Key Binding Site Research Articles

Metabolic pathways, pharmacokinetic, and brain neurochemicals effects of capsaicin: Comprehensively insights from in vivo studies

BackgroundCapsaicin (CAP), a prominent component of chili pepper known for its potent agonistic effects on TRPV1, has attracted significant attention for its diverse physiological effects. Nevertheless, there remains a paucity of data concerning its in vivo distribution, metabolism, pharmacodynamic properties, and influence on the metabolic profile of the brain. MethodsStable isotope tracing, in vitro enzyme incubation, microdialysis coupled with UHPLC-MS/MS techniques were employed to investigate the in vivo metabolic pathways, distribution, and pharmacokinetic properties of CAP, and the potential biases in metabolic pathways was elucidate through molecular docking. Furthermore, the effect of CAP on brain metabolic profiles was assessed using untargeted metabolomics, and spatial visualization analysis was conducted through mass spectrometry imaging. ResultsCAP was distributed predominantly in the kidneys, with lower content in the liver, heart, lungs, brain, and spleen following peripheral administration, and the absorption half-life in the body was about 20 minutes. CAP primarily underwent alkyl terminal dehydrogenation, hydroxylation, and macrocyclization metabolic pathways under the action of CYP2C9, CYP2C19 and CYP2D6, resulting in at least four metabolites. Among them, the hydroxylation products were main metabolites and the dehydrogenation product 16,17-dihydrocapsaicin could interact with the key binding sites Leu515 and Thr550 of TRPV1 like CAP. CAP quickly diffused to various brain regions and the metabolic characteristics in the striatum were relatively different from that in the blood. The distribution of CAP in the brain primarily triggered the release of neurotransmitters in areas associated with reward, cognition, and memory. Both acute and chronic exposure to CAP elevated amino acid levels in cortical regions, while producing contrasting effects on nucleotide metabolites. ConclusionThis study offers an initial in-depth analysis of the distribution patterns, metabolic pathways and pharmacodynamic properties of CAP in the body and brain. These findings established a basis for further studies on CAP's pharmacology properties and its influence on the central nervous system.

Identification of novel salt-enhancing peptides in soy protein and molecular docking studies with transmembrane channel-like 4 (TMC4)

The aim of this study was to rapidly screen novel salt-enhancing peptides from soy protein by virtual screening and molecular docking. Potential salt-enhancing peptides were screened by computerized virtual hydrolysis, bioactivity prediction, toxicity prediction, and water solubility prediction. Sensory evaluation and e-tongue analysis further indicated that the peptides DIF (Asp-Ile-Phe), QPR (Gln-Pro-Arg), MMR (Met-Met-Arg), and DPIY (Asp-Pro-Ile-Tyr) had significant salting enhancing effects. Among them, MMR had the most significant salting effect, replacing at least about 40.35% of NaCl. In addition, a transmembrane channel-like 4 (TMC4) salty receptor model was built, and molecular docking was performed using computational techniques. Glu286, His293, Glu319, and Ser585 were hypothesized to be key binding sites. Molecular dynamics simulations further confirmed the stability of the complex system. This study discovered new salt-enhancing peptides in soy protein and provided a rapid and effective approach for further research in this area.

ACE inhibitory effect and saltiness-enhancing properties of chicken-derived umami peptides: Digestive stability, inhibition kinetics, multiple ligand docking and central composite design

Angiotensin-I-converting enzyme (ACE) inhibitory activity and saltiness-enhancing properties of chicken-derived umami peptides were investigated. DGGRYY and NEFGYSNR were screened and the IC50 values were 28.71 μM and 283.24 μM, indicating their potential as novel ACE inhibitors. DGGRYY and NEFGYSNR have good pH and thermal stability. After gastrointestinal digestion, the ACE-inhibitory activity of DGGRYY retained about 53 %, whereas NEFGYSNR retained about 57 %. The inhibition pattern of both peptides was determined to be uncompetitive, consisting with the result of multiple ligand docking that the binding sites were outside the ACE active pocket. Trp59, Tyr62, Asp121, Arg124, and Ser516 were the key binding sites that contributed to the total binding energy. In addition, saltiness and palatability models were established according to sensory analysis and central composite design. In 0.1 % ~ 0.3 % NaCl solutions, the addition of DGGRYY and NEFGYSNR could enhance the salty intensity and compensate for the palatability loss caused by salt reduction.

Solvation and its influence on the electronic structure and pharmacological activity of 2-fluoro-6-trifluromethyl acetophenone

The molecular framework and vibrational spectra of 2′-Fluoro-6′-Trifluoromethyl Acetophenone (MA3) in diverse solvent environments are being studied using quantum chemistry methods like DFT. The structure was successfully optimized using gas phase and solvent phases such as ethanol, diethyl sulfoxide, chloroform, and diethyl ether. Using FT-Raman and FT-IR techniques, both theoretical and experimental scenarios were examined. The IEFPCM model was used to explore the electronic properties, including HOMO-LUMO gaps, UV–Vis spectra, NBO, Mulliken analysis, and MEP, in various solvents. The TD-DFT approach and IEFPCM model were utilized to replicate the UV spectra. The Fukui function helped locate reactive sites and understand chemical interactions. Comprehensive topological analysis using Multiwfn – 3.8 suite integrated RDG, ALIE, ELF, and LOL to identify key binding sites and weak interactions. The molecular docking studies highlighted the compound’s binding affinities with target proteins, showcasing its potential pharmacological applications. This research underscores the critical role of solvation in determining the electronic and structural properties of MA3, paving the way for its application in drug development and other fields.

Dynamic conformational response of von Willebrand factor to varying shear stress: A hybrid computational approach

This computational study examines the mechanobiological responses of von Willebrand Factor (vWF) to different shear stress levels, emphasizing the unique structural dynamics of its various domains. We introduce a novel coarse-grained model, representing each cluster of six amino acids as a bead, to synthesize the Lattice Boltzmann method with Brownian dynamics. This approach captures the vWF molecule’s conformational adaptability across a spectrum of shear rates, ranging from 5 to 5e + 7s−1, encompassing normal physiological flows to those resembling the high-shear environment of arterial stenosis.Our results reveal domain-specific responses of vWF, particularly in the A2 and A3 domains, which demonstrate significant elongation under elevated shear—reflecting their pivotal roles in clotting processes. Moreover, the study underscores the critical influence of random thermal forces on the molecule’s conformation, with simulations including these forces showing substantially greater conformational variability compared to those without.As shear rates increase, we observe a notable reorganization in the spatial arrangement of vWF domains. This reconfiguration is most evident in the increased separation between the A1 and D’D3 domains under high shear conditions, potentially enhancing the accessibility of platelets to key binding sites on vWF. These findings are paramount for a deeper understanding of vWF’s mechanical behavior in blood clotting and thrombosis, particularly the delicate balance between facilitating platelet adhesion and avoiding excessive stretching that could lead to thrombosis.Our work provides a foundation for future studies investigating vWF behavior in complex flow geometries and its interactions with other blood components. Such insights pave the way for more informed therapeutic strategies targeting vWF function in vascular health and disease, potentially leading to improved treatments for thrombotic disorders.

Novel umami-enhancing peptides of beef M. Semimembranosus hydrolysates and interactions with the T1R1/T1R3 taste receptor

The taste mechanisms of beef umami and umami-enhancing peptides are not well understood. Therefore, novel umami and umami-enhancing peptides from beef M. semimembranosus hydrolysates were explored. Beef hydrolysates treated with Flavourzyme® showed an overall strong umami intensity compared to those treated with Alcalase®, papain, or Protamex®. The peptides were isolated via consecutive separation processes, and 31 potential umami peptides were identified. Molecular docking results showed that WGSEPIRIQ and TERGYSF had considerably low docking energies with the T1R1/T1R3 taste receptor through potential key binding sites for hydrogen bonding, including Ser48, Gly49, and Gln278 in T1R1, and Ser67, Asn68, and Arg247 in the T1R3 subunit. The taste of the identified peptides dissolved in ultrapure water was dominated by sourness. Instead, they demonstrated an umami-enhancing effect in the presence of monosodium glutamate. These results broaden our understanding of the taste mechanisms of beef umami-enhancing peptides and their potential applications as flavoring agents.

Evaluation of Angiotensin-Converting Enzyme 2 Expression In Vivo with Novel 68Ga-Labeled Peptides Originated from the Coronavirus Receptor-Binding Domain.

Angiotensin-converting enzyme 2 (ACE2) is not only a key to the renin-angiotensin-aldosterone system and related diseases, but also the main entry point on cell surfaces for certain coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. By analyzing the different key binding sites from the receptor-binding domain (RBD) of SARS-CoV and SARS-CoV-2, nine new ACE2-targeting peptides (A1 to A9) were designed, synthesized and connected with a chelator, 1,4,7-triazacyclononane-N,N',N''-triacetic acid (NOTA). NOTA-A1, NOTA-A2, NOTA-A4, NOTA-A5, and NOTA-A8 were successfully labeled with [68Ga]Ga3+ and were used for biological evaluation. [68Ga]Ga-NOTA-A2, [68Ga]Ga-NOTA-A5, and [68Ga]Ga-NOTA-A8 showed specific binding to ACE2 via cell assays, and their binding sites and binding capacity were calculated by molecular docking and molecular dynamics simulations. In tumor-bearing mice, A549 tumors were visualized 60 min postinjection of [68Ga]Ga-NOTA-A2, [68Ga]Ga-NOTA-A5, or [68Ga]Ga-NOTA-A8. These peptides also accumulated in the organs with high-level ACE2 expression, confirmed by immunohistochemical stain. Among them, [68Ga]Ga-NOTA-A5 exhibited the highest tumor uptake and tumor/background ratio, and it successfully tracked the increased ACE2 levels in mice tissues after excessive Losartan treatment. In a first-in-human study, the distribution of [68Ga]Ga-NOTA-A5 was evaluated with positron emission tomography/computed tomography (PET/CT) in three participants without adverse events. 68Ga-labeled peptides originated from the coronavirus RBD, with [68Ga]Ga-NOTA-A5 as a typical representative, seem to be safe and effective for the evaluation of ACE2 expression in vivo with PET/CT, facilitating further mechanism investigation and clinical evaluation of ACE2-related diseases.

Site-directed mutagenesis and molecular docking simulations identified the crucial substrate binding site asparagine 101 of xyloglucan endotransglycosylase/hydrolase (XTH) in woody plants

Xyloglucan endotransglycosylase/hydrolase (XTH) is a key enzyme in plant cell wall remodeling. Previous investigations on the angiosperm Populus tomentosa identified 11 PtoXTH proteins with the XTH catalytic motif. Surprisingly, only two (PtoXTH27 and PtoXTH34) exhibited xyloglucan endotransglucosylase (XET) activity, suggesting the presence of additional key substrate binding or catalytic activity sites within XTH proteins. To test this hypothesis, we performed site-directed mutagenesis on selected amino acids in PtoXTH27 and PtoXTH34 and characterized their biochemical properties. Molecular docking simulations and biochemical analyses revealed that N101 is a critical substrate binding site, while Q80, M81, and V180 are essential functional residues influencing XET activity in XTH proteins. Notably, XET-deficient PtoXTH26 regained activity following site-directed mutation, underscoring the significance of these residues. Expanding our study to the gymnosperm Larix kaempferi, we identified two XTH proteins: LkXTH1, which exhibited both the key substrate binding site and XET activity, and LkXTH2, which lacked XET activity. Intriguingly, LkXTH2 regained XET activity after site-directed mutation, highlighting the versatility of the newly identified substrate binding site across different woody plants subphyla. This research provides a theoretical basis for the rapid identification of enzymatically active members within the XTH gene family in woody plants. Furthermore, our findings offer insights into the targeted engineering of XTH enzymes, paving the way for advancements in plant biotechnology and crop improvement.

Isolation and characterization of novel umami peptides from bay scallop (Argopecten irradians) and molecular docking to the T1R1/T1R3 taste receptor

The study aimed to isolate, purify, screen, and identify novel umami peptides from bay scallops. Proteins were hydrolyzed using AP200-A alkaline protease and FF106 flavor protease to obtain umami peptides. Ultrafiltration membranes were employed to separate and purify the peptides from scallop by-products, revealing that fractions smaller than 3 kDa exhibited the highest umami levels. Further purification was achieved using the AKTA system superdexpeptide gel chromatography. The composition of umami peptides was identified using LC-MS/MS technology. Molecular docking identified four types of umami peptides: RPPVVR, APDFGNR, SWLDGK, and RGFGGAR. Hydrogen bonds, electrostatic interactions, and hydrophobic interactions were identified as the primary binding forces between T1R1/T1R3 and the umami peptides, with key binding sites including ASN150, ASP216, ASP219, GLN222, GLU148, GLU217, LEU51, and SER107. These findings supplement existing research on scallop umami peptides and provide insights into the interaction mechanisms between umami receptors and umami peptides.

Virtual Screening and Validation of Affinity DNA Functional Ligands for IgG Fc Segment.

The effective attachment of antibodies to the immune sensing interface is a crucial factor that determines the detection performance of immunosensors. Therefore, this study aims to investigate a novel antibody immobilization material with low molecular weight, high stability, and excellent directional immobilization effect. In this study, we employed molecular docking technology based on the ZDOCK algorithm to virtually screen DNA functional ligands (DNAFL) for the Fc segment of antibodies. Through a comprehensive analysis of the key binding sites and contact propensities at the interface between DNAFL and IgG antibody, we have gained valuable insights into the affinity relationship, as well as the principles governing amino acid and nucleotide interactions at this interface. Furthermore, molecular affinity experiments and competitive binding experiments were conducted to validate both the binding ability of DNAFL to IgG antibody and its actual binding site. Through affinity experiments using multi-base sequences, we identified bases that significantly influence antibody-DNAFL binding and successfully obtained DNAFL with an enhanced affinity towards the IgG Fc segment. These findings provide a theoretical foundation for the targeted design of higher-affinity DNAFLs while also presenting a new technical approach for immunosensor preparation with potential applications in biodetection.

Machine learning-assisted substrate binding pocket engineering based on structural information.

Engineering enzyme-substrate binding pockets is the most efficient approach for modifying catalytic activity, but is limited if the substrate binding sites are indistinct. Here, we developed a 3D convolutional neural network for predicting protein-ligand binding sites. The network was integrated by DenseNet, UNet, and self-attention for extracting features and recovering sample size. We attempted to enlarge the dataset by data augmentation, and the model achieved success rates of 48.4%, 35.5%, and 43.6% at a precision of ≥50% and 52%, 47.6%, and 58.1%. The distance of predicted and real center is ≤4Å, which is based on SC6K, COACH420, and BU48 validation datasets. The substrate binding sites of Klebsiella variicola acid phosphatase (KvAP) and Bacillus anthracis proline 4-hydroxylase (BaP4H) were predicted using DUnet, showing high competitive performance of 53.8% and 56% of the predicted binding sites that critically affected the catalysis of KvAP and BaP4H. Virtual saturation mutagenesis was applied based on the predicted binding sites of KvAP, and the top-ranked 10 single mutations contributed to stronger enzyme-substrate binding varied while the predicted sites were different. The advantage of DUnet for predicting key residues responsible for enzyme activity further promoted the success rate of virtual mutagenesis. This study highlighted the significance of correctly predicting key binding sites for enzyme engineering.

Mechanism of action of plasma-activated water on biomacromolecules in Salmonella Enteritidis: Biological effect, computer simulation, and transcriptomics-based analysis

Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most important causes of foodborne illness in the food industry. In this work, plasma-activated water (PAW) generated from the plasma jet was employed to reduce S. Enteritidis contamination. The antibacterial mechanism of PAW was revealed from biological changes, molecular docking, and transcriptomics. Results revealed that the addition of lactic acid could improve the antibacterial activity and efficiency of PAW, and confirmed the existence and antibacterial activity of free radicals (OH, 1O2, and NO) in PAW. Meanwhile, PAW treatment caused damage to characteristic functional groups of biomolecules, and led to the oxidation of lipids and degradation of DNA. Molecular docking results further suggested that the reactive species could interact with amino acid residues around key binding sites through hydrogen bonding, affecting the stability of structures. Furthermore, the transcriptomics results indicated that PAW is primarily active on bacterial proteins and to a lesser extent on membrane lipids and DNA. Overall, the action mechanism of PAW on biomacromolecules is comprehensively analyzed in this work, and it provides a theoretical basis for the broad application of plasma technology.

MGPPI: multiscale graph neural networks for explainable protein-protein interaction prediction.

Protein-Protein Interactions (PPIs) involves in various biological processes, which are of significant importance in cancer diagnosis and drug development. Computational based PPI prediction methods are more preferred due to their low cost and high accuracy. However, existing protein structure based methods are insufficient in the extraction of protein structural information. Furthermore, most methods are less interpretable, which hinder their practical application in the biomedical field. In this paper, we propose MGPPI, which is a Multiscale graph convolutional neural network model for PPI prediction. By incorporating multiscale module into the Graph Neural Network (GNN) and constructing multi convolutional layers, MGPPI can effectively capture both local and global protein structure information. For model interpretability, we introduce a novel visual explanation method named Gradient Weighted interaction Activation Mapping (Grad-WAM), which can highlight key binding residue sites. We evaluate the performance of MGPPI by comparing with state-of-the-arts methods on various datasets. Results shows that MGPPI outperforms other methods significantly and exhibits strong generalization capabilities on the multi-species dataset. As a practical case study, we predicted the binding affinity between the spike (S) protein of SARS-COV-2 and the human ACE2 receptor protein, and successfully identified key binding sites with known binding functions. Key binding sites mutation in PPIs can affect cancer patient survival statues. Therefore, we further verified Grad-WAM highlighted residue sites in separating patients survival groups in several different cancer type datasets. According to our results, some of the highlighted residues can be used as biomarkers in predicting patients survival probability. All these results together demonstrate the high accuracy and practical application value of MGPPI. Our method not only addresses the limitations of existing approaches but also can assists researchers in identifying crucial drug targets and help guide personalized cancer treatment.

Sarmentol H derived from Sedum sarmentosum Bunge directly targets FXR to mitigate cholestasis by recruiting SRC-1

BackgroundFarnesoid X receptor (FXR) is a vital receptor for bile acids and plays an important role in the treatment of cholestatic liver disease. In addition to traditional bile acid-based steroidal agonists, synthetic alkaloids are the most commonly reported non-steroidal FXR agonists. Sarmentol H is a nor-sesquiterpenoid obtained from Sedum sarmentosum Bunge, and in vitro screening experiments have shown that it might be related to the regulation of the FXR pathway in a previous study. PurposeTo investigate the therapeutic effects of sarmentol H on cholestasis and to determine whether sarmentol H directly targets FXR to mitigate cholestasis. Furthermore, this study aimed to explore the key amino acid residues involved in the binding of sarmentol H to FXR through site-directed mutagenesis. MethodsAn intrahepatic cholestasis mouse model was established to investigate the therapeutic effects of sarmentol H on cholestasis. In vitro experiments, including Co-Ip and FXR-EcRE-Luc assays, were performed to assess whether sarmentol H activates FXR by recruiting the receptor coactivator SRC1. CETSA, SIP, DARTS, and ITC were used to determine the binding of sarmentol H to FXR protein. The key amino acid residues for sarmentol H binding to FXR were analyzed by molecular docking and site-directed mutagenesis. Finally, we conducted in vivo experiments on wild-type and Fxr−/− mice to further validate the anticholestatic target of sarmentol H. ResultsSarmentol H had significant ameliorative effects on the pathological conditions of cholestatic mice induced with ANIT. In vitro experiments suggested that it is capable of activating FXR and regulating downstream signaling pathways by recruiting SRC1. The target validation experiments showed that sarmentol H had the ability to bind to FXR as a ligand (KD = 2.55 μmol/L) and enhance the stability of its spatial structure. Moreover, site-directed mutagenesis revealed that THR292 and TYR365 were key binding sites for sarmentol H and FXR. Furthermore, knockout of the Fxr gene resulted in a significantly higher degree of ANIT-induced cholestatic liver injury than that in wild-type cholestatic mice, and the amelioration of cholestasis or regulatory effects on FXR downstream genes by sarmentol H also disappeared in Fxr−/− cholestatic mice. ConclusionSarmentol H is an FXR agonist. This is the first study to show that it exerts a significant therapeutic effect on cholestatic mice, and can directly bind to FXR and activate it by recruiting the coactivator SRC1.

Resveratrol targeting NRF2 disrupts the binding between KEAP1 and NRF2-DLG motif to ameliorate oxidative stress damage in mice pulmonary infection

Ethnopharmacological relevanceThe root of Polygonum cuspidatum Sieb. et Zucc (PC), known as 'Huzhang' in the Chinese Pharmacopoeia, has been traditionally employed for its anti-inflammatory, antiviral, antimicrobial, and other biological activities. Polydatin (PD) and its aglycone, resveratrol (RES), are key pharmacologically active components responsible for exerting anti-inflammatory and antioxidant effects. However, its specific targets and action mechanisms remain unclear. Aim of the studyThe equilibrium of the KEAP1-NRF2 system serves as the primary protective response to oxidative and electrophilic stresses within the body, particularly in cases of acute lung injury caused by pathogenic microbial infection. In this study, the precise mechanisms by which RES alleviates oxidative stress damage in conjunction with NRF2 activators are discussed. Materials and methodsThe active components from PC were screened to evaluate their potential to inhibit reactive oxygen species (ROS) and activate antioxidant activity dependent on antioxidant response elements (ARE). RES was evaluated for its potential to alleviate the oxidative stress caused by pathogenic microbial infection. Functional probes were designed to study the RES distribution and identify its targets. A lipopolysaccharide (LPS)-induced oxidative injury model was used to evaluate the effects of RES on the KEAP1-NRF2/ARE pathway in RAW 264.7 cells. The interaction between RES and NRF2 was elucidated using drug-affinity responsive target stability (DARTS), cellular thermal shift assays (CETSA), co-immunoprecipitation (Co-IP), and microscale thermophoresis (MST) techniques. The key binding sites were predicted using molecular docking and validated in NRF2-knockdownand reconstructed cells. Finally, protective effects against pulmonary stress were verified in a mouse model of pathogenic infection. ResultsThe accumulation of RES in lung macrophages disrupted the binding between KEAP1 and NRF2, thereby preventing the ubiquitination degradation of NRF2 through its interaction with Ile28 on the NRF2-DLG motif. The activation of NRF2 resulted in the upregulation of nuclear transcription, enhances the expression of antioxidant genes dependent on ARE, suppresses ROS generation, and ameliorates oxidative damage both in vivo and in vitro. ConclusionThese findings shed light on the potential of RES to mitigate oxidative stress damage caused by pathogenic microorganism-induced lung infections and facilitate the discovery of novel small molecule modulators targeting the KEAP1-NRF2 DLG motif interaction.

Molecular Insights into the Effect of Cholesterol on the Binding of Bicarbonate Ions in Band 3 Protein.

Band 3, or anion exchanger 1 (AE1), is one of the indispensable transmembrane proteins involved in the effective respiratory process of the human body and is primarily responsible for the exchange of bicarbonate and chloride anions across the plasma membrane of erythrocyte. However, the molecular mechanism of ion transport of Band 3 is not completely understood, yet. In this work, we systematically investigate the key binding sites of bicarbonate ions in Band 3 and the impact of cholesterol (CHOL) in lipid bilayers on bicarbonate ion binding using all-atom molecular dynamics (MD) simulations. We examine the dynamics of interactions of bicarbonate ions with Band 3 in the microsecond time scale and calculate the binding free energy of the anion in Band 3. The results indicate that the residue R730 of Band 3 is the most probable binding site for bicarbonate ions. CHOL enhances the bicarbonate ion binding by influencing the conformational stability of Band 3 and compressing the volume of the Band 3 cavity. These findings provide some insights into the bicarbonate ion binding in Band 3 and are helpful for understanding the anion exchange of Band 3.

Exploring the link between pyrethroids exposure and dopaminergic degeneration through morphometric, immunofluorescence, and in-silico approaches: the therapeutic role of chitosan-encapsulated curcumin nanoparticles.

Introduction: The synthetic pyrethroid derivative fenpropathrin (FNE), a commonly used insecticide, has been associated with various toxic effects in mammals, particularly neurotoxicity. The study addressed the hallmarks of the pathophysiology of Parkinson's disease upon oral exposure to fenpropathrin (FNE), mainly the alteration of dopaminergic markers, oxidative stress, and molecular docking in rat models. In addition, the protective effect of curcumin-encapsulated chitosan nanoparticles (CRM-Chs-NPs) was also assessed. Methods: In a 60-day trial, 40 male Sprague Dawley rats were divided into 4 groups: Control, CRM-Chs-NPs (curcumin-encapsulated chitosan nanoparticles), FNE (15mg/kg bw), and FNE + CRM-Chs-NPs. Results: FNE exposure induced reactive oxygen species generation, ATP production disruption, activation of inflammatory and apoptotic pathways, mitochondrial function and dynamics impairment, neurotransmitter level perturbation, and mitophagy promotion in rat brains. Molecular docking analysis revealed that FNE interacts with key binding sites of dopamine synthesis and transport proteins. On the other hand, CRM-Chs-NPs mitigated FNE's toxic effects by enhancing mitochondrial dynamics, antioxidant activity, and ATP production and promoting anti-inflammatory and antiapoptotic responses. Conclusion: In summary, FNE appears to induce dopaminergic degeneration through various mechanisms, and CRM-Chs-NPs emerged as a potential therapeutic intervention for protecting the nervous tissue microenvironment.

Disruption of a DNA G-quadruplex causes a gain-of-function SCL45A1 variant relevant to developmental disorders.

SLC45A1 encodes a glucose transporter protein highly expressed in the brain. Mutations in SLC45A1 may lead to neurological diseases and developmental disorders, but its exact role is poorly understood. DNA G-quadruplexes (DNA G4s) are stable structures formed by four guanine bases and play a role in gene regulation and genomic stability. Changes in DNA G4s may affect brain development and function. The mechanism linking alterations in DNA G-quadruplex structures to SLC45A1 pathogenicity remains unknown. In this study, we identify a functional DNA G-quadruplex and its key binding site on SLC45A1 (NM_001080397.3: exon 2: c.449 G>A: p.R150K). This variant results in the upregulation of mRNA and protein expression, which may lead to intellectual developmental disorder with neuropsychiatric features. Mechanistically, the mutation is found to disrupt DNA G-quadruplex structures on SLC45A1, leading to transcriptional enhancement and a gain-of-function mutation, which further causes increased expression and function of the SLC45A1 protein. The identification of the functional DNA G-quadruplex and its effects on DNA G4s may provide new insights into the genetic basis of SLC45A1 pathogenicity and highlight the importance of DNA G4s of SLC45A1 in regulating gene expression and brain development.

The diazirine-mediated photo-crosslinking of collagen improves biomaterial mechanical properties and cellular interactions

In tissue engineering, crosslinking with carbodiimides such as EDC is omnipresent to improve the mechanical properties of biomaterials. However, in collagen biomaterials, EDC reacts with glutamate or aspartate residues, inactivating the binding sites for cellular receptors and rendering collagen inert to many cell types. In this work, we have developed a crosslinking method that ameliorates the rigidity, stability, and degradation rate of collagen biomaterials, whilst retaining key interactions between cells and the native collagen sequence. Our approach relies on the UV-triggered reaction of diazirine groups grafted on lysines, leaving critical amino acid residues intact. Notably, GxxGER recognition motifs for collagen-binding integrins, ablated by EDC crosslinking, were left unreacted, enabling cell attachment, spreading, and colonization on films and porous scaffolds. In addition, our procedure conserves the architecture of biomaterials, improves their resistance to collagenase and cellular contraction, and yields material stiffness akin to that obtained with EDC. Importantly, diazirine-crosslinked collagen can host mesenchymal stem cells, highlighting its strong potential as a substrate for tissue repair. We have therefore established a new crosslinking strategy to modulate the mechanical features of collagen porous scaffolds without altering its biological properties, thereby offering an advantageous alternative to carbodiimide treatment. Statement of significanceThis article describes an approach to improve the mechanical properties of collagen porous scaffolds, without impacting collagen's natural interactions with cells. This is significant because collagen crosslinking is overwhelmingly performed using carbodiimides, which results in a critical loss of cellular affinity. By contrast, our method leaves key cellular binding sites in the collagen sequence intact, enabling cell-biomaterial interactions. It relies on the fast, UV-triggered reaction of diazirine with collagen, and does not produce toxic by-products. It also supports the culture of mesenchymal stem cells, a pivotal cell type in a wide range of tissue repair applications. Overall, our approach offers an attractive option for the crosslinking of collagen, a prominent material in the growing field of tissue engineering.

Characteristics of saltiness-enhancing peptides derived from yeast proteins and elucidation of their mechanism of action by molecular docking

This study aimed to identify saltiness-enhancing peptides from yeast protein and elucidate their mechanisms by molecular docking. Yeast protein hydrolysates with optimal saltiness-enhancing effects were prepared under conditions determined using an orthogonal test. Ten saltiness-enhancing peptide candidates were screened using an integrated virtual screening strategy. Sensory evaluation demonstrated that these peptides exhibited diverse taste characteristics (detection thresholds: 0.13–0.50 mmol/L). Peptides NKF, LGLR, WDL, NMKF, FDSL and FDGK synergistically or additively enhanced the saltiness of a 0.30% NaCl solution. Molecular docking revealed that these peptides predominantly interacted with TMC4 by hydrogen bonding, with hydrophilic amino acids from both peptides and TMC4 playing a pivotal role in their binding. Furthermore, Leu217, Gln377, Glu378, Pro474 and Cys475 were postulated as the key binding sites of TMC4. These findings establish a robust theoretical foundation for salt reduction strategies in food and provide novel insights into the potential applications of yeast proteins.