Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells.

Biomolecules contain various heterogeneities in their structures and local chemical properties, and their functions emerge through the dynamics encoded by these heterogeneities. Molecular dynamics model-based studies will greatly contribute to the elucidation of such chemical/mechanical structure-dynamics-function relationships and the mechanisms that generate them. Coarse-grained molecular dynamics models with appropriately designed nonuniform local interactions play an important role in considering the various phenomena caused by large molecular complexes consisting of various proteins and DNA such as nuclear chromosomes. Therefore, in this chapter, we will introduce a method for constructing a coarse-grained molecular dynamics model that simulates the global behavior of each chromosome in the nucleus of a mammalian cell containing many giant chromosomes.

Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.

Polymer modeling has been playing an increasingly important role in complementing 3D genome experiments, both to aid their interpretation and to reveal the underlying molecular mechanisms. This chapter illustrates an application of Hi-C metainference, a Bayesian approach to explore the 3D organization of a target genomic region by integrating experimental contact frequencies into a prior model of chromatin. The method reconstructs the conformational ensemble of the target locus by combining molecular dynamics simulation and Monte Carlo sampling from the posterior probability distribution given the data. Using prior chromatin models at both 1 kb and nucleosome resolution, we apply this approach to a 30 kb locus of mouse embryonic stem cells consisting of two well-defined domains linking several gene promoters together. Retaining the advantages of both physics-based and data-driven strategies, Hi-C metainference can provide an experimentally consistent representation of the system while at the same time retaining molecular details necessary to derive physical insights.

Hypotensive effect of potent angiotensin-I-converting enzyme inhibitory peptides from corn gluten meal hydrolysate: Gastrointestinal digestion and transepithelial transportation modifications.

The study examined the antihypertensive effect of peptides derived from pepsin-hydrolyzed corn gluten meal, namely KQLLGY and PPYPW, and their in silico gastrointestinal tract digested fragments, KQL and PPY, respectively. KQLLGY and PPYPW showed higher angiotensin I-converting enzyme (ACE)-inhibitory activity and lower ACE inhibition constant (Ki) values when compared to KQL and PPY. Only KQL showed a mild antihypertensive effect in spontaneously hypertensive rats with -7.83 and - 5.71 mmHg systolic and diastolic blood pressure values, respectively, after 8 h oral administration. During passage through Caco-2 cells, KQL was further degraded to QL, which had reduced ACE inhibitory activity. In addition, molecular dynamics revealed that the QL-ACE complex was less stable compared to the KQL-ACE. This study reveals that structural transformation during peptide permeation plays a vital role in attenuating antihypertensive effect of the ACE inhibitor peptide.

Uncovering the pharmacological mechanisms of Patchouli essential oil for treating ulcerative colitis.

ETHNOPHARMACOLOGICAL RELEVANCE: Pogostemonis Herba has long been used in traditional Chinese medicine to treat inflammatory disorders. Patchouli essential oil (PEO) is the primary component of Pogostemonis Herba, and it has been suggested to offer curative potential when applied to treat ulcerative colitis (UC). However, the pharmacological mechanisms of PEO for treating UC remain to be clarified. AIM OF THE STUDY: To elucidate the pharmacological mechanisms of PEO for treating UC. METHODS AND RESULTS: In the present study, transcriptomic and network pharmacology approaches were combined to clarify the mechanisms of PEO for treating UC. Our results reveal that rectal PEO administration in UC model mice significantly alleviated symptoms of UC. In addition, PEO effectively suppressed colonic inflammation and oxidative stress. Mechanistically, PEO can ameliorate UC mice by modulating gut microbiota, inhibiting inflammatory targets (OPTC, PTN, IFIT3, EGFR, and TLR4), and inhibiting the PI3K-AKT pathway. Next, the 11 potential bioactive components that play a role in PEO's anti-UC mechanism were identified, and the therapeutic efficacy of the pogostone (a bioactive component) in UC mice was partially validated. CONCLUSION: This study highlights the mechanisms through which PEO can treat UC, providing a rigorous scientific foundation for future efforts to develop and apply PEO for treating UC.

Role of urea in the retention of DON in soil by clay minerals: Analysis based upon molecular weight.

As a widely used fertilizer, urea significantly promotes the leaching of dissolved organic nitrogen (DON) in soils and aggravates nitrogen contamination in groundwater. Clay minerals are considered the most important factor in retaining DON. However, the effect of urea on the retention of DON with different molecular weights by clay minerals is unknown. In this study, the retention of both low-molecular weight DON (LMWD) and high-molecular weight DON (HMWD) by clay minerals in the presence of urea was investigated. For this purpose, batch adsorption and soil column leaching experiments, characterization analysis (Fourier transform infrared spectroscopy X-ray diffraction, and X-ray photoelectron spectroscopy), and molecular dynamics simulations were carried out. Urea had a positive effect on the adsorption of LMWD, whereas a competitive effect existed for the adsorption of HMWD. The dominant interactions among DON, urea, and clay minerals included H-bonding, ligand exchange, and cation exchange. The urea was preferentially adsorbed on clay minerals and formed a complex, which provided more adsorption sites to LMWD and only a few to HMWD. The presence of urea increased the retention of LMWD and decreased the retention of HMWD in clay minerals. The retention capacity of LMWD increased by 6.9%-12.8%, while that of HMWD decreased by 6.7%-53.1%. These findings suggest that LMWD tended to be trapped in soils, while HMWD was prone to be leached into groundwater, which can be used to evaluate the leaching of DON from soil to groundwater.

PFAS-Biomolecule Interactions: Case Study Using Asclepios Nodes and Automated Workflows in KNIME for Drug Discovery and Toxicology.

The Asclepios suite of KNIME nodes represents an innovative solution for conducting cheminformatics and computational chemistry tasks, specifically tailored for applications in drug discovery and computational toxicology. This suite has been developed using open-source and publicly accessible software. In this chapter, we introduce and explore the Asclepios suite through the lens of a case study. This case study revolves around investigating the interactions between per- and polyfluorinated alkyl substances (PFAS) and biomolecules, such as nuclear receptors. The objective is to characterize the potential toxicity of PFAS and gain insights into their chemical mode of action at the molecular level. The Asclepios KNIME nodes have been designed as versatile tools capable of addressing a wide range of computational toxicology challenges. Furthermore, they can be adapted and customized to accomodate the specific needs of individual users, spanning various domains such as nanoinformatics, biomedical research, and other related applications. This chapter provides an in-depth examination of the technical underpinnings and foundations of these tools. It is accompanied by a practical case study that demonstrates the utilization of Asclepios nodes in a computational toxicology investigation. This showcases the extendable functionalities that can be applied in diverse computational chemistry contexts. By the end of this chapter, we aim for readers to have a comprehensive understanding of the effectiveness of the Asclepios node functions. These functions hold significant potential for enhancing a wide spectrum of cheminformatics applications.

Design of Novel Imidazole Derivatives as Potential Non-nucleoside Reverse Transcriptase Inhibitors Using Molecular Docking and Dynamics Strategies.

Human Immunodeficiency Virus (HIV) has become an epidemic causing Acquired Immunodeficiency Syndrome (AIDS). Highly active antiretroviral therapy (HAART) consists of Nucleoside Reverse Transcriptase Inhibitors (NRTIS), Nucleotide Reverse Transcriptase Inhibitors (NtRTIS), and Non- Nucleoside Reverse Transcriptase Inhibitors (NNRTIS) with HIV Protease Inhibitors (HIV PIs). However, the emergence of resistant strains of NNRTIS necessitates the search for better HIV-1-RT inhibitors. METHODS: In this study, a series of novel imidazoles (SP01-SP30) was designed using molecular docking inside the non-nucleoside inhibitory binding pocket (NNIBP) of the HIV-1-RT (PDB ID-1RT2) using Glide v13.0.137, Autodock Vina, and FlexX v2.1.3. Prime MMGBSA was used to study the free energy of binding of the inhibitors with the target enzyme. Molecular dynamics simulation studies were carried out to discover the dynamic behavior of the protein as well as to unveil the role of the essential amino acids required for the better binding affinity of the inhibitor within the NNIBP of the enzyme. The QikProp software module of Schrodinger and online SwissADME were also used to evaluate the drug-likeliness of these compounds. RESULTS: The imidazole derivative SP08 is predicted to be the most promising design compound that can be considered for further synthetic exploitations to obtain a molecule with the highest therapeutic index against HIV-1-RT. CONCLUSION: The results of the current study demonstrate the robustness of our in-silico drug design strategy that can be used for the discovery of novel HIV-1-RT inhibitors.

Design, In silico Screening, Synthesis, Characterisation and DFT-based Electronic Properties of Dihydropyridine-based Molecule as L-type Calcium Channel Blocker.

BACKGROUND: People of all nationalities and social classes are now affected by the growing issue of hypertension. Over time, there has been a consistent rise in the fatality rate. A range of therapeutic compounds, on the other hand, are often used to handle hypertension. OBJECTIVES: The objectives of this study are first to design potential antihypertensive drugs based on the DHP scaffold, secondly, to analyse drug-likeness properties of the ligands and investigate their molecular mechanisms of binding to the model protein Cav1.2 and finally to synthesise the best ligand. MATERIALS AND METHODS: Due to the lack of 3D structures for human Cav1.2, the protein structure was modelled using a homology modelling approach. A protein-ligand complex's strength and binding interaction were investigated using molecular docking and molecular dynamics techniques. DFT-based electronic properties of the ligand were calculated using the M06-2X/ def2- TZVP level of theory. The SwissADME website was used to study the ADMET properties. RESULTS: In this study, a series of DHP compounds (19 compounds) were properly designed to act as calcium channel blockers. Among these compounds, compound 16 showed excellent binding scores (-11.6 kcal/mol). This compound was synthesised with good yield and characterised. To assess the structural features of the synthesised molecule quantum chemical calculations were performed. CONCLUSION: Based on molecular docking, molecular dynamics simulations, and drug-likeness properties of compound 16 can be used as a potential calcium channel blocker.

Mechanistic Insights into the Evolution of Graphitic Carbon from Sulfur Containing Polar Aromatic Feedstock.

In the realm of carbon fiber research, a variety of structural configurations is noted, comprising crystalline, noncrystalline, and semicrystalline forms. Recent investigations into this domain have revealed an array of intriguing phases of carbon, among which amorphous graphite is the most notable for its unique mechanical, thermal, and electrical properties that arise from its inherent topological disorders. In this study, we utilized the ReaxFF molecular dynamics (MD) simulations to investigate the carbonization and graphitization processes involved in the production of amorphous graphite from benzothiophene, a sulfur-containing polar aromatic precursor. We developed C/H/S ReaxFF force field parameters to describe the high-temperature chemistry of benzothiophene. Our investigation reveals the reaction mechanisms, providing critical insights into the underlying chemical processes toward the formation of amorphous graphite and the structural characteristics of the end products. The formation of volatile gaseous molecules and their continuous elimination led to the development of noncontinuous layered graphite structures analogous to amorphous graphite consisting of pentagons, hexagons, and heptagons. These findings offer unprecedented insights into the carbonization and graphitization processes of sulfur-containing heavy-end aromatic feedstock. This knowledge lays the groundwork for advancing synthesis methods and developing amorphous graphite materials with specific properties.

Electrochemical oxidation of UV filters: A first-principles molecular dynamics study.

A theoretical model is proposed to study the oxidation mechanisms of the organic UV filters BP3 and BP4 during electrochemical water treatment utilizing Car-Parrinello molecular dynamics. Factors such as the amount of solvent to be included and how to design the system with the least possible intervention are discussed. The stages of the proposed model consist of the optimization of the geometries by density functional theory methods, the equilibration of the structure immersed in a water box, the inclusion of the reactive species, and the analysis of the reaction energies of each reaction pathway. The ab-initio molecular dynamics simulations lead to several products, and some trends can be identified, in accordance with the well-known reactivity rules of organic chemistry. The products proposed in this work are intermediates in longer oxidative pathways.

Side-chain-induced changes in aminated chitosan: Insights from molecular dynamics simulations.

Chitosan is a functional polymer with diverse applications in biomedicine, agriculture, water treatment, and beyond. Via derivatization of pristine chitosan, its functionality can be tailored to desired applications, e.g. immobilization of biomolecules. Here, we performed molecular dynamics simulations of three aminated chitosan polymers, where one, two, and three long-distanced side chains have been incorporated. These polymers have been previously synthesized and their properties were investigated experimentally, however, the observed dependencies could not be fully explained on the molecular level. Here, we develop a computational protocol for the simulation of functionalized chitosan polymers and perform advanced analysis of their conformational states, intramolecular interactions, and water binding. We demonstrate that intra- and intermolecular forces, especially hydrogen bonds induced by polymer side chain modifications, modulate dihedral angle conformational states of the polymer backbone and interactions with water. We explain the role of the chemical composition of the functionalized chitosans in their tendency to collapse and reveal the key role of the protonation of the amino group near the polymer backbone on the reduction of polymer collapse. We demonstrate that specific binding of water molecules, especially the intermediate water, is more pronounced in the polymer exhibiting such an amino group.

Identification of Novel Tyrosinase Inhibitors with Nanomolar Potency Using Virtual Screening Approaches.

INTRODUCTION: Hyperpigmentation disorders are caused by excess production of the pigment melanin, catalyzed by the enzyme tyrosinase. Novel tyrosinase inhibitors are needed as therapeutic agents to treat these conditions. METHOD: To discover new inhibitors, we performed a virtual screening of the ZINC20 library containing 1.4 billion compounds. An initial filter for drug-likeness, ADMET properties, and synthetic accessibility reduced the library to 10,217 hits. Quantitative structure-activity relationship (QSAR) modeling of this subset predicted nanomolar inhibitory potency for several chemical scaffolds. Comparative molecular docking studies and rigorous binding energy calculations further prioritized four cysteine-containing dipeptide compounds based on predicted strong binding affinity and mode to tyrosinase. RESULTS: Microsecond-long molecular dynamics simulations provided additional atomistic insights into the stability of inhibitor-enzyme binding interactions. This integrated computational workflow effectively sampled an extremely large chemical space to discover four novel tyrosinase inhibitors with half-maximal inhibitory concentration values below 10 nM. CONCLUSION: Overall, this demonstrates the power of virtual screening and multi-faceted computational techniques to accelerate the discovery of potent bioactive ligands from massive compound libraries by efficiently sampling chemical space.

Design and Synthesis of Benzimidazole Carboxamide Cysteine Protease Inhibitors as Promising Anti-leishmanial Agents.

INTRODUCTION: More than 20 protozoan species of Leishmania are responsible for causing Leishmaniasis, an infection spread by blood-feeding phlebotomine sandflies. A narrow pool of drugs is currently available rendering the current drug stratagem to treat this infection . Development of novel, less toxic, and more effective regimens is thus a need of the hour. Design and synthesis of benzo[d]imidazole carboxamides as agents to combat Leishmaniasis are also required. METHODS: 14 benzo[d]imidazole carboxamides were synthesized and gauged against L. donovani promastigotes and intramacrophage amastigote forms. All of the tested compounds exhibited significant anti-promastigote properties with IC50 well below 10 uM. Compounds 4a, 4b, and 4d, showing the highest anti-parasitic activity against promastigote forms (IC50 0.91- 1.33 µM), were also found to be associated with better anti-leishmanial potential (IC50 0.78- 1.67 µM) against the intramacrophage amastigotes comparable to Amphotericin-B (0.13 µM), a drug used for Leishmaniasis. Compound (4a), namely N-(2-(trifluoromethyl)-1Hbenzo[ d]imidazol-5-yl)benzo[d][1,3]-5-carboxamide-dioxole, was found to be most potent against L. donovani amastigotes among all the tested compounds, and demonstrated better antileishmanial properties (IC50 0.78 µM) when compared to the standard. Compound 4a was also assessed for its toxicity profile against THP-1 human monocytic cells. To establish the molecular target(s) in silico, molecular docking studies were performed against cysteine protease, a putative virulence factor of Leishmania parasites, and nucleoside diphosphate kinase, an enzyme with a critical role in nucleotide recycling, also associated with resistance in Leishmania strains. Compound 4a showed better binding affinity than the standard to these targets; furthermore, the molecular dynamic simulation studies further affirmed the stability of compound 4a, within the active site of the targets. In vitro, cysteine protease inhibitory activity (IC50 8.53 µM) using Bz-Arg-AMC hydrochloride fluorogenic peptide substrate established the promising potential of 4a as a cysteine protease inhibitor. RESULT: Computational ADMET analysis indicated appropriate pharmacokinetic profile and physicochemical characteristics for all members of the synthesized library. CONCLUSION: Both in vitro and in silico studies indicate that the synthesized imidazole carboxamides can act as potent hits and that N-(2-(trifluoromethyl)-1H-benzo[d]imidazol-5- yl)benzo[d][1,3]-5-carboxamide-dioxole 4a can be an effective hit molecule which can be further developed into potent lead molecule (s) to fight Leishmania donovani.

Temperature-Dependent Oxidation Behavior of Silicon Carbide Surface: Reactive Molecular Dynamics Simulations.

The high-temperature oxidation mechanism of silicon carbide (SiC) is crucial for designing thermal protection systems in aircraft. This study explored the oxidative chemical reaction processes and mechanism on SiC surface and interfaces within the temperature range of 300-2300 K by using reactive molecular dynamics simulation. The oxygen impact on the silica (SiOx) growth of the SiC surface was analyzed, which shows a progressive increase of silica thickness. The simulation results indicated that the oxidation process of SiC was a typical passive oxidation mechanism. With the environmental temperature rising and oxygen impact, the increase of oxidation thickness on the SiC surface undergoes three oxidizing reaction processes: little chemical adsorption of oxygen molecules on the initial surface, rapid oxidation of silicon and carbon, and dramatic oxidation of the interface between the oxidation layer and SiC. Additionally, this work studied the mechanism of oxidation thickness growth and chemical diffusion of oxygen. The oxidation rate is weakened according to the oxygen atom diffusion barrier effect of silica repulsion. Moreover, the kinetic parameters were statistically calculated by fitting the growth of Si-O bonds and their reaction rate constants. Subsequently, the activation energy and pre-exponential factors were derived by using the Arrhenius equation to model the chemical reaction kinetics of the thermal oxidation process. The chemical reaction behaviors of the two stages could be concluded as follows: (i) in stage I, the initial oxidation is reaction rate limiting; (ii) in stage II, SiC oxidation is limited by both the oxidation reaction rate and the oxygen diffusion coefficient of the oxidation layer. The activation energy of stage II increased compared with stage I due to the oxygen atoms diffusion barrier between the oxidation layers. This study on the oxidation and ablation mechanism of the SiC surface at the atomic scale would provide insight into understanding thermal oxidation behavior and the design of ceramic materials.

Discovering Effective Chiral Dipeptides against Aß(1-42) Aggregation by the Computational Screening Strategy.

The ß-sheet-breaker (BSB) peptides inhibiting amyloidogenic aggregation have been extensively studied. However, the inhibition efficacy of ultrashort chiral dipeptides remains inadequately understood. In this study, we proposed a computational screening strategy to identify chiral dipeptides as BSB with optimal antiaggregation performance against Aß(1-42) aggregation. We constructed a complete dipeptide library encompassing all possible chiral sequence arrangements and then filtered the library by cascaded molecular docking-molecular dynamics (MD) simulation. Our screening strategy discovered dipeptide DWDP (superscript for chirality) that displayed strong interactions with Aß fibrils and inhibitory effects on Aß aggregation, validated by subsequent experiments. Mechanistic investigation by both MD and replica-exchange molecular dynamics (REMD) simulations revealed that DWDP interacts with Aß by hydrophobic contacts and hydrogen bonds and thus inhibits Aß intermolecular contacts and salt bridge formation, therefore inhibiting Aß aggregation and disrupting Aß aggregates. Totally, our strategy presents a viable approach to discover potential dipeptides with effective antiaggregation ability as potential therapeutic agents for Alzheimer's disease.

Direct Hydrogen Production Promoted by Laser-Induced Water Plasma.

Hydrogen, as a clean energy carrier, plays an important role in addressing the current energy and environmental crisis. However, conventional hydrogen production technologies require extreme reaction conditions, such as high temperature, high pressure, and catalysts. Herein, we study the microscopic mechanism of laser-induced water plasma and subsequent H2 production with real-time time-dependent density functional theory simulations and ab initio molecular dynamics simulations. The results demonstrate that intense laser excites liquid water to generate nonequilibrium plasma in a warm-dense state, which constitutes a superior reaction environment. Subsequent annealing leads to the recombination of energetic reactive particles to generate H2, O2, and H2O2 molecules. Annealing rate and laser wavelength are shown to modulate the product ratio, and the energy conversion efficiency can reach ∼9.2% with an annealing rate of 1.0 K/fs. This work reveals the nonequilibrium atomistic mechanisms of hydrogen production from laser-induced water plasma and shows far-reaching implications for the design of optically controllable hydrogen technology.

Insights into Thermal Conductivity at the MOF-Polymer Interface.

Understanding the thermal conductivity in metal-organic framework (MOF)-polymer composites is crucial for optimizing their performance in applications involving heat transfer. In this work, several UiO66-polymer composites (where the polymer is either PEG, PVDF, PS, PIM-1, PP, or PMMA) are examined using molecular simulations. Our contribution highlights the interface's impact on thermal conductivity, observing an overall increasing trend attributable to the synergistic effect of MOF enhancing polymer thermal conductivity. Flexible polymers such as PEG and PVDF exhibit increased compatibility with the MOF, facilitating their integration with the MOF lattice. However, this integration leads to a moderated enhancement in thermal conductivity compared to polymers that remain separate from the MOF structure, such as PS or PP. This effect can be attributed to alterations in phonon transport pathways and shifts in interfacial interactions between the polymer and MOF. Specifically, the infiltration of the polymer like PEG and PVDF into the MOF disrupted the MOF's ordered network, introducing defects or barriers that hindered phonon propagation. In contrast, nonpolar and rigid polymers like PP, PMMA, PS, and PIM-1 exhibited greater improvements in thermal conductivity when combined with MOFs compared to the flexible polymers PVDF and PEG. Most notably, our analysis identifies a critical interface region within approximately 30-50 Å that profoundly influences thermal conductivity. The interface region, as indicated by the density profile and radius of gyration, is notably shorter but plays a pivotal role in modulating the thermal properties. The sensitivity of the system to these interface characteristics underscores the crucial role of this particular interface area in dictating the thermal conductivity. Our findings emphasize the sensitivity of thermal conductivity in polymer matrices to interface characteristics and highlight the critical role of a specific interface region in modulating thermal properties.

Unraveling the Dual Anti-inflammatory and Antioxidant Mechanisms of Acteoside: Computational Insights and Experimental Validation.

Acteoside (ACT) is one of the primary bioactive ingredients in Cistanche tubulosa (Schenk). Its remarkable efficacy in treating immune-related and inflammatory disorders has garnered significant interest among scientific circles. However, the anti-inflammatory and antioxidant effects of ACT and its underlying molecular mechanisms require further investigation. In this study, pharmacophore-based reverse docking and molecular dynamics simulations identified potential anti-inflammatory targets in silico. Studies conducted in vitro with lipopolysaccharide (LPS)-induced RAW264.7 cells validated the anti-inflammatory properties of ACT. Methyl thiazolyl tetrazolium (MTT) and lactate dehydrogenase (LDH) assays indicated ACT's non-toxic and growth-promoting effects on cells. ACT significantly reduced nitric oxide (NO) and reactive oxygen species (ROS) production and restored levels of antioxidant enzymes. It also decreased pro-inflammatory cytokines. Western blotting assays indicated that ACT inhibited p38, TNF-α, PI3K/AKT, and NF-κB signaling pathways. These findings underscore ACT's ability to mitigate acute inflammation in RAW264.7 cells by modulating key signaling pathways and provide the scientific basis for enhancing the medicinal value of ACT and future drug development.

Quantum Insights into Partially Molecular Imprinted Microspheres for Anticancer Therapeutics: Experimental and Theoretical Studies.

Drug solubility is a determining factor for controlled release, and solubility-dependent release kinetics can be modified by changing the drug's state in the polymer matrix through partial molecular imprinting (PMI), although research in this area remains limited. This novel PMI approach creates nanocavities within the polymer by partially retaining the imprinting molecule and trapping the drug. Such a method holds promise for developing advanced biomaterial-based drug delivery systems for anticancer therapies. In this study, we developed microspheres designed for anticancer drug delivery utilizing PMI to enhance controlled release properties. Poly(vinyl alcohol) (PVA) microspheres were partially imprinted with aspirin (ASP) to create nanocavities for gemcitabine (GEM) molecules, inducing a polymorphic shift of GEM within the polymer matrix. This novel PMI approach enhanced drug release properties by enabling control over the drug crystallinity and release rate. The PVA-ASP-GEM complex showed zero-order release kinetics, releasing 21.6% of GEM over 48 h, maintaining steady state release profile. In contrast, nonimprinted PVA-GEM microspheres exhibited first-order kinetics with a faster release of 46.85% in the same period. Quantum insights from density functional theory (DFT) calculations revealed the superior stability of the PVA-ASP-GEM complex, with a binding free energy of -56.03 kcal/mol, compared to -29.07 kcal/mol for PVA-GEM. Molecular dynamics (MD) simulations demonstrated that ASP's presence created nanocavities that restricted GEM's movement, further contributing to the controlled release. Experimental validation through differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and Raman spectroscopy confirmed the polymorphic transitions within the PVA-ASP-GEM complex. This PMI-based approach offers a promising method for modulating drug release kinetics and improving the stability of anticancer therapeutics, paving the way for innovative biomaterial-based drug delivery systems.

TERRA G-quadruplex stabilization behind the anti-multiple myeloma activity: Novel insights about resveratrol pleiotropic effects.

Resveratrol (RSV) is a nutraceutical compound belonging to the nonflavonoid polyphenol family, whose antioxidants, anti-inflammatory, and antitumoral properties have been widely investigated. The ability of RSV to provide beneficial effects for neurological, cardiovascular, and cancer disorders rekindled the interest to explore the molecular mechanisms behind its pleiotropic effects, which are due to the modulation of coding and noncoding genes involved in many key biological pathways. With a computational approach, including docking studies and thermodynamics calculations followed by 200-ns-long molecular dynamics and a clustering analysis, we hypothesized the stabilizing binding between RSV and G4 structures of telomeric repeat-containing RNA (TERRA), which is a tumor-suppressive long noncoding RNAs (lncRNA) involved in the regulation of telomere maintenance. In vitro studies performed on cellular models of multiple myeloma (MM) strengthened our hypothesis by highlighting that the antiproliferative and apoptotic effect induced by the treatment with RSV is associated with an increase of TERRA transcript and with upregulation of telomeric heterochromatin markers, such as H3K27Me3 and H4K20Me3, and of the hallmark of apoptosis, cleaved-poly(ADP-ribose) polymerase-1. Our results propose innovative insights underlying the multifaceted role of RSV in MM, by pointing out the role of this natural compound in an lncRNA-mediated regulation to counteract cellular immortality.