Enhanced Delivery of Biomolecules into Caco2 Cells Based on the Cell-Penetrating Ability of Keratin Peptides.

Keratin, as a promising bioresource, possesses significant potential for diverse biological applications due to its favorable biocompatibility, low toxicity, biodegradability, and cell adhesion ability. However, there are few studies on the cell-penetrating ability of keratin peptides (KEPs) for biomolecule delivery. Therefore, this study explored the cell-penetrating ability of KEPs with different molecular weights (Mw) on Caco2 cells using fluorescein-labeled insulin (FITC-INS) as the target intracellular biomolecule. The potential cell-penetrating mechanism was elaborated by combining cellular investigation with the physicochemical characterization of KEPs. The result shows that the KEPs <3 kDa (KEP1) exhibited the highest cell-penetrating ability at 2 mg/mL, allowing efficient delivery of FITC-INS into Caco2 cells without covalent bonding. The cellular uptake mechanism was energy-dependent, mainly involving macropinocytosis. The further fractionation of KEP1 reveals that the most effective components consisted of 8-19 amino acids, including specific hydrophobic peptides (e.g., RVVIEPSPVVV and IIIQPSPVVV), PPII amphipathic peptides (e.g., PPPVVVTFP and FIQPPPVVV), and Cys-rich peptides (e.g., LCAPTPCGPTPL and CLPCRPCGPTPL). Additionally, analysis of the secondary and tertiary structure and amino acid composition illustrated that KEP1 exhibited rich hydrophobic residues and disulfide bonds, which probably contributed to its cell-penetrating ability, as opposed to its small particle size and electrostatic interactions. This study reveals the cell-penetrating ability of KEPs, thus highlighting their potential as biomaterials for noncovalently delivering biomolecules.

PepCA: Unveiling protein-peptide interaction sites with a multi-input neural network model.

The protein-peptide interaction plays a pivotal role in fields such as drug development, yet remains underexplored experimentally and challenging to model computationally. Herein, we introduce PepCA, a sequence-based approach for predicting peptide-binding sites on proteins. A primary obstacle in predicting peptide-protein interactions is the difficulty in acquiring precise protein structures, coupled with the uncertainty of polypeptide configurations. To address this, we first encode protein sequences using the Evolutionary Scale Modeling 2 (ESM-2) pre-trained model to extract latent structural information. Additionally, we have developed a multi-input coattention mechanism to concurrently update the encoding of both peptide and protein residues. PepCA integrates this module within an encoder-decoder structure. This model's high precision in identifying binding sites significantly advances the field of computational biology, offering vital insights for peptide drug development and protein science.

Catalytic mechanism study of ATP-citrate lyase during citryl-CoA synthesis process.

ATP-citrate lyase (ACLY) is a critical metabolic enzyme and promising target for drug development. The structure determinations of ACLY have revealed its homotetramer states with various subunit symmetries, but catalytic mechanism of ACLY tetramer and the importance of subunit symmetry have not been clarified. Here, we constructed the free energy landscape of ACLY tetramer with arbitrary subunit symmetries and investigated energetic and conformational coupling of subunits during citryl-CoA synthesis process. The optimal conformational pathway indicates that ACLY tetramer encounters three critical conformational barriers and undergoes a loss of rigid-D2 symmetry to gain an energetic advantage. Energetic coupling of conformational changes and biochemical reactions suggests that these biological events are not independent but rather coupled with each other, showing a comparable energy barrier to the experimental data for the rate-limiting step. These findings could contribute to further research on catalytic mechanism, functional modulation, and inhibitor design of ACLY.

Triple-layered encapsulation of sensitive biomolecules into poly (ε-caprolactone) nanofibers using AC electrospraying.

The incorporation of sensitive bioactive substances such as proteins or DNA into nanofibers poses a significant problem due to the toxicity of most organic solvents. The main idea of this study is to use alternating current electrospraying to create a suspension consisting of polyvinyl alcohol (PVA) capsules containing a bioactive substance dispersed in a solvent system suitable for a water-insoluble biocompatible polymer. In this suspension consisting of PVA capsules and a chloroform/ethanol mixture, poly (ε-caprolactone) (PCL) was dissolved and spun by needle-free electrospinning. The result is a fibrous PCL structure in which PVA capsules containing the bioactive agent are integrated. The PVA capsules protect the bioactive substance from the organic solvents needed to dissolve the PCL. To verify the efficacy of the capsules' protection against chloroform, the green fluorescent protein was first encapsulated into the nanofibers, followed by horseradish peroxidase. Both molecules were shown to retain their bioactivity within the nanofibers.

Lactylome analysis reveals potential target modified proteins in the retina of form-deprivation myopia.

The biological mechanisms underlying the development of myopia have not yet been completely elucidated. The retina is critical for visual signal processing, which primarily utilizes aerobic glycolysis to produce lactate as a metabolic end product. Lactate facilitates lysine lactylation (Kla), a posttranslational modification essential for transcriptional regulation. This study found increased glycolytic flux and lactate accumulation in the retinas of form-deprived myopic guinea pigs. Subsequently, a comprehensive analysis of Kla levels in retinal proteins revealed that Kla was upregulated at 124 sites in 92 proteins and downregulated at three sites in three proteins. Functional enrichment and protein interaction analyses showed significant enrichment in pathways related to energy metabolism, including glutathione metabolism, glycolysis, and the hypoxia-inducible factor-1 signaling pathway. Parallel-reaction monitoring confirmed data reliability. These findings suggest a connection between myopia and retinal energy metabolism imbalance, providing new insights into the pathogenesis of myopia.

Marine Bioactive Molecules as Inhibitors of the Janus Kinases: A Comparative Molecular Docking and Molecular Dynamics Simulation Approach.

A treasure trove of naturally occurring biomolecules can be obtained from sea living organisms to be used as potential antioxidant and anti-inflammatory agents. These bioactive molecules can target signaling molecules involved in the severity of chronic autoimmune diseases such as rheumatoid arthritis (RA). The intracellular tyrosine kinases family, Janus kinases (JAKs, includes JAK1, JAK2, and JAK3), is implicated in the pathogenesis of RA through regulating several cytokines and inflammatory processes. In the present study, we conducted molecular docking and structural analysis investigations to explore the role of a set of bioactive molecules from marine sources that can be used as JAKs' specific inhibitors. Around 200 antioxidants and anti-inflammatory molecules out of thousands of marine molecules found at the Comprehensive Marine Natural Products Database (CMNPD) website, were used in that analysis. The details of the interacting residues were compared to the recent FDA approved inhibitors tofacitinib and baricitinib for data validation. The shortlisted critical amino acids residues of our pharmacophore-based virtual screening were LYS905, GLU957, LEU959, and ASP1003 at JAK1, GLU930 and LEU932 at JAK2, and GLU905 and CYS909 of JAK3. Interestingly, marine biomolecules such as Sargachromanol G, Isopseudopterosin E, Seco-Pseudopterosin, and CID 10071610 showed specific binding and significantly higher binding energy to JAK1 active/potential sites when being compared with the approved inhibitors. In addition, Zoanthoxanthin and Fuscoside E bind to JAK2's critical residues, GLU930 and LEU932. Moreover, Phorbaketal and Fuscoside E appear to be potential candidates that can inhibit JAK3 activity. These results were validated using molecular dynamics simulation for the docked complexes, JAK1(6sm8)/SG, JAK2 (3jy9)/ZAX, and JAK3 (6pjc)/Fuscoside E, where stable and lower binding energy were found based on analyzing set of parameters, discussed below (videos are attached). A promising role of these marine bioactive molecules can be confirmed in prospective preclinical/clinical investigations using rheumatoid arthritis models.

Functionalized metal-organic frameworks with biomolecules for sensing and detection applications of food contaminants.

The increasing demand for toxin-free food, driven by the rise in fast food consumption and changing dietary habits, necessitates advanced and efficient detection methods to address the potential risks associated with contaminated food. Nanomaterial-based detection methods have shown significant promise, particularly using metal-organic frameworks (MOFs) combined with biomolecules. This review article provides an overview of recent advancements in using functionalized metal-organic frameworks (FMOFs) with biomolecules to detect various food contaminants, including heavy metals, antibiotics, pesticides, bacteria, mycotoxins and other chemical contaminants. We discuss the fundamental principles of detecting food contaminants, evaluate existing analytical techniques, and explore the development of biomacromolecule-functionalized MOF-based sensors encompassing colorimetric, optical, electrochemical, and portable variants. The review also examines sensing mechanisms, uses FMOFs as signal probes and carriers for capture probes, and assesses sensitivity. Additionally, we explore the opportunities and challenges in producing FMOFs with biomacromolecules for food contaminant assessment. Future directions include improving sensor sensitivity and specificity, developing more cost-effective production methods, and integrating these technologies into real-world food safety monitoring systems. This work aims to pave the way for innovative and reliable solutions to ensure the safety of our food supply.

Plectin: Dual Participation in Tumor Progression.

The plectin gene can encode a cytoskeletal linking protein, plectin, known for its interaction with three critical components of the cellular cytoskeleton: intermediate filaments, microtubules, and actin filaments. In recent years, more and more studies have reported that plectin is closely related to tumorigenesis and development, exhibiting both tumor-suppressive and tumor-promoting functions. Here, we first introduce the molecular structure and function of plectin, and then we summarize the current understanding of the crucial role of plectin in cancer progression. Finally, we also discuss the possible reasons for the different roles of plectin expression in various types of cancer and highlight the double-edged sword role of plectin in tumor progression. The review aims to deepen the comprehensive understanding of plectin's role in cancer and further help to develop novel therapeutic strategies and drug targets.

'Exerkines': A Comprehensive Term for the Factors Produced in Response to Exercise.

Regular exercise and physical activity are now considered lifestyle factors with positive effects on human health. Physical activity reduces disease burden, protects against the onset of pathologies, and improves the clinical course of disease. Unlike pharmacological therapies, the effects mediated by exercise are not limited to a specific target organ but act in multiple biological systems simultaneously. Despite the substantial health benefits of physical training, the precise molecular signaling processes that lead to structural and functional tissue adaptation remain largely unknown. Only recently, several bioactive molecules have been discovered that are produced following physical exercise. These molecules are collectively called "exerkines". Exerkines are released from various tissues in response to exercise, and play a crucial role in mediating the beneficial effects of exercise on the body. Major discoveries involving exerkines highlight their diverse functions and health implications, particularly in metabolic regulation, neuroprotection, and muscle adaptation. These molecules, including peptides, nucleic acids, lipids, and microRNAs, act through paracrine, endocrine, and autocrine pathways to exert their effects on various organs and tissues. Exerkines represent a complex network of signaling molecules that mediate the multiple benefits of exercise. Their roles in metabolic regulation, neuroprotection, and muscle adaptation highlight the importance of physical activity in maintaining health and preventing disease.

Alternative Pathways in Astrobiology: Reviewing and Synthesizing Contingency and Non-Biomolecular Origins of Terrestrial and Extraterrestrial Life.

The pursuit of understanding the origins of life (OoL) on and off Earth and the search for extraterrestrial life (ET) are central aspects of astrobiology. Despite the considerable efforts in both areas, more novel and multifaceted approaches are needed to address these profound questions with greater detail and with certainty. The complexity of the chemical milieu within ancient geological environments presents a diverse landscape where biomolecules and non-biomolecules interact. This interaction could lead to life as we know it, dominated by biomolecules, or to alternative forms of life where non-biomolecules could play a pivotal role. Such alternative forms of life could be found beyond Earth, i.e., on exoplanets and the moons of Jupiter and Saturn. Challenging the notion that all life, including ET life, must use the same building blocks as life on Earth, the concept of contingency-when expanded beyond its macroevolution interpretation-suggests that non-biomolecules may have played essential roles at the OoL. Here, we review the possible role of contingency and non-biomolecules at the OoL and synthesize a conceptual model formally linking contingency with non-biomolecular OoL theories. This model emphasizes the significance of considering the role of non-biomolecules both at the OoL on Earth or beyond, as well as their potential as agnostic biosignatures indicative of ET Life.

Reviewing advances in nanophotonic biosensors.

Biosensing, a promising branch of exploiting nanophotonic devices, enables meticulous detection of subwavelength light, which helps to analyze and manipulate light-matter interaction. The improved sensitivity of recent high-quality nanophotonic biosensors has enabled enhanced bioanalytical precision in detection. Considering the potential of nanophotonics in biosensing, this article summarizes recent advances in fabricating nanophotonic and optical biosensors, focusing on their sensing function and capacity. We typically classify these types of biosensors into five categories: phase-driven, resonant dielectric nanostructures, plasmonic nanostructures, surface-enhanced spectroscopies, and evanescent-field, and review the importance of enhancing sensor performance and efficacy by addressing some major concerns in nanophotonic biosensing, such as overcoming the difficulties in controlling biological specimens and lowering their costs for ease of access. We also address the possibility of updating these technologies for immediate implementation and their impact on enhancing safety and health.

Hydrophobic solid lipid-based microparticles for the protection of gastric-sensitive hydrophilic active biomolecules for oral administration in the treatment of EPI.

Exocrine Pancreatic Insufficiency (EPI), induced by conditions such as cystic fibrosis, chronic pancreatitis, and Crohn's disease, is a frequently overlooked and underdiagnosed gastrointestinal disorder. It leads to inadequate intestinal digestion due to insufficient secretion of pancreatic juice, resulting in discomfort, pain, and ultimately severe malnutrition. Despite numerous treatments proving ineffective over the past three decades, a strictly hydrophobic solid lipid formulation, administered orally, is proposed in this study to restore digestive function. This technology relies on the hydrophobic nature of the matrix to physically protect the hydrophilic active principle from the gastric environment while enabling its immediate release in the duodenum by targeting the amphiphilic nature of bile salts. Results demonstrate that this formulation effectively protects an acid-sensitive active ingredient during gastric passage (Simulated Gastric Fluid or SGF), facilitating its rapid release upon entering an artificial duodenal environment (Simulated Intestinal Fluid or SIF). Furthermore, it has been demonstrated that the preservation of a protein-based active ingredient extends beyond its primary protein structure to include its functional aspects, such as enzymatic activity. This drug delivery technology could enable the protection of hydrophilic active biomolecules, such as pancreatin, which are sensitive to gastric acidity, while promoting their immediate release upon contact with bile salts in the proximal duodenum, with the ultimate goal of correcting the digestive defect induced by EPI.

Signal amplification in molecular sensing by imprinted polymers.

In the field of sensing, the development of sensors with high sensitivity, accuracy, selectivity, sustainability, simplicity, and low cost remains a key focus. Over the past decades, optical and electrochemical sensors based on molecular imprinting techniques have garnered significant attention due to the above advantages. Molecular imprinting technology utilizes molecularly imprinted polymers (MIPs) to mimic the specific recognition capabilities of enzymes or antibodies for target molecules. Recently, MIP-based sensors rooting in signal amplification techniques have been employed to enhance molecular detection level and the quantitative ability for environmental pollutants, biomolecules, therapeutic compounds, bacteria, and viruses. The signal amplification techniques involved in MIP-based sensors mainly cover nucleic acid chain amplification, enzyme-catalyzed cascade, introduction of high-performance nanomaterials, and rapid chemical reactions. The amplified analytical signals are centered around electrochemical, fluorescence, colorimetric, and surface-enhanced Raman techniques, which can effectively realize the determination of some low-abundance targets in biological samples. This review highlights the recent advancements of electrochemical/optical sensors based on molecular imprinting integrated with various signal amplification strategies and their dedication to the study of trace biomolecules. Finally, future research directions on developing multidimensional output signals of MIP-based sensors and introducing multiple signal amplification strategies are proposed.

Computational Methodologies in Synthesis, Preparation and Application of Antimicrobial Polymers, Biomolecules, and Nanocomposites.

The design and optimization of antimicrobial materials (polymers, biomolecules, or nanocomposites) can be significantly advanced by computational methodologies like molecular dynamics (MD), which provide insights into the interactions and stability of the antimicrobial agents within the polymer matrix, and machine learning (ML) or design of experiment (DOE), which predicts and optimizes antimicrobial efficacy and material properties. These innovations not only enhance the efficiency of developing antimicrobial polymers but also enable the creation of materials with tailored properties to meet specific application needs, ensuring safety and longevity in their usage. Therefore, this paper will present the computational methodologies employed in the synthesis and application of antimicrobial polymers, biomolecules, and nanocomposites. By leveraging advanced computational techniques such as MD, ML, or DOE, significant advancements in the design and optimization of antimicrobial materials are achieved. A comprehensive review on recent progress, together with highlights of the most relevant methodologies' contributions to state-of-the-art materials science will be discussed, as well as future directions in the field will be foreseen. Finally, future possibilities and opportunities will be derived from the current state-of-the-art methodologies, providing perspectives on the potential evolution of polymer science and engineering of novel materials.

Selective and Comparative Study of B/nZVCu-Fe and B/nZVCu-Zn Nanoparticles as Fluorescent Probe for Dopamine in Presence of its Interference Molecules.

This work focuses on the synthesis of Bentonite supported nano zero valent bimetallic nanoparticles (B/nZVCu-M NPs) to be utilized for fast and highly sensitive, reversible, fluorescent determination of dopamine (DA) in the presence of dopamine, other biomolecules and ions. The X-ray Photoelectron Spectroscopy(XPS), Powder X-Ray Diffraction(PXRD) and Scanning Electron Microscopy(SEM) revealed the formation of nanoparticles with size ranging from 15 to 20 nm. The composition was revealed by Fourier Transform Infrared(FTIR) Spectoscopy and Energy Dispersive X-Ray (EDX) Analysis. The Limits of Detection(LOD) were noted to be 5.57nM and 6.07nM. The binding of DA is noted to be reversible with respect to EDTA2-. Furthermore, the developed sensor exhibited good repeatability, satisfactory long-term stability, and was successfully used for the selective detection of dopamine sample with desired recoveries or reversibilities. The main aim of our work is to selectively detect dopamine in presence of its major interferents and biomolecules that are normally present/ co-exist with dopamine in biological systems.

Dynamic Monitoring of Time-Dependent Evolution of Biomolecules Using Quantum Dots-Based Biosensors Assemblies.

The dynamic monitoring of biomolecules that are part of cell membranes generally constitutes a challenge. Electrochemiluminescence (ECL) biosensor assemblies provide clear advantages concerning microscopic imaging. Therefore, this paper proposes and analyzes a quantum dots-based biosensor assembly. Thus, particular attention is granted to biomolecules that are part of cell membranes. Additionally, this paper describes and analyzes a quantum dots-based biosensor assembly, which is used to implement a fully functional color ECL visualization system that allows for cellular and biomolecular structures to be accurately visualized. The related nano-emitter allows the implementation of real-time bioimaging scenarios. Consequently, the proposed approach is thoroughly evaluated relative to the time-dependent evolution of biomolecules. It has been demonstrated that traditionally problematic structures, like the biomolecules that are part of cell membranes, can be studied and monitored relative to their time-dependent dynamic evolution using the proposed solution. The reported research process has been conducted in the realm of cooperation with a specialized biomedical engineering company, and the described results are expected to substantially support a better understanding of the biomolecules' time-dependent dynamic evolution.

Tea-derived exosome-like nanoparticles prevent irritable bowel syndrome induced by water avoidance stress in rat model.

BACKGROUND AND AIM: Exosome-like nanoparticles (ELNs) have emerged as crucial mediators of intercellular communication, evaluated as potential bioactive nutraceutical biomolecules. We hypothesized that oral ELNs have some therapeutic effect on irritable bowel syndrome (IBS). METHODS: In our study, ELNs from tea (Camellia sinensis) leaves were extracted by differential centrifugation. We investigated the role of ELNs by assessing visceral hypersensitivity, body weight, bowel habits, tight junctions, and corticotropin-releasing hormone (CRH) in rats subjected to water avoidance stress (WAS) to mimic IBS with and without ELNs (1 mg/kg per day) for 10 days. RESULTS: The average diameter of ELNs from LCC, FD and MZ tea tree were 165 ± 107, 168 ± 94, and 168 ± 108 nm, the concentration of ELNs were 1.2 × 1013, 1 × 1013, and 1.5 × 1013 particles/mL, respectively. ELNs can be taken up by intestinal epithelial cells. In WAS rats, ELNs significantly restored weight, recovered tight junctions, decreased CRH, and CRH receptor 1 expression levels and inhibited abdominal hypersensitivity in comparison to positive control. CONCLUSIONS: Oral tea-derived ELN improves symptoms of IBS by potentially modulating the CRH pathway.

Detection strategies of infectious diseases via peptide-based electrochemical biosensors.

Infectious diseases have threatened human life for as long as humankind has existed. One of the most crucial aspects of fighting against these infections is diagnosis to prevent disease spread. However, traditional diagnostic methods prove insufficient and time-consuming in the face of a pandemic. Therefore, studies focusing on detecting viruses causing these diseases have increased, with a particular emphasis on developing rapid, accurate, specific, user-friendly, and portable electrochemical biosensor systems. Peptides are used integral components in biosensor fabrication for several reasons, including various and adaptable synthesis protocols, long-term stability, and specificity. Here, we discuss peptide-based electrochemical biosensor systems that have been developed over the last decade for the detection of infectious diseases. In contrast to other reports on peptide-based biosensors, we have emphasized the following points i) the synthesis methods of peptides for biosensor applications, ii) biosensor fabrication approaches of peptide-based electrochemical biosensor systems, iii) the comparison of electrochemical biosensors with other peptide-based biosensor systems and the advantages and limitations of electrochemical biosensors, iv) the pros and cons of peptides compared to other biorecognition molecules in the detection of infectious diseases, v) different perspectives for future studies with the shortcomings of the systems developed in the past decade.

Anticancer efficacy of magnetite nanoparticles synthesized using aqueous extract of brown seaweed Rosenvingea intricata, South Andaman, India.

Cancer is a global issue and hence various efforts are being made. Iron oxide is considered a significant biochemical agent in the biomedical arena for cancer treatment. Marine macroalgae-mediated iron oxides especially, magnetite (Fe3O4) nanoparticles (NPs) are a prospective alternative to diagnose and treat cancer owing to their fluorescent and magnetic properties. We intend to appraise the usability of the aqueous extract of Rosenvingea intricata (R. intricata) in Fe3O4 NPs synthesis and to study their cytotoxic effects against human hepatocarcinoma (Hep3B) and pancreatic (PANC1) cancer cells. In the present study, R. intricata were collected from the coastal region of South Andaman, India. Aqueous extracts of R. intricata were utilized to synthesize Fe3O4 NPs via the co-precipitation method. Phycosynthesized Fe3O4 NPs exhibited wide peak at 400-600 nm from ultraviolet-visible diffused reflectance spectroscopic analysis which validated the formation of NPs. Band edge emission peak at 660 nm in fluorescent spectra confirmed the quantum confinement in Fe3O4 NPs. Fourier transform infrared spectroscopy confirmed the role of R. intricata as a capping and reducing agent with functional groups such as O-H, C-H, C=O, N=O, C=C, C-O, C-N, and C-S arising from amino acids, polysaccharides, aliphatic hydrocarbons, esters, amides, lignins, alkanes, aliphatic amines, and sulfates. Physicochemical properties such as crystallite size (14.36 nm), hydrodynamic size (84.6 nm), irregular morphology, elemental composition, particle size (125 nm), crystallinity, and saturation magnetization (0.90007 emu/g) were obtained from x-ray diffractometer, dynamic light scattering, scanning electron microscopy, energy dispersive x-ray spectrometer, high-resolution transmission electron microscopy, selected area electron diffraction and vibrating sample magnetometer techniques, respectively. The cell viability showed dose-dependent cytotoxic effects and enhanced the apoptosis against Hep3B and PANC1 cancer cells. R. intricata extract capped Fe3O4 NPs could be the most appropriate and effective nanomaterial for cancer treatment and management.