Search Results (484)

This work reports the isolation and structural characterization of 1-(2-aminophenyl)-3-(4-pyridyl)-3-hydroxy-1-propanone (1), a β-hydroxyketone intermediate that crystallized unexpectedly during the base-catalyzed aldol condensation of 2-aminoacetophenone with pyridine-4-carbaldehyde, a reaction intended to afford the corresponding pyridyl chalcone (2). The formation of (1) highlights the sensitivity of Claisen–Schmidt reactions to the electronic and steric features of the substrates and to the applied reaction conditions. Single-crystal X-ray diffraction unambiguously confirmed the molecular structure of (1), revealing a hydrogen-bonding network involving the amino, carbonyl, and β-hydroxyl functionalities. These interactions contribute to the solid-state stabilization of the β-hydroxyketone and hinder its dehydration to chalcone (2). The present results provide experimental insight into the mechanistic landscape of aldol condensations and emphasize the relevance of isolable intermediates as structurally defined precursors for further synthetic transformations. Full article

In situ cancer vaccines activate antitumor immune responses by locally capturing and presenting tumor-derived antigens, in which polymers play a key role as antigen-capturing materials. However, the influence of polymer composition and degree of polymerization (DP) on antigen capture efficiency and protection mechanisms remains insufficiently understood. In this study, the tumor-specific antigen MAGE-A3, highly expressed in esophageal squamous cell carcinoma (ESCC), was employed to investigate antigen capture and stabilization by five representative polymers—chitosan, polyethyleneimine (PEI), alginate, polycaprolactone (PCL), and poly (lactic-co-glycolic acid) (PLGA)—with different DPs, using molecular dynamics simulations and in vitro experiments. All-atom simulations revealed that hydrophobic interactions dominate polymer–antigen binding, while electrostatic interactions from cationic polymers synergistically enhance binding affinity and capture efficiency. Binding free energy analysis showed that van der Waals and electrostatic contributions stabilize the complexes, whereas polar solvation partially counteracts these effects. Experimentally, low-DP chitosan exhibited the highest antigen-capture efficiency (38.9%), attributed to its small molecular size, enabling multipoint binding across the antigen surface. In contrast, high-DP polymers generated pronounced steric hindrance that suppressed antigen–enzyme interactions and inhibited hydrolysis. These findings clarify how polymer composition and chain length jointly regulate antigen capture and protection, providing mechanistic guidance for the rational design of polymer-based in situ cancer vaccines. Full article

Background: Point mutations to the androgen receptor (AR) ligand-binding domain (LBD) are becoming increasingly recognized as a mechanism of therapeutic resistance in castration resistant prostate cancer (CRPC). The present review explores how point mutations induce molecular changes that contribute to the eventual treatment failure of androgen receptor pathway inhibitors (ARPIs) in CRPC. Methods: The PubMed database was searched for structural studies on the AR LBD. Eligible articles included molecular docking analysis and emphasized changes in ligand–receptor interactions after point mutation. Structural data were obtained from the Protein Data Bank (PDB) using the search parameters “Androgen receptor ligand binding domain”, “Homo sapiens”, and “X-ray diffraction”. PDB files of wild-type and point mutant AR LBDs were accumulated for analysis. Results: A functional shift from inhibiting to activating AR has been documented for multiple ARPIs. Crystallography data and in silico evaluation have deciphered how changes in steric hindrance of the AF-2 domain contribute to ARPI loss of function. To combat therapeutic resistance, discovery efforts have begun to consider combination approaches of orthosteric and allosteric inhibitors, as well as compounds that target other AR domains. Although lead compounds have been identified, none have progressed into the clinic. Conclusions: Questions remain regarding the best approach for rationally designing new AR targeting therapeutics. Understanding how structural changes to the AR LBD lead to the failure of clinical therapeutics is a necessary step that should precede drug discovery campaigns. Moreover, computational modeling is a powerful tool that should be leveraged to streamline therapeutic development. Full article

The escalating accumulation of pharmaceutical micropollutants in global water systems represents a significant challenge to current circular economy frameworks, highlighting a critical gap in the management of environmental persistence. Although advanced remediation technologies are often proposed to mitigate this crisis, their engineering optimization is frequently compromised by a reliance on empirical approximations rather than precise physicochemical constants. Addressing this fundamental deficit, this study executes a rigorous determination of mass transfer properties for two ubiquitous contaminants: Butylparaben and Triclosan. Utilizing a high-precision electrolytic conductance method under infinite dilution, we investigated transport dynamics across varying temperature gradients (305.15–319.15 K). Experimental data were subjected to advanced mathematical modeling, where the Modified Robinson–Stokes (MRS) quadratic model significantly outperformed classical linear approaches ($R^2>0.98$), accurately capturing non-ideal solute–solvent interactions. The derived limiting molar conductivities facilitated the calculation of infinite dilution diffusion coefficients via the Nernst–Haskell equation, yielding values of $0.99\times {10}^{-8}$ m²/s for Butylparaben and $0.98\times {10}^{-8}$ m²/s for Triclosan. Furthermore, Stokes–Einstein analysis quantified the hydrodynamic radii, elucidating the steric mechanisms governing the sluggish migration of bulky chlorinated ethers compared to single-ring esters. These precise transport parameters are not merely theoretical values; they are essential inputs for developing accurate computational fate models and designing regenerable separation processes, thereby providing the hard physics required to engineer solutions for the perpetual pollution era. Full article

The precursor infiltration and pyrolysis (PIP) route is widely adopted to fabricate carbon fiber-reinforced silicon carbide (C_f/SiC) composites; however, the atomic-scale restructuring of the pyrolytic carbon/silicon carbide (PyC/SiC) interface during ceramization—and its impact on mechanical integrity—remains elusive. Here, reactive molecular dynamics (ReaxFF MD) simulations elucidate the coupled thermochemical–mechanical evolution of polycarbosilane (PCS) precursors on PyC substrates with orientation angles (OAs) of 0°, 25°, 55°, and 85°. Dynamic pyrolysis triggers a pivotal transition from sp² to sp³ hybridization at the interface. High-OA substrates (55° and 85°) present a dense population of reactive edge sites, fostering extensive cross-interfacial covalent bonding. Subsequent shear loading reveals that these pyrolysis-induced chemical bridges govern failure modes, shifting from interlayer sliding dominated by weak non-bonded interactions (0°) to ductile fracture featuring uniform plasticity and crack deflection. The OA = 55° interface attains a theoretical peak shear strength of 15 GPa and exhibits the most favorable combination of high strength and ductile failure under tensile loading, owing to an optimal balance between reactive site availability and interlayer steric openness. In contrast, the OA = 85° interface, despite comparable peak stress, fails via brittle crack penetration into the SiC matrix. By correlating atomistic structure with macroscopic performance, this study provides a bottom-up framework for engineering C_f/SiC composites via interfacial texturing and optimized pyrolysis protocols. Full article

Linear alkylbenzene (LAB) is the main raw material used to make biodegradable detergents, and its production process is based on aromatic alkylation. HY zeolites that have undergone controlled dealumination and desilication have led industrial standards amongst solid acid catalysts because of their controllable acidity and hierarchical pore structure. Coke formation in such systems can assume a dual role, which is dependent on its condition. Though the over-deposition is known to cause deactivation by blocking the micropores, Bronsted acid-site masking, and diffusion collapse, the low-level deposition could also be done to increase the monoalkylate selectivity by the pore mouth catalysis, steric modulation, and selective suppression of secondary alkylation pathways. The critical review is done on the structural-kinetic interaction that determines the coke evolution in HY-based catalysts. In order to moderate the acid-site density and enhance hydrothermal stability, dealumination (Si/Al optimization of about 2.5 to 30–100) occurs, but to reduce deep-pore coke formation, desilication (interconnected mesopores) is created. The bimodal porosity and regulated acidity are found to be synergistic, as hierarchical HY zeolites produced through successive cycles of steam and alkaline treatments not only show LAB selectivity in excess of 90% but also exhibit much longer catalyst lifetimes. Quantitative research on the beneficial coke regime revealed that it was composed of about 36 wt% hydrogen-rich species, which were localized at the pore mouths, hence enhancing monoalkylation selectivity by 15–40%. Beyond a critical transition window (e.g., 8–12 wt.%), coke formation to condensed polyaromatic and graphitic products leads to fast deactivated coke formation, which is due to percolation limits and transport-controlled kinetics. More advanced techniques of characterization of the coke, e.g., temperature-programmed oxidation (TPO), ²⁷Al MAAS NMR, and UV-Raman spectroscopy, indicate how the coke is changed to highly structured graphitic deposits of high oxidation activation energy. Activity recovery of 85–98% is obtained in regeneration processes, including controlled oxidative calcination, microwave-based and plasma-based processes, and thermal management protocols, and it would be determined by the chemistry of the coke, its spatial distribution, and the regeneration protocols. This paper has developed a mechanistic coke control system by cross-tuning the acidity and development of an effective pore network, which led to a sustainable aromatic alkylation reaction with minimal activity loss, high selectivity, and long life. Full article

Rhizopus oryzae lipase (ROL) is a key enzyme involved in olive oil spoilage and acts as a virulence factor in fungal infections. Natural lipophilic lipase inhibitors are crucial for mitigating economic losses resulting from lipid degradation in stored or decaying olive fruits. This study evaluated a series of enzymatically synthesized piperate esters with varying alkyl chain lengths (butyryl, C4; octyl, C8; dodecyl, C12) for their inhibitory effects on ROL activity. Octyl piperate (C8) demonstrated the highest potency, with IC₅₀ values of 0.05 mg/mL using methods B and C or 0.25 mg/mL using method A. Molecular docking indicated that C8 achieved the most favorable predicted binding energy (Gscore: –11.134 kcal/mol), primarily through hydrophobic interactions (Val329, Ala212, Phe209) and hydrogen bonds with oxyanion hole residues (Ser268, Thr206, Gln241). Molecular dynamics simulations confirmed that C8 maintained stable binding and stabilized the catalytic residues. In comparison, C4 exhibited weaker interactions, and the longer C12 chain induced conformational instability and steric hindrance. These results establish a parabolic structure–activity relationship, identifying the octyl chain (C8) as optimal for ROL inhibition among the tested derivatives. The rational design of lipophilic, biodegradable lipase inhibitors thus positions octyl piperate as a promising candidate for extending olive storage and shelf life, and as a scaffold for developing natural antifungal agents targeting virulent R. oryzae strains. Full article

Tuberculosis, caused by Mycobacterium tuberculosis, remains a global health challenge, particularly due to multidrug-resistant strains. Photodynamic therapy using porphyrin-based photosensitizers offers a promising alternative by targeting the trehalose-rich cell wall of the bacillus. Motivated by prior experimental observations that shorter linkers improve efficacy, this study probes the molecular basis of linker-length-dependent activity in trehalose–porphyrin glycoconjugates. Here, we show that shorter linker lengths are consistent with improved activity in vitro and, in an Ag85B docking model, constrain conformational flexibility, reduce solvent exposure, and promote tighter packing consistent with stronger predicted interactions. Using computational docking, we analyzed binding scores, RMSD variability, steric clashes, and protein–ligand interactions for conjugates docked into Ag85B, a key enzyme in cell wall synthesis. Shorter linkers (0–2 carbons) were found to exhibit superior binding scores, lower RMSD variability, and stronger interactions with residues such as ARG 43, including unique π–cation interactions. In contrast, longer linkers displayed increased flexibility, reduced binding specificity, and greater solvent exposure. These findings, which support our experimental observations, suggest a molecular basis for linker-dependent efficacy and provide a framework for designing next-generation porphyrin-based therapeutics for tuberculosis treatment. Full article

Polypyrrole-based functional composites are increasingly explored and extensively adopted for energy storage, sensing, and environmental applications due to their tunable electronic properties, chemical versatility, and mechanical stability. However, rational optimization of these composites requires a unified understanding of electronic, mechanical, thermal, and chemical behavior at the atomic scale, which underlies their multifunctional behavior, and remains fragmented. Notably, Density Functional Theory (DFT) provides indispensable atomistic insight into the electronic, mechanical, thermal, and chemical interactions that govern the performance of multifunctional materials. To bridge these gaps, this review presents a comprehensive assessment of recent DFT and time-dependent DFT (TD-DFT) studies that elucidate the electronic, mechanical, thermal, and chemical characteristics of polypyrrole and its hybrid composites. Key theoretical descriptors, including electronic structure modulation, charge transfer behavior, adsorption energetics, interfacial binding energies, hydrogen bond formation, and charge redistribution, are critically assessed to establish structure–property relationships across diverse functional systems. Considerable attention is given to interfacial interactions, doping strategies, and composite architectures that govern durability, conductivity, and chemical stability. By consolidating current atomistic insights and identifying existing limitations, this review provides a coherent framework for rational material design. Notably, it presents the first systematic quantification of dopant steric effects in PPy multifunctional composites, linking atomistic-scale modifications to the optimization of functional properties in next-generation applications. Full article

The $\beta$-sheet, consisting of several $\beta$-strands, is one of the most important secondary structures of proteins. Most $\beta$-sheets differ greatly from the fully extended, all-trans form due to twisting and/or bending. When looked at in the direction of the $\beta$-strands rather than along the hydrogen bonds, the twist is usually right-handed. Although numerous studies have investigated the origin of the right-handed twist of $\beta$-sheets or $\beta$-strands in proteins, there is no common agreement about its causes. The twist can be seen from the dihedral angles in the Ramachandran plot. Here, we discuss the opposing roles of the dihedral angles $\varphi$ and $\psi$. The key role is played by the angle $\varphi$, which is controlling the distance between the carbonyl group of the backbone and the side chain of the next amino acid. There are two antisymmetric effects: the change in $\varphi$ in the clockwise direction is initiated by a ${\mathrm{C}}_{\beta }$… O clash and delimited by a subsequent ${\mathrm{C}}_{\beta }$… NH clash, while the opposite relationship holds for the counter-clockwise change in $\psi$. The impact of the twist on tertiary structures is examined. The understanding of the molecular effects within a strand is deepened by 3D computer images and ball–and–stick models. The use of (tangible) physical models is highlighted in view of teaching structural biology to undergraduate students. Full article

Background/Objectives: ASXL1 is a chromatin-associated gene implicated in both hematologic malignancies and neurodevelopmental disorders, including Bohring–Opitz syndrome (BOS). Although many ASXL1 variants are well classified, a substantial proportion remain variants of uncertain significance (VUS), complicating molecular diagnosis and genetic counseling. The objective of this study was to evaluate whether structural context can inform the interpretation of selected ASXL1 missense variants in a clinical setting. Methods: We describe a 17-year-old female with clinical features consistent with BOS carrying the heterozygous ASXL1 variant p.Q1448R, currently classified as benign under ACMG/AMP guidelines. Three-dimensional in silico structural modeling was performed using AlphaFold3 and available crystallographic data. Three additional ASXL1 missense variants classified as VUS in ClinVar (p.R265H, p.T297M, and p.Y358C) were also analyzed. Evolutionary conservation, domain localization, and residue-level interactions were assessed. Results: Structural modeling indicated that the p.Q1448R substitution alters polar interactions and introduces a steric constraint near a conserved PHD-type zinc finger domain. Variants p.R265H and p.T297M affected stabilizing interactions within the DEUBAD, which is involved in BAP1 activation, while p.Y358C altered a polar microenvironment adjacent to a chromatin-interacting region. All analyzed variants, except p.T297M, localized to evolutionarily conserved regions. Conclusions: This study demonstrates that in silico structural analysis can provide complementary, domain-level insights for the interpretation of ASXL1 missense variants that remain classified as benign, likely benign or VUS under current frameworks. Such approaches may assist in prioritizing variants for further functional evaluation and refining molecular interpretation when experimental data are limited. Full article

The broadly neutralizing monoclonal antibody 3D1 potently neutralizes SADS-CoV by targeting a conserved epitope within the heptad repeat 1 (HR1) domain of the viral spike protein. Structural and biophysical analyses demonstrate that 3D1 binds with high affinity to a specific linear β-turn motif (residues A804–N809) in HR1. High-resolution crystallography reveals that this motif sits within a deep, electrostatically complementary paratope groove. Critically, 3D1 binding competitively inhibits the essential interaction between HR1 and HR2. Notably, its recognition is not dependent on HR1’s native helical conformation, as it maintains strong binding to conformationally constrained, stapled helical peptides. Collectively, the data indicate that 3D1 neutralizes by capturing a pre-hairpin intermediate state of HR1—a transition state between prefusion and postfusion forms—thereby sterically blocking the formation of the stable postfusion six-helix bundle that is essential for membrane fusion. This work defines a precise, structure-dependent neutralizing epitope and elucidates a mechanism of action that involves trapping a key fusion intermediate, offering a valuable template for the design of broad-spectrum coronavirus therapeutics. Full article

The development of effective inhalable drugs remains a key challenge in the treatment of pulmonary diseases, due to the physiological barriers of the respiratory tract and the lack of predictive models that accurately reproduce the human lung environment. In this context, liposomes (LP) have emerged as promising nanocarriers for pulmonary drug delivery due to their high biocompatibility, surfactant-like composition, capacity to encapsulate both hydrophilic and lipophilic drugs, and potential to provide sustained drug release while reducing systemic toxicity. This study evaluates the influence of size and PEGylation on their physicochemical properties, cytotoxicity, interaction with the pulmonary mucus, and cellular internalisation. LP of 100 nm (LP 100), 200 nm (LP 200), and 600 nm (LP 600) were characterised physiochemically and evaluated in pulmonary cell lines (A549 and Calu-3) exposed in liquid–liquid interface (LLI) and air–liquid interface (ALI) by nebulisation. In addition, artificial pulmonary mucus (APM) was employed to analyse LP penetration through the pulmonary mucus barrier. Results indicate that LP 100 exhibits greater colloidal stability, lower cytotoxicity, and sustained migration through the APM over time with respect to larger particles. PEGylation of LP 100 (LP-PEG) further increases their stability and ability to penetrate the APM, although cellular internalisation is reduced due to the steric effect of the PEG coating. These findings highlight the importance of adjusting the size and surface modifications of LPs according to the therapeutic target of the drug, optimising their persistence on the epithelial surface or their cellular uptake. Full article

Cancer metastasis, the spread of tumour cells from the primary site to distant organs, is responsible for over 90% of cancer deaths, yet effective treatments remain elusive due to incomplete understanding of the molecular drivers involved. Podocalyxin (PODXL), a protein overexpressed in many aggressive cancers, links the cell membrane to the internal skeleton through its interaction with Ezrin, an actin cytoskeleton cross-linker. Despite its therapeutic relevance, the PODXL–Ezrin interface remains structurally uncharacterised and pharmacologically intractable. Here, we employed an integrated computational approach combining protein–protein docking, molecular dynamics (MD) simulations, and virtual screening to investigate the structural basis of the PODXL–Ezrin interaction. Using AlphaFold-predicted structures, we modelled PODXL and Ezrin complexes, revealing that PODXL’s cytoplasmic domain stabilises upon Ezrin binding, with Arg495 mediating temporally distinct electrostatic interactions essential for initial complex assembly. Particularly, we characterised the R495W missense mutation in PODXL’s Ezrin-binding domain, demonstrating that substitution of arginine with bulky, hydrophobic tryptophan may allosterically destabilise Ezrin’s dormant conformation. This mutation slightly increases the intramolecular distance between the F3 subdomain and C-terminal domain from 2.59 Å to 3.40 Å, thus leading to potential partial unmasking of the Thr567 phosphorylation site that could plausibly prime Ezrin for activation. Molecular dynamics simulations in the WT state with a total simulation time of 100 ns revealed enhanced structural rigidity and reduced radius of gyration fluctuations in the mutant complex, consistent with a potential “locked,” activation-prone state that amplifies oncogenic signalling. Through virtual screening, we identified NSC305787 as a selective destabiliser of the R495W mutant complex by disrupting key Trp495–pre-C-terminal loop Ezrin interactions and causing steric hindrance to PIP2 recruitment. Our findings identified mutation-dependent changes in drug binding that can guide the development and repurposing of compounds for targeting PODXL-related cancers and improve patient outcomes in PODXL-altered malignancies. Full article

The interface between synthetic materials and biological systems is a critical determinant of performance in medical devices and biosensors. This review examines the evolution of biointerface science through the lens of self-assembled monolayers (SAMs) of thiols on gold, a model system that offers atomic-level control over surface chemistry. We trace the field from the foundational structural characterization to the establishment of empirical design rules for bio-inertness. While early theoretical models attributed protein resistance to steric repulsion forces in polymer brushes, contemporary understanding has shifted toward the “water barrier” hypothesis, which posits that tightly bound interfacial water prevents direct biomolecular contact. We highlight recent studies that extend these concepts into “realistic” crowded biological environments. Their work reveals that fouling surfaces in crowded media generate a “viscous interphase layer” (VIL) that extends tens of nanometers into solution, whereas zwitterionic surfaces maintain a robust hydration shell that prevents this accumulation. Furthermore, this hydration barrier is shown to fundamentally alter bacterial mechanics, forcing microorganisms into a reversible, tethered “hovering” state at a significant biological interaction distance (>100 nm) from the surface, effectively precluding biofilm nucleation. These insights underscore that the future of antifouling material design lies in the precise engineering of interfacial hydration structures. Full article