Molecular docking and molecular dynamics simulation analyses of urea with ammoniated and ammoxidized lignin

Towards new bioactive fluorine-containing 1,3,4-oxadiazole-amide derivatives: synthesis, antibacterial activity, molecular docking and molecular dynamics simulation study

Through the approach of molecular hybridization, this study rationally designed and synthesized new trifluoromethyl-1,3,4-oxadiazole amide derivatives, denoted as 1a-1n. The findings reveal that these novel molecules exhibit potent inhibitory effects against various bacterial strains. Thereinto, compounds 1c, 1d, 1i, 1j and 1n, demonstrate relatively superior antimicrobial performance against B. cereus FM314, with a minimum inhibitory concentration (MIC) of 0.03907 μg/mL. Molecular docking analysis suggests the potential importance of the Ser57 and Thr125 amino acid residues (PDB ID: 4EI9) in contributing to the inhibitory activity against B. cereus. The consistency of these results was further corroborated through subsequent molecular dynamics simulations and MMPBSA validations. The insights gained from this study serve to facilitate the rational design and efficient development of novel eco-friendly antimicrobial inhibitors based on the trifluoromethyl-1,3,4-oxadiazole amide scaffold.

Water-compatible cross-linked pyrrolidone acrylate pressure-sensitive adhesives with persistent adhesion for transdermal delivery: Synergistic effect of hydrogen bonding and electrostatic force

Poor skin adhesion and mechanical properties are common problems of pressure-sensitive adhesive (PSA) in transdermal drug delivery system (TDDS). Its poor water compatibility also causes the patch to fall off after sweating or soaking in the application site. To solve this problem, poly (2-Ethylhexyl acrylate-co-N-Vinyl-2-pyrrolidone-co-N-(2-Hydroxyethyl)acrylamide) (PENH), a cross-linked pyrrolidone polyacrylate PSA, was designed to improve the adhesion and water resistance of PSA through electrostatic force and hydrogen bonding system. The structure of PENH was characterized by 1H NMR, FTIR, DSC, and other methods. The mechanism was studied by FTIR, rheological test, and molecular simulation. The results showed that the PENH patch could adhere to human skin for more than 10 days without cold flow, and it could still adhere after sweating or water contact. In contrast, the commercial PSA Duro-Tak® 87-4098 and Duro-Tak® 87-2852 fell off completely on the 3rd and 6th day, respectively, and Duro-Tak® 87-2510 showed a significant dark ring on the second day. Mechanism studies have shown that the hydrogen bond formed by 2-ethylhexyl acrylate (2-EHA), N-vinyl-2-pyrrolidinone (NVP), and N-(2-Hydroxyethyl)acrylamide (HEAA) enhances cohesion, the interaction with skin improves skin adhesion, and the electrostatic interaction with water or drug molecules enhances the ability of water absorption and drug loading. Due to the synergistic effect of hydrogen bonds and electrostatic force, PENH can maintain high cohesion after drug loading or water absorption. PENH provides a choice for the development of water-compatible patches with long-lasting adhesion. STATEMENT OF SIGNIFICANCE: Based on the synergistic effect of hydrogen bonding and electrostatic force, a hydrogen-bonded, cross-linked pyrrolidone acrylate pressure-sensitive adhesive for transdermal drug delivery was designed and synthesized, which has high adhesion and cohesive strength and is non-irritating to the skin. The patch can be applied on the skin surface continuously for more than 10 days without the phenomenon of "dark ring", and the patch can remain adherent after the patient sweats or bathes. This provides a good strategy for choosing a matrix for patches that require prolonged administration.

Understanding Lignin Dissolution with Urea and the Formation of a Lignin Nano-Aggregate: A Multiscale Approach

This study employs a combined computational and experimental approach to elucidate the mechanisms governing the interaction between lignin and urea, impacting lignin dissolution and subsequent aggregation behavior. Molecular dynamics (MD) simulations reveal how the urea concentration and temperature influence lignin conformation and interactions. Higher urea concentrations and temperatures promote lignin dispersion by disrupting intramolecular interactions and enhancing solvation. Density functional theory (DFT) calculations quantitatively assess the interaction energy between lignin and urea, supporting the findings from MD simulations. Anti-solvent precipitation demonstrates that increasing the urea concentration hinders the self-assembly of lignin nanoclusters. The findings provide valuable insights for optimizing lignin biorefinery processes by tailoring the urea concentration and temperature for efficient extraction and dispersion. Understanding the influence of urea on lignin behavior opens up avenues for designing novel lignin-based materials with tailored properties. This study highlights the potential for the synergetic application of MD simulations and DFT calculations to unravel complex material interactions at the atomic level.

Self-Adhesive and Conductive Dual-Network Polyacrylamide Hydrogels Reinforced by Aminated Lignin, Dopamine, and Biomass Carbon Aerogel for Ultrasensitive Pressure Sensor

Conductive hydrogels have attracted extensive interest owing to its potential in soft robotics, electronic skin, and human monitoring. However, insufficient mechanical properties, lower adhesivity, and unsatisfactory conductivity seriously hinder potential applications in this emerging field. Herein, a highly elastic conductive hydrogel with a combination of favorable mechanical properties, self-adhesiveness, and excellent electrical performance was achieved by the synergistic effect of aminated lignin (AL), polydopamine (PDA), polyacrylamide (PAM) chains, and biomass carbon aerogel (C-SPF). In detail, AL was applied to induce slow oxidative polymerization of DA for preparing the sticky hydrogel containing PDA. Then, C-SPF carbon aerogel was used as a matrix to construct a dual-network structured composite hydrogel by combining with the hydrogels derived from PDA, AL, and PAM. The as-prepared conductive hydrogel displayed excellent mechanical performance, strong adhesive strength, and repeatable adhesivity. The prepared hydrogel-based pressure sensor possessed fast response (0.6 s loading and 0.8 s unloading stress time), high response (maximum RCR = 1.8 × 10⁴), wide working pressure range (from 0 to 240.0 kPa), and excellent durability (stable 500 compression cycles with 30% deformation). In addition, the prepared sensor also displayed ultrahigh sensitivity (170 kPa^-1), which was near 4 orders of magnitude higher than the conventional lignin-modified PAM hydrogels. The multiple interactions between hydrogel components and the mechanical properties of hydrogel were also verified by molecular dynamics investigation. Moreover, the excellent cytocompatibility and antibacterial activity of this composite hydrogel ensured high potential in various applications such as human/machine interaction, artificial intelligence, personal healthcare, and wearable devices.

Cancer metabolism control by natural products: Pyruvate kinase M2 targeting therapeutics

Glycolysis is the primary source of energy for cancer growth and metastasis. The shift in metabolism from mitochondrial oxidative phosphorylation to aerobic glycolysis is called the Warburg effect. Cancer progression due to aerobic glycolysis is often associated with the activation of oncogenes or the loss of tumor suppressors. Therefore, inhibition of glycolysis is one of the effective strategies in cancer control. Pyruvate kinase M2 (PKM2) is a key glycolytic enzyme overexpressed in breast, prostate, lung, colorectal, and liver cancers. Here, we discuss published studies regarding PKM2 inhibitors from natural products that are promising drug candidates for cancer therapy. We have highlighted the potential of natural PKM2 inhibitors for various cancer types. Moreover, we encourage researchers to evaluate the combinational effects between natural and synthetic PKM2 inhibitors. Also, further high-quality studies are needed to firmly establish the clinical efficacy of natural products.

Mechanism insight on drug skin delivery from polyurethane hydrogels: Roles of molecular mobility and intermolecular interaction

Though polyurethane (PU) hydrogel had great potential in topical drug delivery system, drug skin delivery behavior from hydrogel and the underlying molecular mechanism were still unclear. In this study, PU and Carbomer (CP as control) hydrogels were prepared with lidocaine (LID) and ofloxacin (OFX) as model drugs. In vitro skin permeation and tissue distribution study were conducted to evaluate the drug delivery behaviors. The underlying molecular mechanisms were characterized by drug release with octanol as release medium, rheological study, ATR-FTIR, NMR, and molecular simulation. The results showed that the skin permeation amount of LID-PU (45.50 ± 7.12 μg) was lower than LID-CP (45.50 ± 7.12 μg). And the LID diffusion coefficient of PU (26.21 μg/h^0.5) was also lower than CP (31.30 μg/h^0.5), which attributed to H-bonding between LID (-CONH) and PU (-NHCOO). However, the OFX-PU showed a higher skin permeation amount (10.06 ± 1.29 μg) than OFX-CP (5.28 ± 1.39 μg). And the OFX-PU also showed a higher diffusion coefficient (30.0 μg/h^0.5) than OFX-CP (21.37 μg/h^0.5), which was caused by increased mobility of hydrogel when interaction action site was C-O-C in PU. In conclusion, drug skin delivery behavior from PU hydrogel was controlled by molecular mobility and intermolecular interaction, which clarified the influence of the functional group of PU hydrogel on drug skin delivery behavior and broadened our understanding of PU hydrogel application in topical drug delivery system.

Discovery of novel SecA inhibitors against "Candidatus Liberibacter asiaticus" through virtual screening and biological evaluation

"Candidatus Liberibacter asiaticus" (Ca. L. asiaticus) is the causal agent of Huanglongbing disease of citrus and current study focuses on the discovery of novel small-molecule inhibitors against SecA protein of Ca. L. asiaticus. In this study, homologous modeling was used to construct the three-dimensional structure of SecA. Then, molecular docking-based virtual screening and two rounds of in vitro bacteriostatic experiments were utilized to identify novel small-molecule inhibitors of SecA. Encouragingly, 93 compounds were obtained and two of them (P684-2850, P684-3808) showed strong antimicrobial activities against Liberibacter crescens BT-1 in bacteriostatic experiments. Finally, molecular dynamics simulations were employed to explore the binding modes of the receptor-ligand complexes. Results in MD simulations showed that compound P684-3808 was relatively stable during simulation, while compound P684-2850 left the binding pocket. Compound P684-3808 might be suitable as a lead compound for further development of antimicrobial compounds against SecA of Ca. L. asiaticus.

Mechanisms of Metabolic Reprogramming in Cancer Cells Supporting Enhanced Growth and Proliferation

Cancer cells alter metabolic processes to sustain their characteristic uncontrolled growth and proliferation. These metabolic alterations include (1) a shift from oxidative phosphorylation to aerobic glycolysis to support the increased need for ATP, (2) increased glutaminolysis for NADPH regeneration, (3) altered flux through the pentose phosphate pathway and the tricarboxylic acid cycle for macromolecule generation, (4) increased lipid uptake, lipogenesis, and cholesterol synthesis, (5) upregulation of one-carbon metabolism for the production of ATP, NADH/NADPH, nucleotides, and glutathione, (6) altered amino acid metabolism, (7) metabolism-based regulation of apoptosis, and (8) the utilization of alternative substrates, such as lactate and acetate. Altered metabolic flux in cancer is controlled by tumor-host cell interactions, key oncogenes, tumor suppressors, and other regulatory molecules, including non-coding RNAs. Changes to metabolic pathways in cancer are dynamic, exhibit plasticity, and are often dependent on the type of tumor and the tumor microenvironment, leading in a shift of thought from the Warburg Effect and the “reverse Warburg Effect” to metabolic plasticity. Understanding the complex nature of altered flux through these multiple pathways in cancer cells can support the development of new therapies.

Research Progress in Lignin-Based Slow/Controlled Release Fertilizer

As a skeleton component of plants, lignin is an organic macromolecule polymer that can be regenerated and naturally degraded. Annually, plant growth produces about 150 billion tons of lignin. In industrial processes such as paper and biomass-refining industry, large amounts of lignin are formed as by-products. Most of technical lignins are directly combusted to obtain heat, which not only is a waste of organic matter but also leads to environmental pollution and other issues. Interestingly, lignin can be used as slow-release carriers and coating materials for fertilizers due to its excellent slow release properties as well as chelating and other functionalities. Preparation of lignin-based slow/controlled release fertilizers can be achieved by sustainable chemical (ammoxidation, Mannich reaction, and other chemical modifications), coating (without or with chemical modification), and chelation modifications. This Review systematically summarizes the methods, mechanisms, and application of the above methods for preparing lignin-based slow/controlled release fertilizers. Although the evaluation standards and methods of lignin-based slow/controlled release fertilizers are not perfect, it is believed that more and more scholars will pay more attention to them to accelerate the development and application of lignin-based slow/controlled release fertilizers, so as to improve their relevant standards. In short, there is an urgent need to improve the preparation process of lignin-based slow/controlled release fertilizers and application as lignin-based slow/controlled release fertilizers to production practice as soon as possible.

Poly(l-Lactic Acid)/Pine Wood Bio-Based Composites

Bio-based composites made of poly(l-lactic acid) (PLLA) and pine wood were prepared by melt extrusion. The composites were compatibilized by impregnation of wood with γ-aminopropyltriethoxysilane (APE). Comparison with non-compatibilized formulation revealed that APE is an efficient compatibilizer for PLLA/wood composites. Pine wood particles dispersed within PLLA act as nucleating agents able to start the growth of PLLA crystals, resulting in a faster crystallization rate and increased crystal fraction. Moreover, the composites have a slightly lower thermal stability compared to PLLA, proportional to filler content, due to the lower thermal stability of wood. Molecular dynamics was investigated using the solid-state ¹H NMR technique, which revealed restrictions in the mobility of polymer chains upon the addition of wood, as well as enhanced interfacial adhesion between the filler and matrix in the composites compatibilized with APE. The enhanced interfacial adhesion in silane-treated composites was also proved by scanning electron microscopy and resulted in slightly improved deformability and impact resistance of the composites.

Investigation of Effect of Isopropyl Palmitate on Drug Release from Transdermal Patch and Molecular Dynamics Study

Chemical penetration enhancers are widely used in transdermal drug delivery system. However, few studies have focused on changes of concentration in chemical penetration enhancers. In this study, the effect of concentrations of enhancers on drug release and its mechanism were investigated. Zolmitriptan (ZOL) was used as a model drug and isopropyl palmitate (IPP) was used as a model enhancer to investigate drug release behaviors in pressure-sensitive adhesives (PSAs). The IPP concentrations were 2, 5, 10, 12, and 15%. Drug release percents increased by 4.8, 11.5, 16, 15.1, and 14.8%, respectively. Interestingly, the linear relationship between concentrations of IPP and release percents was improved in the 0-10% and remained unchanged in the 10-15%. Moreover, thermal and rheology studies were performed to investigate changes of the fluidity of PSAs. FT-IR and molecular dynamics simulation were conducted to confirm the interaction strength among ZOL, IPP, and PSAs. The results elucidated that IPP increased fluidity of PSAs and vied for drug from PSAs. As a result, the interaction among three components played a major role in changing release behaviors of ZOL, but the increased fluidity only worked in the concentration of less than 10%.