Identification of RNA­dependent liquid­liquid phase separation proteins using an artificial intelligence strategy.

RNA-dependent liquid-liquid phase separation (LLPS) proteins play critical roles in cellular processes such as stress granule formation, DNA repair, RNA metabolism, germ cell development, and protein translation regulation. The abnormal behavior of these proteins is associated with various diseases, particularly neurodegenerative disorders like amyotrophic lateral sclerosis and frontotemporal dementia, making their identification crucial. However, conventional biochemistry-based methods for identifying these proteins are time-consuming and costly. Addressing this challenge, our study developed a robust computational model for their identification. We constructed a comprehensive dataset containing 137 RNA-dependent and 606 non-RNA-dependent LLPS protein sequences, which were then encoded using amino acid composition, composition of K-spaced amino acid pairs, Geary autocorrelation, and conjoined triad methods. Through a combination of correlation analysis, mutual information scoring, and incremental feature selection, we identified an optimal feature subset. This subset was used to train a random forest model, which achieved an accuracy of 90% when tested against an independent dataset. This study demonstrates the potential of computational methods as efficient alternatives for the identification of RNA-dependent LLPS proteins. To enhance the accessibility of the model, a user-centric web server has been established and can be accessed via the link: http://rpp.lin-group.cn.

Alleviation potential of green-synthesized selenium nanoparticles for cadmium stress in Solanum lycopersicum L: modulation of secondary metabolites and physiochemical attributes.

KEY MESSAGE: Selenium nanoparticles reduce cadmium absorption in tomato roots, mitigating heavy metal effects. SeNPs can efficiently help to enhance growth, yield, and biomolecule markers in cadmium-stressed tomato plants. In the present study, the effects of selenium nanoparticles (SeNPs) were investigated on the tomato plants grown in cadmium-contaminated soil. Nanoparticles were synthesized using water extract of Nigella sativa and were characterized for their size and shape. Two application methods (foliar spray and soil drench) with nanoparticle concentrations of 0, 100, and 300 mg/L were used to observe their effects on cadmium-stressed plants. Growth, yield, biochemical, and stress parameters were studied. Results showed that SeNPs positively affected plant growth, mitigating the negative effects of cadmium stress. Shoot length (SL), root length (RL), number of branches (NB), number of leaves per plant (NL), and leaf area (LA) were significantly reduced by cadmium stress but enhanced by 45, 51, 506, 208, and 82%, respectively, by soil drench treatment of SeNPs. Similarly, SeNPs increased the fruit yield (> 100%) and fruit weight (> 100%), and decreased the days to fruit initiation in tomato plants. Pigments were also positively affected by the SeNPs, particularly in foliar treatment. Lycopene content was also enhanced by the addition of NPs (75%). Furthermore, the addition of SeNPs improved the ascorbic acid, protein, phenolic, flavonoid, and proline contents of the tomato plants under cadmium stress, whereas stress enzymes also showed enhanced activities under cadmium stress. It is concluded from the present study that the addition of selenium nanoparticles enhanced the growth and yield of Cd-stressed plants by reducing the absorption of cadmium and increasing the stress management of plants.

Synthesis and in Silico Docking Studies of Ethyl 2-(2-Arylidene-1-alkylhydrazinyl)thiazole-4-carboxylates as Antiglycating Agents.

Ethyl 2-(2-arylidene-1-alkylhydrazinyl)thiazole-4-carboxylates (1a-k) were synthesized by alkylation on HN- of ethyl 2-(2-arylidenehydrazinyl)thiazole-4-carboxylates. The proposed structures (1a-k) are corroborated by spectro-analytical techniques like UV, FT-IR, 1 H-, 13 C-NMR and HR-MS. All synthesized compounds were screened for their antiglycation and antioxidant assays. The in vitro antiglycation results revealed promising activity of compounds 1a, 1b, 1d, 1e, 1f, 1g, 1j and 1k with IC50 values 0.0004±1.097-17.22±0.538 µM when compared to standard, aminoguanidine (IC50 =25.50±0.337 µM). Among all tested compounds 1j and 1k are the best antiglycating agents with IC50 values 1.848±0.646 and 0.0004±1.097 µM, respectively. The in-silico studies also agree with these results where binding energy for 1j and 1k was found to be -9.25 and -8.42 kcal/mol with calculated dissociation constants of 0.16 and 0.67 µM, respectively. The antiglycation results demonstrate the application of these compounds in reducing diabetic complications.

Subtractive proteomics-based vaccine targets annotation and reverse vaccinology approaches to identify multiepitope vaccine against Plesiomonas shigelloides.

Plesiomonas shigelloides, an aquatic bacterium belonging to the Enterobacteriaceae family, is a frequent cause of gastroenteritis with diarrhea and gastrointestinal severe disease. Despite decades of research, discovering a licensed and globally accessible vaccine is still years away. Developing a putative vaccine that can combat the Plesiomonas shigelloides infection by boosting population immunity against P. shigelloides is direly needed. In the framework of the current study, the entire proteome of P. shigelloides was explored using subtractive genomics integrated with the immunoinformatics approach for designing an effective vaccine construct against P. shigelloides. The overall stability of the vaccine construct was evaluated using molecular docking, which demonstrated that MEV showed higher binding affinities with toll-like receptors (TLR4: 51.5 ± 10.3, TLR2: 60.5 ± 9.2) and MHC receptors(MHCI: 79.7 ± 11.2 kcal/mol, MHCII: 70.4 ± 23.7). Further, the therapeutic efficacy of the vaccine construct for generating an efficient immune response was evaluated by computational immunological simulation. Finally, computer-based cloning and improvement in codon composition without altering amino acid sequence led to the development of a proposed vaccine. In a nutshell, the findings of this study add to the existing knowledge about the pathogenesis of this infection. The schemed MEV can be a possible prophylactic agent for individuals infected with P. shigelloides. Nevertheless, further authentication is required to guarantee its safeness and immunogenic potential.

Silybum marianum: An Overview of its Phytochemistry and Pharmacological Activities with Emphasis on Potential Anticancer Properties.

Silybum marianum (SM) belongs to the family Asteraceae, which holds therapeutic significance in medicinal chemistry. Phytochemistry analysis revealed an abundance of active constituents, particularly silymarin, composed of polyphenols and flavonolignans. Silymarin is majorly found in leaves, seeds, and fruits and is comprised of seven flavonolignans. Silymarin derivatives, specifically silybin, were reported for their medicinal properties. This review summarizes the studies conducted to evaluate SM's pharmacological properties and proposed mechanisms. SM exhibited anticancer properties due to being capable of modifying the induction of apoptosis, inhibiting the STAT3 pathway, decreasing the transcription of various growth factors, impeding the growth of 4T1 cells and inducing cell cycle arrest in various types of cancers, i.e., skin cancer, liver cancer, breast cancer, ovarian cancer etc. Silymarin and its derivatives protect the liver and ameliorate various immune-mediated and autoimmune hepatic diseases. Moreover, antimicrobial, antidiabetic, cardioprotective, nephroprotective, and neuroprotective activities were also reported. Based on testified in vitro and in vivo studies, SM can serve as an alternative to cure various pathological ailments.

Novel Coumarin Derivatives as Potential Urease Inhibitors for Kidney Stone Prevention and Antiulcer Therapy: From Synthesis to In Vivo Evaluation.

The presence of ammonium ions in urine, along with basic pH in the presence of urease-producing bacteria, promotes the production of struvite stones. This causes renal malfunction, which is manifested by symptoms such as fever, nausea, vomiting, and blood in the urine. The involvement of urease in stone formation makes it a good target for finding urease enzyme inhibitors, which have the potential to be developed as lead drugs against kidney stones in the future. The documented ethnopharmacology of coumarin 2-one against bacterial, fungal and viral strains encouraged us to synthesize new derivatives of coumarins by reacting aromatic aldehydes with 4-aminocoumarin. The synthesized compounds (2a to 11a) were evaluated for their antimicrobial, in vitro, and in silico properties against the urease enzyme. The study also covers in vivo determination of the synthesized compounds with respect to different types of induced ulcers. The molecular docking study along with extended MD simulations (100 ns each) and MMPBSA study confirmed the potential inhibitory candidates as evident from computed ∆Gbind (3a = -11.62 and 5a = -12.08 Kcal/mol) against the urease enzyme. The in silico analyses were augmented by an enzymatic assay, which revealed that compounds 3a and 5a had strong inhibitory action, with IC50 of 0.412 µM (64.0% inhibition) and 0.322 µM (77.7% inhibition), respectively, compared to standard (Thiourea) with 82% inhibition at 0.14 µM. Moreover, the most active compound, 5a, was further tested in vivo for antiulcer activity by different types of induced ulcers, including pyloric ligation-, ethanol-, aspirin-, and histamine-induced ulcers. Compound 5a effectively reduced gastric acidity, lipid peroxidation, and ulceration in a rat model while also inhibiting gastric ATPase activity, which makes it a promising candidate for ulcer treatment. As a result of the current research, 3a and 5a may be used as new molecules for developing potent urease inhibitors. Additionally, the compound 3a showed antibacterial activity against Staphylococcus aureus and Salmonella typhimurium, with zones of inhibition of 41 ± 0.9 mm and 35 ± 0.9 mm, respectively. Compound 7a showed antibacterial activity against Staphylococcus aureus and Salmonella typhimurium, with zones of inhibition of 30 ± 0.8 mm and 42 ± 0.8 mm, respectively. These results prove that the synthesized compounds also possess good antibacterial potential against Gram-positive and Gram-negative bacterial strains.

Preparation and investigation of a novel combination of Solanum nigrum-loaded, arabinoxylan-cross-linked ß-cyclodextrin nanosponges for the treatment of cancer: in vitro, in vivo, and in silico evaluation.

Introduction: Cancer contributes to a high mortality rate worldwide spanning its diversity from genetics to resistant therapeutic response. To date emerging strategies to combat and manage cancer are particularly focused on the development of targeted therapies as conventional treatments account for the destruction of normal cells as well. In this regard, medicinal plant-based therapies are quite promising in imposing minimal side effects; however, limitations like poor bioavailability and stability of bioactive phytochemicals are associated with them. In parallel, nanotechnology provides nominal solution to deliver particular therapeutic agent without compromising its stability. Methods: In this study, Solanum nigrum, an effective medicinal plant, loaded arabinoxylan cross-linked ß-cyclodextrin nanosponges (SN-AXCDNS) were designed to evaluate antitumor activity against breast cancer. Therefore, SN-AXCDNS were prepared by using cross-linker melt method and characterized by physicochemical and pharmacological parameters. Results: Hydrodynamic size, zeta potential and entrapment efficiency (EE%) were estimated as 226 ± 4 nm, -29.15 ± 5.71 mV and 93%, respectively. Surface morphology of nanocomposites showed spherical, smooth, and porous form. Antitumor pharmacological characterization showed that SN loaded nanosponge demonstrated higher cytotoxicity (22.67 ± 6.11 µg/mL), by inducing DNA damage as compared to void SN extract. Flow cytometry analysis reported that encapsulated extract promoted cell cycle arrest at sub-G1 (9.51%). Moreover, in vivo analysis demonstrates the reduction in tumor weight and 85% survival chances in nanosponge treated mice featuring its effectiveness. In addition, in silico analysis revealed that ß-cyclodextrin potentially inhibits MELK in breast cancer cell lines (B.E = -10.1 Kcal/mol). Conclusion: Therefore, findings of current study elucidated the therapeutic potential of ß-cyclodextrin based nanosponges to be an alternative approach regarding the delivery and solubilization of antitumor drugs.

Fabrication of Highly Robust and Conductive Ion Gels Based on the Combined Strategies of Double-Network, Composite, and High-Functionality Cross-Linkers.

A robust hybrid ion gel is fabricated utilizing the combined strategies of double-network (DN), composite, and high-functionality cross-linkers. The charged poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) constructs the DN skeleton, with graphene oxide (GO) and N,N'-methylenebisacrylamide (MBA) being the cross-linkers for the first and second networks, respectively. The ionic liquid, either 1-ethyl-3-methylimidazolium dicyanamide ([EMIm][DCA]) or 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4]), is locked in the network to offer the high conductivity. Compared to the DN PAMPS ion gel without nanoparticles and the hybrid DN ion gel with unconnected silica nanoparticles, the present ion gel exhibits a significantly higher tensile strength (3.2 ± 0.1 MPa) and an excellent compressive strength (26 ± 1 MPa). The [EMIm][DCA] ion gel has a high conductivity close to that of its neat ionic liquids. The conductivity of the gel is sensitive to deformation and temperature, which leads to potential applications in sensing body movements, pulse, and temperature change.

Reduced Graphene Oxide/Alumina, A Good Accelerant for Cellulose-Based Artificial Nacre with Excellent Mechanical, Barrier, and Conductive Properties.

In this article, a simple strategy was employed to fabricate bioinspired hybrid composite with carboxymethyl cellulose (CMC), graphene oxide, and reduced graphene oxide/alumina (rGO/Al) by a facile solution casting method. The tensile strength and toughness of rGO/Al-CMC-GO can reach 586.6 ± 12 MPa, 12.1 ± 0.44 MJm-3, respectively, due to the interface strengthening of alumina, which is 1.43 and 12 times higher than steel and about 4.3 and 6.7 times that of nature nacre. The artificial nacre hybrid composite is conductive due to the introduction of rGO/Al on the surface. Interestingly this structure can also be coated on the surface of cotton thread to give the thread good mechanical performance and conductivity. Additionally, the artificial nacre has better fire shielding and gas barrier properties. The oxygen permeability (OP) for 1% rGO/Al-CMC decreased from 0.0265 to 0.003 mLµm m-2 day-1 kpa-1, the water vapor permeability (WVP) decreased from 0.363 to 0.205 gmmm-2 day-1 kpa-1 when the concentration increased from 1% rGO/Al to 6% rGO/Al. It is believed this work provided a simple and feasible strategy to fabricate ultrastrong and ultratough graphene-based artificial nacre multifunctional materials.

Bio-Based Artificial Nacre with Excellent Mechanical and Barrier Properties Realized by a Facile In Situ Reduction and Cross-Linking Reaction.

Demands for high strength integrated materials have substantially increased across various kinds of industries. Inspired by the relationship of excellent integration of mechanical properties and hierarchical nano/microscale structure of the natural nacre, a simple and facile method to fabricate high strength integrated artificial nacre based on sodium carboxymethylcellulose (CMC) and borate cross-linked graphene oxide (GO) sheets has been developed. The tensile strength and toughness of cellulose-based hybrid material reached 480.5 ± 13.1 MPa and 11.8 ± 0.4 MJm-3 by a facile in situ reduction and cross-linking reaction between CMC and GO (0.7%), which are 3.55 and 6.55 times that of natural nacre. This hybrid film exhibits better thermal stability and flame retardancy. More interestingly, the hybrid material showed good water stability compared to that in the original water-soluble CMC. This type of hybrid has great potential applications in aerospace, artificial muscle, and tissue engineering.

Preparation and characterization of bio-based hybrid film containing chitosan and silver nanowires.

A bio-based hybrid film containing chitosan (CS) and silver nanowires (AgNWs) has been prepared by a simple casting technique. X-ray diffraction (XRD), Fourier infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and UV-visible spectroscopy were employed to characterize the structure of bio-based film. The bio-based hybrid film showed unique performance compared with bare chitosan film. The incorporated nano-silver could improve the strength properly. The results revealed that AgNWs in CS film, improved its tensile strength more than 62% and Young modulus 55% compared with pure chitosan film. On the other hand tensile strength was increased 36.7% with AgNPs. Importantly, the film also exhibited conductivity and antibacterial properties, which may expand its future application.