO-1 Signaling Pathway

Atopic dermatitis (AD) is one of the most common chronic inflammatory skin diseases. AD pathogenesis is associated with increased oxidative stress, impairment of the skin barrier, and activation of the immune response. Rosmarinic acid (RA), a caffeic acid ester, is known for its anti-inflammatory and antioxidant properties. However, the effects of RA on Dermatophagoides farinae extract (DfE)-induced AD-like skin inflammation, as well as its ability to regulate oxidative stress through the Nrf2/HO-1 pathway in TNF-α/IFN-γ-treated keratinocytes, remain unclear. We investigated RA activity in a DfE-induced AD-like skin inflammation mouse model and IFN-γ/TNF-α-stimulated keratinocytes. We found that RA attenuates DfE-induced inflammation by decreasing dermatitis scores and serum inflammatory marker levels and mast cell infiltration. Additionally, RA significantly suppressed IFN-γ/TNF-α-induced chemokine production in keratinocytes and reduced Th cytokine levels in concanavalin A-stimulated splenocytes. Importantly, RA also increased Nrf2/HO-1 expression in TNF-α/IFN-γ-treated keratinocytes. In conclusion, this study demonstrated that RA effectively alleviates DfE-induced AD-like skin lesions by reducing the levels of inflammatory cytokines and chemokines. Furthermore, RA promotes Nrf2/HO-1 signaling in keratinocytes, which may help mitigate DfE-induced oxidative stress, thereby alleviating AD-like skin inflammation. These findings highlight the potential of RA as a therapeutic agent for treating AD and other skin inflammation.

An in vivo and in silico probing of the protective potential of betaine against sodium fluoride-induced neurotoxicity

Excessive fluoride exposure beyond the tolerable limit may adversely impacts brain functionality. Betaine (BET), a trimethyl glycine, possesses antioxidant, anti-inflammatory and anti-apoptotic functions, although the underlying mechanisms of the role of BET on fluoride-induced neurotoxicity remain unelucidated. To assess the mechanism involved in the neuro-restorative role of BET on behavioural, neurochemical, and histological changes, we employed a rat model of sodium fluoride (NaF) exposure. Animals were treated with NaF (9 mg/kg) body weight (bw) only or co-treated with BET (50 and 100 mg/kg bw) orally uninterrupted for 28 days. We obtained behavioural phenotypes in an open field, performed negative geotaxis, and a forelimb grip test, followed by oxido-inflammatory, apoptotic, and histological assessment. Behavioural endpoints indicated lessened locomotive and motor and heightened anxiety-like performance and upregulated oxidative, inflammatory, and apoptotic biomarkers in NaF-exposed rats. Co-treatment with BET significantly enhanced locomotive, motor, and anxiolytic performance, increased the antioxidant signalling mechanisms and demurred oxidative, inflammatory, and apoptotic biomarkers and histoarchitectural damage in the cerebrum and cerebellum cortices mediated by NaF. The in-silico analysis suggests that multiple hydrogen bonds and hydrophobic interactions of BET with critical amino acid residues, including arginine (ARG380 and ARG415) in the Keap1 Kelch domain, which may disrupt Keap1-Nrf2 complex and activate Nrf2. This may account for the observed increased in the Nrf2 levels, elevated antioxidant response and enhanced anti-inflammatory response. The BET-Keap1 complex was also observed to exhibit structural stability and conformational flexibility in solvated biomolecular systems, as indicated by the thermodynamic parameters computed from the trajectories obtained from a 100 ns full atomistic molecular dynamics simulation. Therefore, BET mediates neuroprotection against NaF-induced cerebro-cerebellar damage through rats' antioxidant, anti-inflammatory, and anti-apoptotic activity, which molecular interactions with Keap1-Nrf2 may drive.

Bioactive proteins and antioxidant peptides from Litsea cubeba fruit meal: Preparation, characterization and ameliorating function on high-fat diet-induced NAFLD through regulating lipid metabolism, oxidative stress and inflammatory response

Non-alcoholic fatty liver disease (NAFLD) plays an increasingly significant threat to human health. In this study, the processing by-products of Litsea cubeba fruit meal were defatted by ultrasound-assisted methods, then the acetone-precipitated protein of L. cubeba (LCP) was obtained and structural analysis was performed. LCP was hydrolyzed by a two-step sequential hydrolysis method using alcalase and papain. Subsequently, antioxidant peptide fraction (IV2) was isolated and identified from the resultant hydrolysate through membrane ultrafiltration, Sephadex G-15 chromatography, and liquid chromatograph mass spectrometer (LC-MS). Animal experimentation indicated the potential of IV2 to mitigate hepatic steatosis. Moreover, IV2 could effectively reduce oxidative stress-induced damage by modulating the Keap1-Nrf2 pathway to activate downstream heme oxygenase-1 (HO-1) and NAD(P) H quinone oxidoreductase 1 (NQO1). Integrating metabolomics and transcriptomics revealed enrichment in pathways associated with glycerolipid metabolism and fatty acid β-oxidation, suggesting the principal mechanisms underlying IV2's ameliorative effects on NAFLD. Transcriptome sequencing identified 3092 up-regulated and 3010 down-regulated genes following IV2 treatment. Interaction analyses based on different lipid compositions (DELs) and differentially expressed genes (DEGs) indicated that IV2 primarily alleviated hepatic steatosis by modulating peroxisome proliferator-activated receptor α (PPAR-α) related pathways, thereby augmenting fatty acid β-oxidation within liver cells. These results indicate that IV2 shows potential in improving high-fat diet (HFD)-induced NAFLD, with improved fatty acid β-oxidation and reduced triglyceride biosynthesis emerging as underlying mechanisms.

Machine learning methods for unveiling the potential of antioxidant short peptides in goat milk-derived proteins during in vitro gastrointestinal digestion

Milk serves as an important dietary source of bioactive peptides, offering notable benefits to individuals. Among the antioxidant short peptides (di- and tripeptides) generated from gastrointestinal digestion are characterized by enhanced bioavailability and bioaccessibility, while assessing them individually presents a labor-intensive and expensive challenge. Based on 4 distinct types of AA descriptors (physicochemical, 3-dimensional structural, quantum, and topological attributes) and genetic algorithms for feature selection, 1 and 4 machine learning-predicted models separately for di- and tripeptides with 2,2-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt radical scavenging capacity exhibited excellent fitting and prediction ability with random forest regression as machine learning algorithm. Intriguingly, the electronic properties of N-terminal AA were considered as only factor affecting the antioxidant capacity of dipeptides containing both tyrosine and tryptophan. Four peptides from the potential di- and tripeptides exhibited highly predicted values by the constructed predicted models. Subsequently, a total of 45 dipeptides and 52 tripeptides were screened by a customized workflow in goat milk during in vitro simulated digestion. In addition to 5 known antioxidant dipeptides, 9 peptides were quantified during digestion, exhibiting concentrations ranging from 0.04 to 1.78 mg L-1. Particularly noteworthy was the promising in vivo functionality of antioxidant dipeptides with N-terminal tyrosine, supported by in silico assays. Overall, this investigation explored crucial molecular properties influencing antioxidant short peptides and high-throughput screening potential peptides with antioxidant activity from goat milk aided by machine learning, thereby facilitating the discovery of novel functional peptides from milk-derived proteins and paving the way for understanding their metabolites during digestion.

Cytoprotective Effects of Antioxidant Peptides from Red Californian Worm (Eisenia foetida) Hydrolysate on Differentiated Caco-2 Cells

BACKGROUND/OBJECTIVES

When prooxidants outweigh antioxidants, oxidative stress can occur, causing an accumulation of reactive oxygen species (ROS). This process can lead to cellular damage and plays a role in the development of numerous health conditions. This study aimed to investigate the cytoprotective effects on differentiated Caco-2 cells of hydrolysates derived from the red Californian worm (WH) and their fractions, identify the peptides responsible for this effect, and elucidate the mechanisms involved.

METHODS

The WH was obtained through hydrolysis with Alcalase 2.4 L and subsequently fractionated to two fractions (F > 3 kDa and F < 3 kDa) using a ceramic membrane with a molecular weight cutoff of 3 kDa. The peptides found in the F < 3 kDa fraction, demonstrating the highest cytoprotective activity, were then sequenced via liquid chromatography-mass spectrometry analysis (LC-MS/MS), and molecular docking was conducted to elucidate the underlying antioxidant mechanisms.

RESULTS

The hydrolysate of Eisenia foetida and its F < 3 kDa fraction exhibited no cytotoxicity, protected the cells from H2O2-induced oxidative stress (50% increase viability), preserved cell viability by restoring their redox status (ROS: 20% decrease, and glutathione (GSH): recovered to basal control levels) and cell cycle distribution, and decreased apoptosis (16%). Twenty-eight peptides were identified, with five showing antioxidant activity through stable interactions with myeloperoxidase (MPO) and Kelch-like ECH-associated protein 1 (Keap-1), KPEDWDDR being the peptide that presented the highest affinity with both molecules (-7.9 and -8.8 kCal/mol, respectively).

CONCLUSIONS

These results highlight the WH as a potential source of bioactive peptides for the management of oxidative stress.

Synthesis and Bioevaluation of New Stable Derivatives of Chrysin-8-C-Glucoside That Modulate the Antioxidant Keap1/Nrf2/HO-1 Pathway in Human Macrophages

Background/Objectives: The beneficial effects of the flavonoid chrysin can be reduced by its poor oral bioavailability. It has been shown that chrysin-8-C-glucoside (1) has a better absorption capability. The aim of this study was to evaluate the antioxidant and anti-inflammatory activity of this glucoside, as well as the respective hexa-acetate derivative 1a and the hexa-ethyl carbonate derivative 1b since the inclusion of moieties in bioactive molecules may increase or modify their biological effects. Methods: THP-1 macrophages were used to determine the viability in the presence of chrysin derivatives, and non-cytotoxic concentrations were selected. Subsequently, lipopolysaccharide (LPS)-induced reactive oxygen species (ROS) production and inflammatory mediators were examined. The involvement of chrysin derivatives with the Keap1 and Nrf2 antioxidant system was determined by docking and Western blotting studies. Results: Our data demonstrated, for the first time, that pretreatment with the three compounds caused a significant reduction in LPS-induced reactive oxygen species (ROS) production and pro-inflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin 1β (IL-1β) levels, as well as in cyclooxygenase 2 (COX-2) expression. The mechanisms underlying these protective effects were related, at least in part, to the competitive molecular interactions of these phenolic compounds with Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2), which would allow the dissociation of Nrf2 and its translocation into the nucleus and the subsequent up-regulation of hemo-oxygenase 1 (HO-1) expression. Conclusions: Compared to the 8-C-glucoside parent chrysin, compound 1a exhibited the strongest antioxidant and anti-inflammatory activity. We hypothesized that the incorporation of an acetate group (1a) may reduce its polarity and, thus, increase membrane permeability, leading to better pharmacological activity. These findings support the potential use of these phenolic compounds as Nrf2 activators against oxidative-stress-related inflammatory diseases.

Computational Assessment of Carotenoids as Keap1-Nrf2 Protein-Protein Interaction Inhibitors: Implications for Antioxidant Strategies

The Keap1-Nrf2 pathway is an essential system that maintains redox homeostasis and modulates key metabolic processes, including metabolism of amino acids to promote the synthesis of antioxidant enzymes. Inhibitors of the protein-protein interaction (PPI) between Keap1 and Nrf2 have emerged as a promising strategy for developing novel classes of antioxidant agents that selectively activate this pathway without off-target effects. Carotenoids, a large family of lipophilic isoprenoids synthesized by all photosynthetic organisms, are well-known for their antioxidant activities. However, the ability of carotenoids to inhibit the Keap1-Nrf2 PPI through the involvement of specific amino acid residues has not yet been revealed. We utilized molecular docking, molecular dynamic simulations, and pharmacokinetic prediction techniques to investigate the potential of eight oxygenated carotenoids, known as xanthophylls, to inhibit Keap1. Among the compounds investigated, fucoxanthin and astaxanthin established multiple hydrogen-bonding and hydrophobic interactions within the Kelch domain of Keap1, showing remarkable binding affinities. Furthermore, fucoxanthin and astaxanthin displayed the ability to form a stable complex with Keap1 and fit into the binding pocket of its Kelch domain. These analyses led to the identification of critical amino acid residues in the binding pocket of Keap1 which are involved in the interaction with carotenoid xanthophylls. Our analyses further revealed that fucoxanthin and astaxanthin demonstrate a favorable safety profile and possess pharmacokinetic properties consistent with acceptable drug-like characteristics. These findings lay the preliminary foundation for developing a novel class of Keap1-Nrf2 PPI inhibitors with potential applications against oxidative stress-related diseases.

Oleanolic acid alleviating ischemia-reperfusion injury in rat severe steatotic liver via KEAP1/NRF2/ARE

Severe steatosis in donor livers is contraindicated for transplantation due to the high risk of ischemia-reperfusion injury (IRI). Although Ho-1 gene-modified bone marrow mesenchymal stem cells (HO-1/BMMSCs) can mitigate IRI, the role of gut microbiota and metabolites in this protection remains unclear. This study aimed to explore how gut microbiota and metabolites contribute to HO-1/BMMSCs-mediated protection against IRI in severe steatotic livers. Using rat models and cellular models (IAR20 and THLE-2 cells) of steatotic liver IRI, this study revealed that ischemia-reperfusion led to significant liver and intestinal damage, heightened immune responses, impaired liver function, and altered gut microbiota and metabolite profiles in rats with severe steatosis, which were partially reversed by HO-1/BMMSCs transplantation. Integrated microbiome and metabolome analyses identified gut microbial metabolite oleanolic acid as a potential protective agent against IRI. Experimental validation showed that oleanolic acid administration alone alleviated IRI and inhibited ferroptosis in both rat and cellular models. Network pharmacology and molecular docking implicated KEAP1/NRF2 pathway as a potential target of oleanolic acid. Indeed, OA experimentally upregulated NRF2 activity, which underlies its inhibition of ferroptosis and protection against IRI. The gut microbial metabolite OA protects against IRI in severe steatotic liver by promoting NRF2 expression and activity, thereby inhibiting ferroptosis.

WNK1 Interaction with KEAP1 Promotes NRF2 Stabilization to Enhance the Oxidative Stress Response in Hepatocellular Carcinoma

Cellular oxidative stress plays a key role in the development and progression of hepatocellular carcinoma (HCC). A better understanding of the processes that regulate reactive oxygen species (ROS) homeostasis could uncover improved strategies for treating HCC. Herein, we identified protein kinase with-no-lysine kinase 1 (WNK1) as an antioxidative factor and therapeutic target in HCC. In human HCC, WNK1 expression was increased and correlated with poor patient prognosis. WNK1 knockdown significantly inhibited cell proliferation and xenograft tumor growth. Mechanistically, WNK1 competed with nuclear factor erythroid 2-related factor 2 (NRF2) for binding with the partial Kelch domain of Kelch-like ECH-associated protein 1 (KEAP1), reducing NRF2 ubiquitination and promoting NRF2 accumulation and nuclear translocation to increase antioxidant response. WNK1 silencing increased H2O2-induced apoptosis and inhibited cell growth by elevating ROS levels, which could be rescued by treatment with the antioxidant N-acetylcysteine and NRF2 activator tert-butylhydroquinone. Liver-specific WNK1 knockout mouse models of HCC substantiated that WNK1 promoted HCC development by regulating ROS levels. WNK463, an inhibitor of the WNK kinase family, suppressed HCC progression and altered the redox status. These findings suggest that WNK1 plays a critical role in HCC development and progression and that the WNK1-oxidative stress axis may be a promising therapeutic target for HCC. Significance: Inhibiting WNK1 induces NRF2 degradation and reduces the oxidative stress response to suppress hepatocellular carcinoma growth, indicating that targeting the WNK1-KEAP1-NRF2 axis is a potential strategy to treat liver cancer.

Identification and molecular mechanisms of novel antioxidant peptides from fermented broad bean paste: A combined in silico and in vitro study

This study aimed to investigate the antioxidative and cytoprotective activity of antioxidant peptides from fermented broad bean paste (FBBP) and explore their potential molecular mechanisms using a combined in silico and in vitro approach. Seven novel antioxidant peptides (VSRRFIYYL, SPAIPLP, PVPPPGG, KKDGYWWAKFK, LAWY, LGFMQF, and LPGCP) identified by integrated approaches of peptidomics and in silico bioinformatic analysis were synthesized, exhibiting strong antioxidant potential against in vitro radicals. Molecular docking results suggested that these peptides could form stable hydrogen bonds and solvent-accessible surface with key amino acid residues of Keap1, thus potentially regulating the Keap1-Nrf2 pathway by occupying the Nrf2-binding site on Keap1. Additionally, they exhibited strong cellular antioxidant activity and could protect HepG2 cells from AAPH-induced oxidative injury by reducing reactive oxygen species and MDA accumulation. This study firstly unraveled the molecular mechanisms of antioxidant peptides from FBBP, and provided a new theoretical basis for the high-value utilization of FBBP.

A facile strategy for the construction of a phage display cyclic peptide library for the selection of functional macrocycles

Cyclic peptides represent invaluable scaffolds in biological affinity, providing diverse collections for discovering functional molecules targeting challenging biological entities and protein-protein interactions. The field increasingly focuses on developing cyclization strategies and chemically modified combinatorial libraries in conjunction with M13 phage display, to identify macrocyclic peptide inhibitors for traditionally challenging targets. Here, we introduce a cyclization strategy utilizing ortho-phthalaldehyde (OPA) for the discovery of active macrocycles characterized by asymmetric scaffolds with side-chain cyclization. Through this approach, aldehyde groups attached to free molecules sequentially attack the ε-amine of lysine and the thiol of cysteine, facilitating the rapid cyclization of genetically encoded linear precursor libraries displayed on phage particles. The construction of a 109-member library and subsequent screening successfully identified cyclic peptide binders targeting three therapeutically relevant proteins: PTP1B, NEK7, and hKeap1. The results confirm the efficacy in rapidly obtaining active ligands with micromolar potency. This work provides a fast and efficient operable high-throughput platform for screening functional peptide macrocycles, which hold promise for broad application in therapeutics, chemically biological probes, and disease diagnosis.

Tumor suppressor KEAP1 promotes HSPA9 degradation, controlling mitochondrial biogenesis in breast cancer

The oxidative-stress-related protein Kelch-like ECH-associated protein 1 (KEAP1) is a substrate articulator of E3 ubiquitin ligase, which plays an important role in the ubiquitination modification of proteins. However, the function of KEAP1 in breast cancer and its impact on the survival of patients with breast cancer remain unclear. Our study demonstrates that KEAP1, a positive prognostic factor, plays a crucial role in regulating cell proliferation, apoptosis, and cell cycle transition in breast cancer. We investigate the underlying mechanism using human tumor tissues, high-throughput detection technology, and a mouse xenograft tumor model. KEAP1 serves as a key regulator of cellular metabolism, the reprogramming of which is one of the hallmarks of tumorigenesis. KEAP1 has a significant effect on mitochondrial biogenesis and oxidative phosphorylation by regulating HSPA9 ubiquitination and degradation. These results suggest that KEAP1 could serve as a potential biomarker and therapeutic target in the treatment of breast cancer.

Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation

Research in the human genome sciences generates a substantial amount of genetic data for hundreds of thousands of individuals, which concomitantly increases the number of variants of unknown significance (VUS). Bioinformatic analyses can successfully reveal rare variants and variants with clear associations with disease-related phenotypes. These studies have had a significant impact on how clinical genetic screens are interpreted and how patients are stratified for treatment. There are few, if any, computational methods for variants comparable to biological activity predictions. To address this gap, we developed a machine learning method that uses protein three-dimensional structures from AlphaFold to predict how a variant will influence changes to a gene's downstream biological pathways. We trained state-of-the-art machine learning classifiers to predict which protein regions will most likely impact transcriptional activities of two proto-oncogenes, nuclear factor erythroid 2 (NFE2L2)-related factor 2 (NRF2) and c-Myc. We have identified classifiers that attain accuracies higher than 80%, which have allowed us to identify a set of key protein regions that lead to significant perturbations in c-Myc or NRF2 transcriptional pathway activities.

Preparation and identification of antioxidant peptides from Quasipaa spinosa skin through two-step enzymatic hydrolysis and molecular simulation

Frog skin, a by-product of Quasipaa Spinosa farming, is rich in protein and potentially a valuable raw material for obtaining antioxidant peptides. This study used papain combined with acid protease to digest frog skin in a two-step enzymatic hydrolysis method. Based on a single factor and response surface experiments, experimental conditions were optimized, and the degree of hydrolysis was 30 %. A frog skin hydrolysate (QSPH-Ⅰ-3) was obtained following ultrafiltration and gel filtration chromatography. IC50 for DPPH, ABTS, and hydroxyl radical scavenging capacities were 1.68 ± 0.05, 1.20 ± 0.14 and 1.55 ± 0.11 mg/mL, respectively. Peptide sequences (17) were analyzed and, through molecular docking, peptides with low binding energies for KEAP1 were identified, which might affect the NRF2-KEAP1 pathway. These findings suggest protein hydrolysates and antioxidant peptide derivatives might be used in functional foods.

Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases

Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for this is the scarcity of ligands binding various E3 ligases and the paucity of structural data available, which complicates ligand design across the family. In this study, we aim to progress PROTAC discovery by proposing a shortlist of E3 ligases that can be prioritized for covalent targeting by performing systematic structural ligandability analysis on a chemoproteomic dataset of potentially reactive cysteines across hundreds of E3 ligases. One of the goals of this study is to apply AlphaFold (AF) models for ligandability evaluations, as for a vast majority of these ligases an experimental structure is not available in the protein data bank (PDB). Using a combination of pocket features, AF model quality and additional aspects, we propose a shortlist of E3 ligases and corresponding cysteines that can be prioritized to potentially discover covalent ligands and expand the PROTAC toolbox.

Structurally manipulated antioxidant peptides derived from wheat bran: Preparation and identification

Bioactive peptide's development is facing two challenges in terms of its lower yield and limited understanding of structurally orientated functionality. Therefore, peptides were prepared from wheat bran via a cocktail enzyme for achieving a higher level of hydrophobic amino acids than traditional method. The obtained peptides exhibited great antioxidant activities against H2O2-induced oxidative stress in HepG2 cells. Among them, 91 bioactive peptides were selected through the virtual screening, and their N-terminal and C-terminal contained many hydrophobic amino acids. Then the peptides with capacity to interact with Keap1 were identified by in silico simulation, because Keap1 acts as a sensor of redox insults. The results revealed that peptides DLDW and DLGL demonstrated the highest binding affinities, and a bridge was formed between Asp of DLGL and Arg415 of Klech domain, contributing to interfering Keap1-Nrf2 interaction. These findings implied a potential application of wheat bran peptides as nutraceuticals and health-promoting ingredients.

Anti-Inflammatory Therapeutic Mechanisms of Isothiocyanates: Insights from Sulforaphane

Isothiocyanates (ITCs) belong to a group of natural products that possess a highly reactive electrophilic -N=C=S functional group. They are stored in plants as precursor molecules, glucosinolates, which are processed by the tyrosinase enzyme upon plant tissue damage to release ITCs, along with other products. Isolated from broccoli, sulforaphane is by far the most studied antioxidant ITC, acting primarily through the induction of a transcription factor, the nuclear factor erythroid 2-related factor 2 (Nrf2), which upregulates downstream antioxidant genes/proteins. Paradoxically, sulforaphane, as a pro-oxidant compound, can also increase the levels of reactive oxygen species, a mechanism which is attributed to its anticancer effect. Beyond highlighting the common pro-oxidant and antioxidant effects of sulforaphane, the present paper was designed to assess the diverse anti-inflammatory mechanisms reported to date using a variety of in vitro and in vivo experimental models. Sulforaphane downregulates the expression of pro-inflammatory cytokines, chemokines, adhesion molecules, cycloxyhenase-2, and inducible nitric oxide synthase. The signalling pathways of nuclear factor κB, activator protein 1, sirtuins 1, silent information regulator sirtuin 1 and 3, and microRNAs are among those affected by sulforaphane. These anti-inflammatory actions are sometimes due to direct action via interaction with the sulfhydryl structural moiety of cysteine residues in enzymes/proteins. The following are among the topics discussed in this paper: paradoxical signalling pathways such as the immunosuppressant or immunostimulant mechanisms; crosstalk between the oxidative and inflammatory pathways; and effects dependent on health and disease states.

The antioxidant peptides from walnut protein hydrolysates and their protective activity against alcoholic injury

In this study, walnut protein was hydrolyzed, separated by ultrafiltration, purified by RP-HPLC, identified by LC-MS/MS, and screened by molecular docking to finally obtain three novel antioxidant peptides HGEPGQQQR (1189.584 Da), VAPFPEVFGK (1089.586 Da) and HNVADPQR (949.473 Da). These three peptides exhibited excellent cellular antioxidant activity (CAA) with EC50 values of 0.0120 mg mL-1, 0.0068 mg mL-1, and 0.0069 mg mL-1, respectively, which were superior to that of the positive control GSH (EC50: 0.0122 mg mL-1). In the ethanol injury model, three antioxidant peptides enhanced the survival of cells treated with ethanol from 47.36% to 62.69%, 57.06% and 71.64%, respectively. Molecular docking results showed that the three antioxidant peptides could effectively bind to Keap1, CYP2E1 and TLR4 proteins. These results suggested that walnut-derived antioxidant peptides could be potential antioxidants and hepatoprotective agents for application in functional foods.

Novel antioxidant peptides identified from coix seed by molecular docking, quantum chemical calculations and invitro study in HepG2 cells

The aim of the study was to identify potent antioxidant peptides sourced from coix seed, analyze the structure-activity relationship through molecular docking and quantum chemical calculation. Molecular docking results showed that among thirteen peptides selected in silico, eight had favourable binding interaction with the Keap1-Kelch domain (2FLU). Promising peptides with significant binding scores were further evaluated using quantum calculation. It was shown that peptide FFDR exhibited exceptional stability, with a high energy gap of 5.24 eV and low Highest Occupied Molecular Orbitals (HOMO) and Lowest Unoccupied Molecular Orbitals (LUMO) values. Furthermore, FFDR displayed the capacity to enhance the expression of Nrf2-Keap1 antioxidant genes (CAT, SOD, GSH-Px) and improved cellular redox balance by increasing reduced glutathione (GSH) while reducing oxidized glutathione (GSSG) and malonaldehyde (MDA) levels. These findings highlight the potential of coix seed peptides in developing novel, effective and stable antioxidant-based functional foods.

Sunflower seed-derived bioactive peptides show antioxidant and anti-inflammatory activity: From in silico simulation to the animal model

The evolving field of food technology is increasingly dedicated to developing functional foods. This study explored bioactive peptides from sunflower protein isolate (SPI), obtained from defatted flour, a by-product of the oil processing industry. SPI underwent simulated gastrointestinal digestion and the obtained peptide-enriched fraction (PEF) showed antioxidant properties in vivo, in zebrafish. Among the peptides present in PEF identified by mass spectrometry analysis, we selected those with antioxidant properties by in silico evaluation, considering their capability to interact with Keap1, key protein in the regulation of antioxidant response. The selected peptides were synthesized and evaluated in a cellular model. As a result, DVAMPVPK, VETGVIKPG, TTHTNPPPEAE, LTHPQHQQQGPSTG and PADVTPEEKPEV activated Keap1/Nrf2 pathway leading to Antioxidant Response Element-regulated enzymes upregulation. Since the crosstalk between Nrf2 and NF-κB is well known, the potential anti-inflammatory activity of the peptides was assessed and principally PADVTPEEKPEV showed good features both as antioxidant and anti-inflammatory molecule.

Exploring of multi-functional umami peptides from Stropharia rugosoannulata: Saltiness-enhancing effect and mechanism, antioxidant activity and potential target sites

Umami peptides enhance flavor and offer potential health benefits. We analyzed the taste-value profiles of five novel umami peptides from Stropharia rugosoannulata using E-tongue, exhibiting significant saltiness characteristics. While the peptides PHEMQ and SEPSHF exhibited higher saltiness, their mixture with salt did not enhance saltiness compared to individual peptides. Surprisingly, SGCVNEL, which was initially weak in saltiness, showed remarkably enhanced saltiness when mixed with salt, possibly due to have strong binding with receptors. Molecular docking elucidated the salt-forming mechanism of TMC4, highlighting the P2-domain and hydrogen bonds' role in the composite structure stability. Evaluation of the antioxidant activity evaluation demonstrated dose-dependent effects primarily through free radical scavenging via the single-electron transfer potential mechanism for SGCVNEL, EPLCNQ, and ESCAPQL. Docking experiments with antioxidant targets revealed varied binding stabilities, indicating diverse antioxidant effects of the peptides. These findings provide valuable insights into the exploration and application of versatile bioactive flavor peptides.

Natural products as non-covalent and covalent modulators of the KEAP1/NRF2 pathway exerting antioxidant effects

By controlling several antioxidant and detoxifying genes at the transcriptional level, including NAD(P)H quinone oxidoreductase 1 (NQO1), multidrug resistance-associated proteins (MRPs), UDP-glucuronosyltransferase (UGT), glutamate-cysteine ligase catalytic (GCLC) and modifier (GCLM) subunits, glutathione S-transferase (GST), sulfiredoxin1 (SRXN1), and heme-oxygenase-1 (HMOX1), the KEAP1/NRF2 pathway plays a crucial role in the oxidative stress response. Accordingly, the discovery of modulators of this pathway, activating cellular signaling through NRF2, and targeting the antioxidant response element (ARE) genes is pivotal for the development of effective antioxidant agents. In this context, natural products could represent promising drug candidates for supplementation to provide antioxidant capacity to human cells. In recent decades, by coupling in silico and experimental methods, several natural products have been characterized to exert antioxidant effects by targeting the KEAP1/NRF2 pathway. In this review article, we analyze several natural products that were investigated experimentally and in silico for their ability to modulate KEAP1/NRF2 by non-covalent and covalent mechanisms. These latter represent the two main sections of this article. For each class of inhibitors, we reviewed their antioxidant effects and potential therapeutic applications, and where possible, we analyzed the structure-activity relationship (SAR). Moreover, the main computational techniques used for the most promising identified compounds are detailed in this survey, providing an updated view on the development of natural products as antioxidant agents.

Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives

Kelch-like proteins (KLHLs) are a large family of BTB-containing proteins. KLHLs function as the substrate adaptor of Cullin 3-RING ligases (CRL3) to recognize substrates. KLHLs play pivotal roles in regulating various physiological and pathological processes by modulating the ubiquitination of their respective substrates. Mounting evidence indicates that mutations or abnormal expression of KLHLs are associated with various human diseases. Targeting KLHLs is a viable strategy for deciphering the KLHLs-related pathways and devising therapies for associated diseases. Here, we comprehensively review the known KLHLs inhibitors to date and the brilliant ideas underlying their development.

Dioxinodehydroeckol: A Potential Neuroprotective Marine Compound Identified by In Silico Screening for the Treatment and Management of Multiple Brain Disorders

Neurodegenerative disorders such as Alzheimer's disease (AD), Glioblastoma multiforme (GBM), Amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD) are some of the most prevalent neurodegenerative disorders in humans. Even after a variety of advanced therapies, prognosis of all these disorders is not favorable, with survival rates of 14-20 months only. To further improve the prognosis of these disorders, it is imperative to discover new compounds which will target effector proteins involved in these disorders. In this study, we have focused on in silico screening of marine compounds against multiple target proteins involved in AD, GBM, ALS, and PD. Fifty marine-origin compounds were selected from literature, out of which, thirty compounds passed ADMET parameters. Ligand docking was performed after ADMET analysis for AD, GBM, ALS, and PD-associated proteins in which four protein targets Keap1, Ephrin A2, JAK3 Kinase domain, and METTL3-METTL14 N6-methyladenosine methyltransferase (MTA70) were found to be binding strongly with the screened compound Dioxinodehydroeckol (DHE). Molecular dynamics simulations were performed at 100 ns with triplicate runs to validate the docking score and assess the dynamics of DHE interactions with each target protein. The results indicated Dioxinodehydroeckol, a novel marine compound, to be a putative inhibitor among all the screened molecules, which might be effective against multiple target proteins involved in neurological disorders, requiring further in vitro and in vivo validations.

Cyclic Peptide Keap1-Nrf2 Protein-Protein Interaction Inhibitors: Design, Synthesis, and In Vivo Treatment of Acute Lung Injury

Directly blocking the Keap1-Nrf2 pathway is a promising strategy for the mitigation of acute lung injury (ALI). Peptide Keap1-Nrf2 inhibitors have been reported to have a high Keap1 binding affinity. However, these inhibitors showed weak activity in cells and/or animals. In this study, we designed a series of linear peptides from an Nrf2-based 9-mer Ac-LDEETGEFL-NH2. To improve the cellular activity, we further designed cyclic peptides based on the crystal complex of Keap1 with a linear peptide. Among them, cyclic 9-mer ZC9 targeting Keap1 showed a better affinity (KD2 = 51 nM). Specifically, it exhibited an acceptable water solubility (>38 mg/mL), better cell permeability, cell activity, and metabolic stability (serum t1/2 > 24 h). In the in vitro LPS-induced oxidative damages and ALI model, ZC9 showed significant dose-response reversal activity without apparent toxicity. In conclusion, our results suggested ZC9 as a lead cyclic peptide targeting the Keap1-Nrf2 pathway for ALI clinical treatment.

Ascorbic acid mitigates the impact of oxidative stress in a human model of febrile seizure and mesial temporal lobe epilepsy

Prolonged febrile seizures (FS) in children are linked to the development of temporal lobe epilepsy (MTLE). The association between these two pathologies may be ascribed to the long-term effects that FS exert on neural stem cells, negatively affecting the generation of new neurons. Among the insults associated with FS, oxidative stress is noteworthy. Here, we investigated the consequences of exposure to hydrogen peroxide (H2O2) in an induced pluripotent stem cell-derived neural stem cells (iNSCs) model of a patient affected by FS and MTLE. In our study, we compare the findings from the MTLE patient with those derived from iNSCs of a sibling exhibiting a milder phenotype defined only by FS, as well as a healthy individual. In response to H2O2 treatment, iNSCs derived from MTLE patients demonstrated an elevated production of reactive oxygen species and increased apoptosis, despite the higher expression levels of antioxidant genes and proteins compared to other cell lines analysed. Among the potential causative mechanisms of enhanced vulnerability of MTLE patient iNSCs to oxidative stress, we found that these cells express low levels of the heat shock protein HSPB1 and of the autophagy adaptor SQSTM1/p62. Pre-treatment of diseased iNSCs with the antioxidant molecule ascorbic acid restored HSBP1 and p62 expression and simultaneously reduced the levels of ROS and apoptosis. Our findings suggest the potential for rescuing the impaired oxidative stress response in diseased iNSCs through antioxidant treatment, offering a promising mechanism to prevent FS degeneration in MTLE.

Screening approaches for the identification of Nrf2-Keap1 protein-protein interaction inhibitors targeting hot spot residues

Protein-protein interactions (PPIs) play a crucial role in most biological processes and are important targets in the development of therapeutic agents. However, small molecule drug discovery that targets PPIs remains very challenging. Targeting hot spot residues is considered the best option for inhibiting such interactions, but there are few examples of how knowledge of hot spots can be used in high throughput screening to find hit compounds. A substrate adaptor protein for a ubiquitin ligase complex, Kelch-like ECH-associated protein 1 (Keap1), negatively modulates the expression of genes involved in cellular protection against oxidative stress. Here, we focused on three arginine hot spot residues in the Keap1 substrate binding pocket (Arg380, Arg415, and Arg483), and screened the carboxylic acid library owned by Japan Tobacco Inc. for compounds that interact with the arginine residues in differential scanning fluorescence assays. Furthermore, we identified several small molecule compounds that specifically bind to the Keap1 Kelch domain hot spots by comparing binding to alanine mutant proteins (R380A, R415A, and R483A) with binding to the wild-type protein using surface plasmon resonance (SPR) screening. These compounds inhibited the protein-protein interaction between the Keap1 Kelch domain and the nuclear factor erythroid 2-related factor 2 (Nrf2) peptide, and the ubiquitination of Nrf2 catalyzed by the Cul3/RINGBox 1 E3 ligase. In addition, the binding mode of one compound (Compound 4) was determined by X-ray crystallography after validation of binding by isothermal titration calorimetry, native mass spectrometry, and nuclear magnetic resonance. Compound 4 had favorable thermodynamic properties, and noncovalently bound to Keap1 with a stoichiometry of 1:1. Our results suggest that Compound 4 could potentially be developed into effective therapeutic or preventive agents for a variety of diseases and conditions such as oxidative stress response, inflammation, and carcinogenesis. We believe that the use of a set of complementary biophysical techniques including the SPR assay with single alanine mutant of hot spots provides opportunities to identify hit compounds for developing inhibitors of PPIs.

Involvement of the Keap1-Nrf2-ARE pathway in the antioxidant activity of sinomenine

Sinomenine is a pure alkaloid isolated from Sinomenium acutum. This study is aimed to investigate the critical role of the nuclear factor erythroid 2-related factor 2 (Nrf2)-kelch-like ECH-associated protein-1(Keap1)-antioxidant response element (ARE) antioxidative signaling pathway in protecting sinomenine against H2O2-induced oxidative injury. Cytotoxicity and antioxidant experiments to initially determine the protective effects of sinomenine show that sinomenine has no effect on the decreased cell viability and presents similar potency in scavenging all three free radicals. The binding affinity between sinomenine and Keap1 was determined via fluorescence polarization assay, with IC50 of 13.52 μM. Quantum chemical calculation and theoretical simulation illustrated that sinomenine located into the Nrf2-binding site of Keap1 via hydrophobic and hydrogen interactions, showing high stability and binding affinity. On the basis of the stable binding of sinomenine with Keap1, sinomenine efficiently induced nuclear translocation of Nrf2, and increased in ARE activity in a concentration-dependent manner. Quantitative polymerase chain reaction provided further evidences that sinomenine-induced protection upregulated ARE-dependent genes, such as NAD(P)H quinone oxidoreductase 1, hemeoxygenase-1, and glutamate-cysteine ligase modifier subunit. Western blot confirmed that sinomenine increased the expressions of these antioxidative enzymes. Taken together, in vitro and in silico evaluations demonstrate that sinomenine inhibits the binding of Keap1 to Nrf2, promotes the nuclear accumulation of Nrf2 and thus leads to the upregulated expressions of Nrf2-dependent antioxidative genes. Our findings also highlight the use of sinomenine for pharmacological or therapeutic regulation of the Nrf2-Keap1-ARE system, which is a novel strategy to prevent the progression of oxidative injury.

Purification and Identification of Peptides from Hydrilla verticillata (Linn. f.) Royle with Cytoprotective and Antioxidative Effect against H2O2-Treated HepG2 Cells

Antioxidant peptides were purified from Hydrilla verticillata (Linn. f.) Royle (HVR) protein hydrolysate by ultrafiltration, gel filtration chromatography, and semipreparative reversed-phase HPLC and identified by UPLC-ESI-MS/MS. Therein, TCLGPK and TCLGER were selected to be synthesized, and they displayed desirable radical-scavenging activity to ABTS (99.20 ± 0.56-99.20 ± 0.43%), DPPH (97.32 ± 0.59-97.56 ± 0.97%), hydroxyl radical (54.32 ± 1.27-70.42 ± 2.01%), and superoxide anion (42.93 ± 1.46-52.62 ± 1.11%) at a concentration of 0.96 μmol/mL. They possessed a cytoprotective effect against H2O2-induced oxidative stress in HepG2 cells in a dose-dependent manner. 1.6 μmol/mL of the two peptides could perfectly protect HepG2 cells from H2O2-induced injury. The TCLGPK exhibited higher antioxidant activity and cytoprotective effect than TCLGER. Western blot and molecular docking results indicated that the two peptides achieved antioxidant ability and cytoprotective effect by combining with Kelch-like ECH-associated protein 1 (Keap1) to activate the Keap1-nuclear factor erythroid 2-related factor 2 (Nrf2)-antioxidant response elements signaling pathway, leading to the activity and expression of the related antioxidases in the pathway significantly up-regulating and the intracellular reactive oxygen species level, lipid peroxidation, and cell apoptosis rate significantly down-regulating.

Redox Homeostasis and Nrf2-Regulated Mechanisms Are Relevant to Male Infertility

Infertility represents a significant global health challenge, affecting more than 12% of couples worldwide, and most cases of infertility are caused by male factors. Several pathological pathways are implicated in male infertility. The main mechanisms involved are driven by the loss of reduction-oxidation (redox) homeostasis and the resulting oxidative damage as well as the chronic inflammatory process. Increased or severe oxidative stress leads to sperm plasma membrane and DNA oxidative damage, dysregulated RNA processing, and telomere destruction. The signaling pathways of these molecular events are also regulated by Nuclear factor-E2-related factor 2 (Nrf2). The causes of male infertility, the role of oxidative stress in male infertility and the Keap1-Nrf2 antioxidant pathway are reviewed. This review highlights the regulatory role of Nrf2 in the balance between oxidants and antioxidants as relevant mechanisms to male fertility. Nrf2 is involved in the regulation of spermatogenesis and sperm quality. Establishing a link between Nrf2 signaling pathways and the regulation of male fertility provides the basis for molecular modulation of inflammatory processes, reactive oxygen species generation, and the antioxidant molecular network, including the Nrf2-regulated antioxidant response, to improve male reproductive outcomes.