Search Results (912)

Background: The candidate therapeutic peptide TnP demonstrates broad, system-level regulatory capacity, revealed through integrated network analysis from transcriptomic data in zebrafish. Our study primarily identifies TnP as a multifaceted modulator of drug metabolism, wound healing, proteolytic activity, and pigmentation pathways. Results: Transcriptomic profiling of TnP-treated larvae following tail fin amputation revealed 558 differentially expressed genes (DEGs), categorized into four functional networks: (1) drug-metabolizing enzymes (cyp3a65, cyp1a) and transporters (SLC/ABC families), where TnP alters xenobiotic processing through Phase I/II modulation; (2) cellular trafficking and immune regulation, with upregulated myosin genes (myhb/mylz3) enhancing wound repair and tlr5-cdc42 signaling fine-tuning inflammation; (3) proteolytic cascades (c6ast4, prss1) coupled to autophagy (ulk1a, atg2a) and metabolic rewiring (g6pca.1-tg axis); and (4) melanogenesis-circadian networks (pmela/dct-fbxl3l) linked to ubiquitin-mediated protein turnover. Key findings highlight TnP’s unique coordination of rapid (protease activation) and sustained (metabolic adaptation) responses, enabled by short network path lengths (1.6–2.1 edges). Hub genes, such as nr1i2 (pxr), ppara, and bcl6aa/b, mediate crosstalk between these systems, while potential risks—including muscle hypercontractility (myhb overexpression) or cardiovascular effects (ace2-ppp3ccb)—underscore the need for targeted delivery. The zebrafish model validated TnP-conserved mechanisms with human relevance, particularly in drug metabolism and tissue repair. TnP’s ability to synchronize extracellular matrix remodeling, immune resolution, and metabolic homeostasis supports its development for the treatment of fibrosis, metabolic disorders, and inflammatory conditions. Conclusions: Future work should focus on optimizing tissue-specific delivery and assessing genetic variability to advance clinical translation. This system-level analysis positions TnP as a model example for next-generation multi-pathway therapeutics. Full article

The glucagon-like peptide-1 receptor (GLP-1R), which belongs to the class B1 G protein-coupled receptor (GPCR) family, is an important target for treatment of metabolic disorders, including type 2 diabetes and obesity. The growing interest in GLP-1R-based therapies is driven by the development of various functional agonists as well as the huge commercial market. Thus, understanding the structural details of ligand-induced signaling are important for developing improved GLP-1R drugs. Here, we investigated the conformational dynamics of the receptor in complex with a selection of prototypical functional agonists, including CHU-128 (small molecule-biased), danuglipron (small molecule balanced), and Peptide 19 (peptide balanced), which exhibit unique, distinct binding modes and induced helix packing. Furthermore, our all-atom molecular dynamics (MD) simulations revealed atomic feature how different those ligands led to signaling pathway preference. Our findings offer valuable insights into the mechanistic principle of GLP-1R activation, which are helpful for the rational design of next-generation GLP-1R drug molecules. Full article

Conventional methods for generating knock-out or knock-in mammalian cell models using CRISPR-Cas9 genome editing often require tedious single-cell clone selection and expansion. In this study, we develop and optimise rapid and robust strategies to engineer homozygous fluorescent reporter knock-in cell pools with precise genome editing, circumventing clonal variability inherent to traditional approaches. To reduce false-positive cells associated with random integration, we optimise the design of donor DNA by removing the start codon of the fluorescent reporter and incorporating a self-cleaving T2A peptide system. Using fluorescence-assisted cell sorting (FACS), we efficiently identify and isolate the desired homozygous fluorescent knock-in clones, establishing stable cell pools that preserve parental cell line heterogeneity and faithfully reflect endogenous transcriptional regulation of the target gene. We evaluate the knock-in efficiency and rate of undesired random integration in the electroporation method with either a dual-plasmid system (sgRNA and donor DNA in two separate vectors) or a single-plasmid system (sgRNA and donor DNA combined in one vector). We further demonstrate that coupling our single-plasmid construct with an integrase-deficient lentivirus vector (IDLV) packaging system efficiently generates fluorescent knock-in reporter cell pools, offering flexibility between electroporation and lentivirus transduction methods. Notably, compared to the electroporation methods, the IDLV system significantly minimises random integration. Moreover, the resulting reporter cell lines are compatible with most of the available genome-wide sgRNA libraries, enabling unbiased CRISPR screens to identify key transcriptional regulators of a gene of interest. Overall, our methodologies provide a powerful genetic tool for rapid and robust generation of fluorescent reporter knock-in cell pools with precise genome editing by CRISPR-Cas9 for various research purposes. Full article

Spurred by the enormous therapeutic success of glucagon-like peptide-1 receptor (GLP-1R) agonists (GLP1-RAs) against diabetes and obesity, glucagon family receptor pharmacology has garnered a tremendous amount of interest. Glucagon family receptors, e.g., the glucagon receptor itself (GCGR), the GLP-1R, and the glucose-dependent insulinotropic peptide receptor (GIPR), belong to the incretin receptor superfamily, i.e., receptors that increase blood glucose-dependent insulin secretion. All incretin receptors are class B1 G protein-coupled receptors (GPCRs), coupling to the G_s type of heterotrimeric G proteins which activates adenylyl cyclase (AC) to produce cyclic adenosine monophosphate (cAMP). Most GPCRs undergo desensitization, i.e., uncouple from G proteins and internalize, thanks to interactions with the βarrestins (arrestin-2 and -3). Since the βarrestins can also mediate their own G protein-independent signaling, any given GPCR can theoretically signal (predominantly) either via G proteins or βarrestins, i.e., be a G protein- or βarrestin-“biased” receptor, depending on the bound ligand. A plethora of experimental evidence suggests that the GLP-1R does not undergo desensitization in physiologically relevant tissues in vivo, but rather, it produces robust and prolonged cAMP signals. A particular property of constant cycling between the cell membrane and caveolae/lipid rafts of the GLP-1R may underlie its lack of desensitization. In contrast, GIPR signaling is extensively mediated by βarrestins and the GIPR undergoes significant desensitization, internalization, and downregulation, which may explain why both agonists and antagonists of the GIPR exert the same physiological effects. Here, we discuss this evidence and make a case for the GLP-1R being a phenotypically or functionally G_s-selective receptor. We also discuss the implications of this for the development of GLP-1R poly-ligands, which are increasingly pursued for the treatment of obesity and other diseases. Full article

The global escalation of organic waste generation, coupled with rising protein demand and environmental pressure, necessitates innovative, circular approaches to resource management. Hermetia illucens (Black Soldier Fly, BSF) has emerged as a leading candidate for integrated waste-to-resource systems. This review examines BSF biological and genomic adaptations underpinning waste conversion efficiency, comparative performance of BSF bioconversion versus traditional treatments, nutritional and functional attributes, techno-economic, regulatory, and safety barriers to industrial scale-up. Peer-reviewed studies were screened for methodological rigor, and data on life cycle traits, conversion metrics, and product compositions were synthesized. BSF larvae achieve high waste reductions, feed-conversion efficiencies and redirect substrate carbon into biomass, yielding net CO₂ emissions as low as 12–17 kg CO₂ eq ton⁻¹, an order of magnitude below composting or vermicomposting. Larval biomass offers protein, lipids (notably lauric acid), micronutrients, chitin, and antimicrobial peptides, with frass serving as a nutrient-rich fertilizer. Pathogen and antibiotic resistance gene loads decrease during bioconversion. Key constraints include substrate heterogeneity, heavy metal accumulation, fragmented regulatory landscapes, and high energy and capital demands. BSF systems demonstrate superior environmental and nutritional performance compared to conventional waste treatments. Harmonized safety standards, feedstock pretreatment, automation, and green extraction methods are critical to overcoming scale-up barriers. Interdisciplinary innovation and policy alignment will enable BSF platforms to realize their full potential within circular bio-economies. Full article

Cold environments challenge the structural and functional integrity of membrane proteins, requiring specialized adaptations to maintain activity under low thermal energy. Here, we investigate the molecular basis of cold tolerance in the peptide transporter PepT1 from the Antarctic icefish (Chionodraco hamatus, ChPepT1) using molecular dynamics simulations, binding free energy calculations (MM/GBSA), and dynamic network analysis. We compare ChPepT1 to its human ortholog (hPepT1), a non-cold-adapted variant, to reveal key features enabling psychrophilic function. Our simulations show that ChPepT1 displays enhanced global flexibility, particularly in domains adjacent to the substrate-binding site and the C-terminal domain (CTD). While hPepT1 loses substrate binding affinity as temperature increases, ChPepT1 maintains stable peptide interactions across a broad thermal range. This thermodynamic buffering results from temperature-sensitive rearrangement of hydrogen bond networks and more dynamic lipid interactions. Importantly, we identify a temperature-responsive segment (TRS, residues 660–670) within the proximal CTD that undergoes an α-helix to coil transition, modulating long-range coupling with transmembrane helices. Dynamic cross-correlation analyses further suggest that ChPepT1, unlike hPepT1, reorganizes its interdomain communication in response to temperature shifts. Our findings suggest that cold tolerance in ChPepT1 arises from a combination of structural flexibility, resilient substrate binding, and temperature-sensitive interdomain dynamics. These results provide new mechanistic insight into thermal adaptation in membrane transporters and offer a framework for engineering proteins with enhanced functionality in extreme environments. Full article

Diabetes mellitus and atrial fibrillation (AF) frequently coexist, creating a complex bidirectional relationship that exacerbates cardiovascular risk and challenges clinical management. Diabetes fosters a profibrotic, pro-inflammatory, and proarrhythmic atrial substrate through a constellation of pathophysiologic mechanisms, including metabolic remodeling, oxidative stress, mitochondrial dysfunction, ion channel dysregulation, and autonomic imbalance, thereby promoting AF initiation and progression. Conventional rhythm control strategies remain less effective in diabetic individuals, underscoring the need for innovative, substrate-targeted interventions. In this context, sodium–glucose cotransporter 2 (SGLT2) inhibitors and glucagon-like peptide-1 (GLP-1) receptor agonists have emerged as promising agents with pleiotropic antiarrhythmic properties, modulating fibrosis, inflammation, and mitochondrial integrity. Moreover, advances in anti-inflammatory, antifibrotic, and ion channel-modulating therapeutics, coupled with novel mitochondrial-targeted strategies, are reshaping the therapeutic landscape. Multi-omics approaches are further refining our understanding of diabetes-associated AF, facilitating precision medicine and biomarker-guided interventions. This review delineates the molecular nexus linking diabetes and AF, critically appraises emerging rhythm control strategies, and outlines translational avenues poised to advance individualized management in this high-risk population. Full article

The increasing circulation of multi-drug-resistant pathogens, coupled with the sluggish development of new antibiotics, is weakening our capacity to combat human infections, resulting in elevated death tolls. To address this worldwide crisis, antimicrobial peptides (AMPs) are viewed as promising substitutes or adjuvants for combating bacterial infections caused by multidrug-resistant organisms. Here, the antimicrobial activity and structural characterization of a novel 13-amino acid cationic peptide named RKW (RKWILKWLRTWKK-NH2), designed based on known AMPs sequences and the identification of a key tryptophan-rich structural motif, were described. RKW displayed a broad-spectrum and potent antimicrobial and antibiofilm activity against Gram-positive and Gram-negative pathogens, including ESKAPE bacteria and fungi with minimal inhibitory concentrations (MBC) ranging from 5 µM to 20 μM. Structural results by fluorescence and Circular Dichroism (CD) spectroscopy revealed that the peptide was folded into a regular α-helical conformation in a membrane-like environment, remaining stable in a wide range of pH and temperature for at least 48 h of incubation. Furthermore, RKW showed low toxicity in vitro against mammalian fibroblast cells, indicating its potential as a promising candidate for the development of new antimicrobial or antiseptic strategies. Full article

Vibrational analysis of peptides in solution and the theoretical determination of the effects of the microenvironment on infrared and Raman spectra are of key importance in many fields of chemical interest. In this work, we present a computational study combining static quantum mechanical calculations with ab initio molecular dynamics simulations to investigate the vibrational behavior of three peptide models in both the gas phase and in explicit water, under non-periodic boundary conditions. The vibrational spectra of the main amide bands, namely amide I-III and A, were analyzed using a time–frequency approach based on the wavelet transform, which allows the resolution of transient frequency shifts and mode couplings along the trajectories. This combined approach enabled us to perform a time-resolved vibrational analysis revealing how vibrational frequencies, especially of the C=O and N–H stretching modes, evolve over time due to dynamical microsolvation. These fluctuations modulate vibrational couplings and lead to spectral broadening and frequency shifts that correlate with the local structuring of the solvent. In conclusion, our results highlight how the proposed protocol allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, the peptide backbone, and its microenvironment. Full article

Metabolic labeling with deuterated water is used in combination with liquid-chromatography coupled with mass spectrometry to study the turnover rates of individual proteins in vivo. This technique and bioinformatics tools for data analysis quantify the turnover rates of thousands of proteins. Turnover rates change during organismal growth and respond to alterations in the environment and diet. The accurate and statistically significant determination of the turnover rate changes of a protein depend on the variations in the turnover rates of the peptides of the protein. One of the systematic factors contributing to this variability is the dependence of the turnover rates on the number of exchangeable hydrogens of the peptides. This variability (by reducing the statistical power) reduces biological interpretability. Here, we propose a computational approach to eliminate the dependence of the turnover rates on the number of exchangeable hydrogens. This approach enhances the accuracy of turnover rate estimation and may help to support more accurate assessments of biological dynamics and disease mechanisms. Full article

This study explores the identification, characterization, and biological evaluation of angiotensin I-converting enzyme (ACE)-inhibitory peptides derived from enzymatic hydrolysates of crucian carp swim bladders. Following sequential purification by size-exclusion and reversed-phase chromatography, two bioactive peptides—Hyp-Gly-Ala-Arg (Hyp-GAR) and Gly-Ala-Hyp-Gly-Ala-Arg (GA-Hyp-GAR)—were identified using ultra-high-performance liquid chromatography coupled with linear ion trap–Orbitrap tandem mass spectrometry. The synthetic peptides demonstrated potent ACE-inhibitory activity in vitro, with IC₅₀ values of 12.2 μM (Hyp-GAR) and 4.00 μM (GA-Hyp-GAR). Molecular docking and enzyme kinetics confirmed competitive inhibition through key interactions with ACE active site residues and zinc coordination. In vivo antihypertensive activity was evaluated in spontaneously hypertensive rats, revealing that GA-Hyp-GAR significantly reduced systolic blood pressure in a dose-dependent manner. At a dose of 36 mg/kg, GA-Hyp-GAR reduced systolic blood pressure by 60 mmHg—an effect comparable in magnitude and timing to that of captopril. Mechanistically, GA-Hyp-GAR modulated levels of angiotensin II, bradykinin, endothelial nitric oxide synthase, and nitric oxide. A 90-day subchronic oral toxicity study in mice indicated no significant hematological, biochemical, or histopathological alterations, supporting the peptide’s safety profile. These findings suggest that GA-Hyp-GAR is a promising natural ACE inhibitor with potential application in functional foods or as a nutraceutical for hypertension management. Full article

Background/Objectives: Glucagon-like peptide-1 receptor agonists (GLP-1RAs), which were originally developed for managing type 2 diabetes by enhancing insulin secretion and reducing appetite, have emerged as promising candidates in alcohol use disorder (AUD). These medications offer a dual mechanism of action that aligns with the multifaceted nature of addiction by targeting both peripheral metabolic and central reward pathways. This review focused on the current clinical trials and real-world evidence regarding the effects of GLP-1RAs as novel therapeutics for AUD. We also discussed early but encouraging results from clinical trials in AUD, observational and real-world evidence, safety profiles, psychiatric considerations, and future directions leading beyond GLP-1RAs. Methods: A comprehensive English-language literature search was conducted per PRISMA guidelines across PubMed, Medline, Google Scholar, Web of Science, and trial registries. Using targeted keywords, we identified relevant clinical and observational studies on GLP-1RAs for alcohol use disorder, excluding off-topic or non-English works and assessing all studies for eligibility. Results: Out of 1080 records identified, seven studies met the inclusion criteria. The findings from recent clinical trials, large-scale observational studies, and real-world evidence suggest that GLP-1RAs may significantly reduce alcohol consumption, cravings, and alcohol-related hospitalizations. Their central effect on reward processing, coupled with a generally favorable safety profile, supports their potential therapeutic role beyond metabolic disorders. Conclusions: Emerging evidence positions GLP-1RAs as a promising new pharmacologic approach for managing AUD. Ongoing and future research should prioritize larger, longer-duration randomized controlled trials that include diverse populations, with specific attention to treatment motivation, co-occurring psychiatric conditions, and long-term outcomes. Full article

A prime role of biological membranes is to form barriers for material transport into and out of cells. Membranes consist of phospholipids with polar heads, which are presented to the aqueous solutions, and hydrophobic tails that form the membrane core. This construct prevents the permeation of hydrophilic, well-solvated molecules across the lipid hydrophobic barrier. The barrier is not absolute, and several approaches are available for efficient translocation. Channels and pumps enable selective and efficient transport across membranes. Another transport mechanism is passive permeation, in which permeants, without assistance, directly transport across membranes. Passive transport is coupled to transient defects in the membrane structure that make crossing the hydrophobic bilayer easier—for example, displacements of head groups from aqueous solution–membrane interface into the membrane core. The defects, in turn, are rare unless assisted by passively permeating molecules such as cell-penetrating peptides that distort the membrane structure. One possible defect is a phospholipid molecule with a head pointing to the hydrophobic core. This membrane distortion allows head group flipping from one layer to the other. We show computationally, using atomically detailed simulations and the Milestoning theory, that the presence of a cell-penetrating peptide in a membrane greatly increases phospholipid flip-flop rate and hence defect formation and the permeability of membranes. Full article

In recent years, bifunctional ingredients extracted and utilized from waste by-products as raw materials have received significant attention in the food production process. Previous studies have found that bovine livers possess both antioxidant and emulsifying potential; therefore, enhancing these dual properties is a current research focus. In this study, three different types of polyphenols (epigallocatechin gallate [EGCG], gallic acid [GA] and tannin [TA]) provide a reference on how to achieve better complexation of polyphenols with bovine liver hydrolysates (BLHs). Based on the molecular weight results, it was shown that the bovine liver peptides bind to polyphenols to form complexes with higher molecular weights. Furthermore, the binding affinities among the three complexes were as follows: TA > EGCG > GA. The emulsions stabilized by the coupling compounds contained more homogeneous and dense droplets (optical microscopy). Both the antioxidant properties and the emulsifying activity of all complexes were superior to those of bovine liver hydrolysates (BLHs) (p < 0.05), confirming synergistic effects that either flavonoids, phenolic acids or tannins possess with bovine liver hydrolysates. This combination provides an effective strategy for developing novel foods with specific functions. Full article

G-protein-coupled receptors (GPCRs) are a group of various membrane proteins that mediate essential physiological processes by translating extracellular signals into intracellular responses. The β2-Adrenergic Receptor (β2-AR), a key GPCR, plays a critical role in smooth muscle relaxation, bronchodilation, and cardiovascular function, making it an important therapeutic target for diseases such as asthma and hypertension. Diketopiperazines (DPKs), as cyclic peptides, have shown promise as scaffolds for inhibiting protein interactions and modulating receptor activity, offering a potential alternative to traditional small-molecule inhibitors with reduced side effects. In this study, five DPK derivatives were selected from the PubChem database and evaluated for their binding affinity to the 3D structure of β2-AR (PDB ID = 2RH1) through molecular docking studies using AutoDock 4.6 and MGLTools. The binding energy and hydrogen bond formation of each compound were evaluated to determine their interaction efficiency. Among the compounds, tryptophan-proline diketopiperazine (compound 3) exhibited the highest binding affinity with a binding energy of −5.89 kcal/mol. This enhanced interaction is attributed to the aromatic nature of tryptophan, which promotes strong π-π stacking interactions, and the rigidity of proline, which optimally fits within the receptor’s binding pocket. Hydrophobic interactions further stabilized the complex. These findings highlight compound 3 as a promising β2-AR modulator, providing valuable insights for the design of peptide-based inhibitors targeting β2-AR-related pathologies. Full article