Elucidation of Molecular Interactions Between Drug-Polymer in Amorphous Solid Dispersion by a Computational Approach Using Molecular Dynamics Simulations

Introduction

Amorphous drug dispersion is frequently used to enhance the solubility and dissolution of poorly water-soluble drugs, thereby improving their oral bioavailability. The dispersion of these drugs into polymer matrix can inhibit their recrystallization. The inter-molecular interactions between drug and polymer plays a role in the improvement of the dissolution rate, solubility, and physical stability of drug.

Aim

This study aims to investigate the formation and interactions of ritonavir (RTV)/poloxamer (PLX) amorphous formulation using a computational approach via molecular dynamics (MD) simulations, which mimicked solvent evaporation and melt-quenching method.

Methods

TheRoot Mean Square Deviation (RMSD) value, Root Mean Square Fluctuation (RMSF), Radial Distribution Function (RDF), Radius of Gyration (Rg), Solvent Accessible Surface Area (SASA), and hydrogen bond interactions were analyzed to determine interaction mechanisms between RTV and PLX in amorphous solid dispersion.

Results

The pi-alkyl bonds between RTV and PLX were formed after simulations of solvent evaporation, while the hydrogen bond interactions of RTV-PLX was observed during melt method simulations. These results indicate the successful formulation of amorphous solid dispersion (ASD) from RTV and PLX. The RMSD values obtained from the solvent evaporation, melt-cooling-A, melt-cooling-B, and melt-cooling-C methods were 3.33 Å, 1.97 Å, 1.30 Å, and 1.29 Å, respectively, while the average RMSF values were 2.65 Å, 1.04 Å, 1.05 Å, and 1.07 Å, respectively. This indicates that the suppression of translational motion of RTV from the melt method can be stronger than solvent evaporation caused by the intermolecular interactions of RTV-PLX.

Conclusion

MD simulations helped in understanding the formation and interaction mechanisms of ASD formulations that were difficult to detect by experimental approaches.

Combating Cariogenic Streptococcus mutans Biofilm Formation and Disruption with Coumaric Acid on Dentin Surface

Streptococcus mutans, the primary cause of dental caries, relies on its ability to create and sustain a biofilm (dental plaque) for survival and pathogenicity in the oral cavity. This study was focused on the antimicrobial biofilm formation control and biofilm dispersal potential of Coumaric acid (CA) against Streptococcus mutans on the dentin surface. The biofilm was analyzed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) viability assay, microtiter plate assay, production of extracellular polymeric substances (EPSs), florescence microscopy (surface coverage and biomass μm2) and three-dimensional (3D) surface plots. It was observed that CA at 0.01 mg/mL reduced bacterial growth by 5.51%, whereases at 1 mg/mL, a significant (p < 0.05) reduction (98.37%) was observed. However, at 1 mg/mL of CA, a 95.48% biofilm formation reduction was achieved, while a 73.45% biofilm dispersal (after 24 h. treatment) was achieved against the preformed biofilm. The MTT assay showed that at 1 mg/mL of CA, the viability of bacteria in the biofilm was markedly (p < 0.05) reduced to 73.44%. Moreover, polysaccharide (EPS) was reduced to 24.80 μg/mL and protein (EPS) to 41.47 μg/mL. ImageJ software (version 1.54 g) was used to process florescence images, and it was observed that the biofilm mass was reduced to 213 (μm2); the surface coverage was reduced to 0.079%. Furthermore, the 3D surface plots showed that the untreated biofilm was highly dense, with more fibril-like projections. Additionally, molecular docking predicted a possible interaction pattern of CA (ligand) with the receptor Competence Stimulating Peptide (UA159sp, PDB ID: 2I2J). Our findings suggest that CA has antibacterial and biofilm control efficacy against S. mutans associated with dental plaque under tested conditions.

Tapioca Starch Improves the Quality of Virgatus nemipterus Surimi Gel by Enhancing Molecular Interaction in the Gel System

The gel prepared using Nemipterus virgatus (N. virgatus) surimi alone still has some defects in texture and taste. Complexing with polysaccharides is an efficient strategy to enhance its gel properties. The main objective of this study was to analyze the relationship between the gel quality and molecular interaction of N. virgatus surimi gel after complexing with tapioca starch. The results make clear that the gel strength, hardness, and chewiness of surimi gel were increased by molecular interaction with tapioca starch. At the appropriate addition amount (12%, w/w), the surimi gel had an excellent gel strength (17.48 N), water-holding capacity (WHC) (89.01%), lower cooking loss rate (CLR) (0.95%), and shortened T2 relaxation time. Microstructure analysis indicated that the addition of tapioca starch facilitated even distribution in the gel network structure, resulting in a significant reduction in cavity diameter, with the minimum diameter reduced to 20.33 μm. In addition, tapioca starch enhanced the hydrogen bonding and hydrophobic interaction in the gel system and promoted the transformation of α-helix to β-sheet (p < 0.05). Correlation analysis showed that the increased physicochemical properties of surimi gel were closely related to the enhanced noncovalent interactions. In conclusion, noncovalent complexation with tapioca starch is an efficient strategy to enhance the quality of surimi gel.

Preparation of Hot-Melt-Extruded Solid Dispersion Based on Pre-Formulation Strategies and Its Enhanced Therapeutic Efficacy

In this study, an amorphous solid dispersion containing the poorly water-soluble drug, bisacodyl, was prepared by hot-melt extrusion to enhance its therapeutic efficacy. First, the miscibility and interaction between the drug and polymer were investigated as pre-formulation strategies using various analytical approaches to obtain information for selecting a suitable polymer. Based on the calculation of the Hansen solubility parameter and the identification of the single glass transition temperature (Tg), the miscibility between bisacodyl and all the investigated polymers was confirmed. Additionally, the drug-polymer molecular interaction was identified based on the comprehensive results of dynamic vapor sorption (DVS), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, and a comparison of the predicted and experimental values of Tg. In particular, the hydroxypropyl methylcellulose (HPMC)-based solid dispersions, which exhibited large deviation between the calculated and experimental values of Tg and superior physical stability after DVS experiments, were selected as the most appropriate solubilized bisacodyl formulations due to the excellent inhibitory effects on precipitation based on the results of the non-sink dissolution test. Furthermore, it was shown that the enteric-coated tablets containing HPMC-bisacodyl at a 1:4 ratio (w/w) had significantly improved in vivo therapeutic laxative efficacy compared to preparations containing un-solubilized raw bisacodyl in constipation-induced rabbits. Therefore, it was concluded that the pre-formulation strategy, using several analyses and approaches, was successfully applied in this study to investigate the miscibility and interaction of drug-polymer systems, hence resulting in the manufacture of favorable solid dispersions with favorable in vitro and in vivo performances using hot-melt extrusion processes.

Probing Molecular Packing of Amorphous Pharmaceutical Solids Using X-ray Atomic Pair Distribution Function and Solid-State NMR

The structural investigation of amorphous pharmaceuticals is of paramount importance in comprehending their physicochemical stability. However, it has remained a relatively underexplored realm primarily due to the limited availability of high-resolution analytical tools. In this study, we utilized the combined power of X-ray pair distribution functions (PDFs) and solid-state nuclear magnetic resonance (ssNMR) techniques to probe the molecular packing of amorphous posaconazole and its amorphous solid dispersion at the molecular level. Leveraging synchrotron X-ray PDF data and employing the empirical potential structure refinement (EPSR) methodology, we unraveled the existence of a rigid conformation and discerned short-range intermolecular C-F contacts within amorphous posaconazole. Encouragingly, our ssNMR 19F-13C distance measurements offered corroborative evidence supporting these findings. Furthermore, employing principal component analysis on the X-ray PDF and ssNMR data sets enabled us to gain invaluable insights into the chemical nature of the intermolecular interactions governing the drug-polymer interplay. These outcomes not only furnish crucial structural insights facilitating the comprehension of the underlying mechanisms governing the physicochemical stability but also underscore the efficacy of synergistically harnessing X-ray PDF and ssNMR techniques, complemented by robust modeling strategies, to achieve a high-resolution exploration of amorphous structures.

Molecular basis for cellular retinoic acid-binding protein 1 in modulating CaMKII activation

Introduction: Cellular retinoic acid (RA)-binding protein 1 (CRABP1) is a highly conserved protein comprised of an anti-parallel, beta-barrel, and a helix-turn-helix segment outside this barrel. Functionally, CRABP1 is thought to bind and sequester cytosolic RA. Recently, CRABP1 has been established as a major mediator of rapid, non-genomic activity of RA in the cytosol, referred to as "non-canonical" activity. Previously, we have reported that CRABP1 interacts with and dampens the activation of calcium-calmodulin (Ca2+-CaM)-dependent kinase 2 (CaMKII), a major effector of Ca2+ signaling. Through biophysical, molecular, and cellular assays, we, herein, elucidate the molecular and structural mechanisms underlying the action of CRABP1 in dampening CaMKII activation. Results: We identify an interaction surface on CRABP1 for CaMKII binding, located on the beta-sheet surface of the barrel, and an allosteric region within the helix segment outside the barrel, where both are important for interacting with CaMKII. Molecular studies reveal that CRABP1 preferentially associates with the inactive form of CaMKII, thereby dampening CaMKII activation. Alanine mutagenesis of residues implicated in the CaMKII interaction results in either a loss of this preference or a shift of CRABP1 from associating with the inactive CaMKII to associating with the active CaMKII, which corresponds to changes in CRABP1's effect in modulating CaMKII activation. Conclusions: This is the first study to elucidate the molecular and structural basis for CRABP1's function in modulating CaMKII activation. These results further shed insights into CRABP1's functional involvement in multiple signaling pathways, as well as its extremely high sequence conservation across species and over evolution.

Plasmon Resonance Energy Transfer Nanoruler for Pinpointing Molecular Distance and Interaction on the Living Cell Membrane

Developing novel strategies to measure nanoscale distance and molecular interaction on a living cell membrane is of great significance but challenging. Here we develop a model of a linker-free plasmon resonance energy transfer, termed "PRET nanoruler", which is composed of a single-sized nanogold-antibody conjugates donor (G26@antiCD71) and a fluorophore-labeled XQ-2d aptamer receptor (XQ-2d-Cy3), that produces a separation distance (r) dependent energy transfer (ηPRET). Both the theoretical finite element simulation and experiments evidence the observable PRET between single G26NPs and XQ-2d-Cy3. Regardless of the size of ηPRET, we could confirm r is less than 5 nm, the separation of two binding sites is in the range of 13.0-18.0 nm. There is a competitive binding of Tf and XQ-2d-Cy3 on CD71 receptors. PRET nanoruler realizes the estimation of the nanoscale separation distance, and determines the molecular interaction and competitive binding. It is an alternative tool for observing nanoscale single molecular events in the future.

Enhanced Oral Bioavailability of Rivaroxaban-Loaded Microspheres by Optimizing the Polymer and Surfactant Based on Molecular Interaction Mechanisms

This study aimed to develop microspheres using water-soluble carriers and surfactants to improve the solubility, dissolution, and oral bioavailability of rivaroxaban (RXB). RXB-loaded microspheres with optimal carrier (poly(vinylpyrrolidone) K30, PVP) and surfactant (sodium lauryl sulfate (SLS)) ratios were prepared. 1H NMR and Fourier transform infrared (FTIR) analyses showed that drug-excipient and excipient-excipient interactions affected RXB solubility, dissolution, and oral absorption. Therefore, molecular interactions between RXB, PVP, and SLS played an important role in improving RXB solubility, dissolution, and oral bioavailability. Formulations IV and VIII, containing optimized RXB/PVP/SLS ratios (1:0.25:2 and 1:1:2, w/w/w), had significantly improved solubility by approximately 160- and 86-fold, respectively, compared to RXB powder, with the final dissolution rates improved by approximately 4.5- and 3.4-fold, respectively, compared to those of RXB powder at 120 min. Moreover, the oral bioavailability of RXB was improved by 2.4- and 1.7-fold, respectively, compared to that of RXB powder. Formulation IV showed the highest improvement in oral bioavailability compared to RXB powder (AUC, 2400.8 ± 237.1 vs 1002.0 ± 82.3 h·ng/mL). Finally, the microspheres developed in this study successfully improved the solubility, dissolution rate, and bioavailability of RXB, suggesting that formulation optimization with the optimal drug-to-excipient ratio can lead to successful formulation development.

Investigation of the binding interactions mechanism between zein with chrysin by multispectroscopic techniques

As a natural carrier protein, zein was intensively studied for the construction of a flavonoid delivery system. Chrysin has presented superior tumor-resistant, anti-inflammatory, and anti-oxidation potentials among the flavonoid candidates in clinical practice. However, due to inadequate research, the binding mechanism and structural affinity of zein to chrysin are still indeterminate. Therefore, multispectral methods were employed to explore the molecular interaction of zein and chrysin in this work. These techniques showed that chrysin reduced the intrinsic fluorescence of zein via a static process and that the interaction between zein and chrysin was mainly driven spontaneously by hydrophobic forces. Additionally, the experimental results revealed the changed microenvironment in the vicinity of tyrosine and affected secondary structure in the presence of chrysin, indicating zein's conformation were altered by chrysin. This work provided comprehensive insight into the combination of plant-derived protein (zein) and flavonoids (chrysin) and helped rationalize the protection, transportation, and release of chrysin through a zein-based delivery system.

Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity

The study of molecular recognition patterns is crucial for understanding the interactions between inorganic (nano)particles and biomolecules. In this review we focus on hydroxyls (OH) exposed at the surface of oxide particles (OxPs) which can play a key role in molecular initiating events leading to OxPs toxicity. We discuss here the main analytical methods available to characterize surface OH from a quantitative and qualitative point of view, covering thermogravimetry, titration, ζ potential measurements, and spectroscopic approaches (NMR, XPS). The importance of modelling techniques (MD, DFT) for an atomistic description of the interactions between membranes/proteins and OxPs surfaces is also discussed. From this background, we distilled a new approach methodology (NAM) based on the combination of IR spectroscopy and bioanalytical assays to investigate the molecular interactions of OxPs with biomolecules and membranes. This NAM has been already successfully applied to SiO₂ particles to identify the OH patterns responsible for the OxPs' toxicity and can be conceivably extended to other surface-hydroxylated oxides.

Expression Pattern and Ligand Binding Characteristics Analysis of Chemosensory Protein SnitCSP2 from Sirex nitobei

Sirex nitobei is an important wood-boring wasp to conifers native to Asia, causing considerable economic and ecological damage. However, the current control means cannot achieve better efficiency, and it is expected to clarify the molecular mechanism of protein-ligand binding for effective pest control. This study analyzed the expression pattern of CSP2 in S. nitobei (SnitCSP2) and its features of binding to the screened ligands using molecular docking and dynamic simulations. The results showed that SnitCSP2 was significantly expressed in female antennae. Molecular docking and dynamic simulations revealed that SnitCSP2 bound better to the host plant volatile (+)-α-pinene and symbiotic fungal volatiles terpene and (-)-globulol than other target ligands. By the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, the free binding energies of the three complexes were calculated as -44.813 ± 0.189 kJ/mol, -50.446 ± 0.396 kJ/mol, and -56.418 ± 0.368 kJ/mol, and the van der Waals energy was found to contribute significantly to the stability of the complexes. Some key amino acid residues were also identified: VAL13, GLY14, LYS61, MET65, and LYS68 were important for the stable binding of (+)-α-pinene by SnitCSP2, while for terpenes, ILE16, ALA25, TYR26, CYS29, GLU39, THR37, and GLY40 were vital for a stable binding system. We identified three potential ligands and analyzed the interaction patterns of the proteins with them to provide a favorable molecular basis for regulating insect behavioral interactions and developing new pest control strategies.

Selective polypeptide ligand binding to the extracellular surface of the transmembrane domains of the class B GPCRs GLP-1R and GCGR

Crystal and cryo-EM structures of the glucagon-like peptide-1 receptor (GLP-1R) and glucagon receptor (GCGR) bound with their peptide ligands have been obtained with full-length constructs, indicating that the extracellular domain (ECD) is indispensable for specific ligand binding. This article complements these data with studies of ligand recognition of the two receptors in solution. Paramagnetic NMR relaxation enhancement measurements using dual labeling with fluorine-19 probes on the receptor and nitroxide spin labels on the peptide ligands provided new insights. The glucagon-like peptide-1 (GLP-1) was found to interact with GLP-1R by selective binding to the extracellular surface. The ligand selectivity toward the extracellular surface of the receptor was preserved in the transmembrane domain (TMD) devoid of the ECD. The dual labeling approach further provided evidence of cross-reactivity of GLP-1R and GCGR with glucagon and GLP-1, respectively, which is of interest in the context of medical treatments using combinations of the two polypeptides.

ISOTHERMAL TITRATION CALORIMETRY (ITC) AS A PROMISING TOOL IN PHARMACEUTICAL NANOTECHNOLOGY

Isothermal titration calorimetry (ITC) is a technique for evaluating the thermodynamic profiles of connection between two molecules, allowing the experimental design of nanoparticles systems with drugs and/or biological molecules. Taking into account the relevance of ITC, we conducted, therefore, an integrative revision of the literature, from 2000 to 2023, on the main purposes of using this technique in pharmaceutical nanotechnology. The search were carried out in the Pubmed, Sciencedirect, Web of Science, and Scifinder databases using the descriptors "Nanoparticles", "Isothermal Titration Calorimetry", and "ITC". We have observed that the ITC technique has been increasingly used in pharmaceutical nanotechnology, seeking to understand the interaction mechanisms in the formation of nanoparticles. Additionally, to understand the behavior of nanoparticles with biological materials (proteins, DNA, cell membranes, among others), thereby helping to understand the behavior of nanocarriers in vivo studies. As a contribution, we intended to reveal the importance of ITC in the laboratory routine, which is itself a quick and easy technique to obtain relevant results that help to optimize the nanosystems formulation process.

Molecular interaction between plants and Trichoderma species against soil-borne plant pathogens

Trichoderma spp. (Hypocreales) are used worldwide as a lucrative biocontrol agent. The interactions of Trichoderma spp. with host plants and pathogens at a molecular level are important in understanding the various mechanisms adopted by the fungus to attain a close relationship with their plant host through superior antifungal/antimicrobial activity. When working in synchrony, mycoparasitism, antibiosis, competition, and the induction of a systemic acquired resistance (SAR)-like response are considered key factors in deciding the biocontrol potential of Trichoderma. Sucrose-rich root exudates of the host plant attract Trichoderma. The soluble secretome of Trichoderma plays a significant role in attachment to and penetration and colonization of plant roots, as well as modulating the mycoparasitic and antibiosis activity of Trichoderma. This review aims to gather information on how Trichoderma interacts with host plants and its role as a biocontrol agent of soil-borne phytopathogens, and to give a comprehensive account of the diverse molecular aspects of this interaction.

Selenium Organic Content Prediction in Jengkol (Archidendron pauciflorum) and Its Molecular Interaction with Cardioprotection Receptors PPAR-γ, NF-κB, and PI3K

Selenium (Se) is a trace mineral found in plants with a distinct sulfuric odor that is cardioprotective and reported to have low toxicity. West Java, Indonesia, has a variety of plants with a distinct odor that are consumed raw, such as jengkol (Archidendron pauciflorum). This study is conducted to determine the Se content of jengkol using the fluorometric method, where the jengkol extract is separated, and the Se content is detected using high-pressure liquid chromatography (HPLC), combined with fluorometry. Two fractions with the highest Se concentration (A and B) are found and characterized using liquid chromatography mass spectrometry to predict the organic Se content by comparing the results with those in the external literature. The Se content of fraction (A) is found to be selenomethionine (m/z 198), gamma glutamyl-methyl-selenocysteine-(GluMetSeCys; m/z 313), and the Se-sulfur (S) conjugate of cysteine-selenoglutathione (m/z 475). Furthermore, these compounds are docked on receptors involved in cardioprotection. The receptors are peroxisome proliferator-activated receptor-γ (PPAR-γ), nuclear factor kappa-B (NF-κB), and phosphoinositide 3-kinase (PI3K/AKT). The interaction of receptor and ligan that has the lowest binding energy of the docking simulation is measured with molecular dynamic simulation. MD is performed to observe bond stability and conformation based on root mean square deviation, root mean square fluctuation, radius gyration, and MM-PBSA parameters. The results of the MD simulation show that the stability of the complex organic Se compounds tested with the receptors is lower than that of the native ligand, while the binding energy is lower than that of the native ligand based on the MM-PSBA parameter. This indicates that the predicted organic Se in jengkol, i.e., gamma-GluMetSeCys to PPAR-γ, gamma-GluMetSeCys AKT/PI3K, and Se-S conjugate of cysteine-selenoglutathione to NF-κB, has the best interaction results and provides a cardioprotection effect, compared to the molecular interaction of the test ligands with the receptors.

Molecular Interaction of Pea Glutelin and Lipophilic Bioactive Compounds: Structure-Binding Relationship and Nano-/Microcomplexation

This study investigated the impact of ionic strength and lipophilicity of bioactive compounds on their interaction with the alkaline soluble pea glutelin fraction (ASF) using the fluorescence quenching technique. A Stern-Volmer quenching constant, KD, of 8.9 ± 0.10, 5.3 ± 0.06, 4.0 ± 0.01, 1.1 ± 0.00, 0.9 ± 0.02, and 0.1 ± 0.00 (×104 M-1) was observed for curcumin-ASF (CuASF), astaxanthin-ASF (AsASF), cholecalciferol-ASF (ChASF), β-carotene-ASF (βCaASF), coenzyme Q10-ASF (Q10ASF), and β-sitosterol-ASF (βSiASF) complexes, respectively. An increase in ionic strength did not significantly change KD, the effective quenching constant K, and the bimolecular quenching rate constant KQ. However, it changed the mode of interaction of the ASF with cholecalciferol, β-carotene, coenzyme Q10, and β-sitosterol from static to static-dynamic quenching. Transmission electron microscopy showed that the morphology formed with protein (spherical nanocomplexes, microaggregates, or fiber-like particles) differed among the compounds. The favorable binding of CuASF, AsASF, ChASF, and βCaASF complexes provides stable matrices for formulating protein-based delivery systems for lipophilic nutraceuticals.

Characterization of Co-amorphous Carvedilol-Maleic Acid System Prepared by Solvent Evaporation

The aim of this study was to enhance the solubility and stability of the water-insoluble drug carvedilol (CAR) with maleic acid (MLE) to create a co-amorphous system by a solvent evaporation method. Phase diagrams of co-amorphous CAR-MLE, constructed from peak height in the Fourier-transform infrared (FTIR) spectra and the glass transition temperature (Tg) from differential scanning calorimetry (DSC) measurements, revealed that the optimal molar ratio of CAR to MLE was 2:1. The FTIR spectra indicated that the secondary amine-derived peak of CAR and the carboxy group-derived peak of MLE disappeared in the CAR:MLE (2:1) co-amorphous system. DSC measurements showed that the endothermic peaks associated with the melting of CAR and MLE disappeared and a Tg at 43 °C was apparent. Furthermore, the solubility of CAR tested using the shaking flask method for 24 h at 37 °C was 1.2 μg/mL, whereas that of the co-amorphous system was approximately three times higher, at 3.5 μg/mL. Finally, the stability was evaluated by powder- X-ray diffraction at 40 °C; no clear diffraction peaks originating from crystals were observed in the amorphous state until after approximately 3 months of storage. These results indicate that co-amorphization of CAR with MLE improved the solubility of CAR while maintaining its stability in an amorphous form.

Considerations on the Kinetic Processes in the Preparation of Ternary Co-Amorphous Systems by Milling

In non-strongly interacting co-amorphous systems, addition of a polymer, to further stabilize the co-amorphous systems, may influence the phase behavior between the components. In this study, the evolution of the composition of the amorphous phase in the ternary system carvedilol (CAR)-tryptophan (TRP)-hydroxypropylmethyl cellulose (HPMC) was investigated, based upon previously formed and characterized binary systems to which the third component was added (CAR - TRP + HPMC, CAR - HPMC + TRP and TRP - HPMC + CAR). Ball milling was used as the preparation method for all binary and ternary systems. The influence of the milling time on the co-amorphous systems was monitored by DSC and XRPD. Addition of HPMC reduced the miscibility of CAR with TRP due to hydrogen bond formation between CAR and polymer. These bonds became dominant for the interaction pattern. In addition, when CAR or TRP exceeded the miscibility limit in HPMC, phase separation and eventually crystallization of CAR and TRP was observed. All ternary co-amorphous systems eventually reached the same composition, albeit following different paths depending on the initially used binary system.

GAP-43 closely interacts with BDNF in hippocampal neurons and is associated with Alzheimer's disease progression

Introduction

Growth-associated protein 43 (GAP-43) is known as a neuronal plasticity protein because it is widely expressed at high levels in neuronal growth cones during axonal regeneration. GAP-43 expressed in mature adult neurons is functionally important for the neuronal communication of synapses in learning and memory. Brain-derived neurotrophic factor (BDNF) is closely related to neurodegeneration and synaptic plasticity during the aging process. However, the molecular mechanisms regulating neurodegeneration and synaptic plasticity underlying the pathogenesis and progression of Alzheimer's disease (AD) still remain incompletely understood.

Methods

Remarkably, the expressions of GAP-43 and BDNF perfectly match in various neurons in the Human Brain Atlas database. Moreover, GAP-43 and BDNF are highly expressed in a healthy adults' hippocampus brain region and are inversely correlated with the amyloid beta (Aβ), which is the pathological peptide of amyloid plaques found in the brains of patients with AD.

Results

These data led us to investigate the impact of the direct molecular interaction between GAP-43 and BDNF in hippocampal neuron fate. In this study, we show that GAP-43 and BDNF are inversely associated with pathological molecules for AD (Tau and Aβ). In addition, we define the three-dimensional protein structure for GAP-43 and BDNF, including the predictive direct binding sites via analysis using ClusPro 2.0, and demonstrate that the deprivation of GAP-43 and BDNF triggers hippocampal neuronal death and memory dysfunction, employing the GAP-43 or BDNF knock-down cellular models and 5XFAD mice.

Conclusion

These results show that GAP-43 and BDNF are direct binding partners in hippocampal neurons and that their molecular signaling might be potential therapeutic targets for AD.

Mammal comparative tendon biology: advances in regulatory mechanisms through a computational modeling

There is high clinical demand for the resolution of tendinopathies, which affect mainly adult individuals and animals. Tendon damage resolution during the adult lifetime is not as effective as in earlier stages where complete restoration of tendon structure and property occurs. However, the molecular mechanisms underlying tendon regeneration remain unknown, limiting the development of targeted therapies. The research aim was to draw a comparative map of molecules that control tenogenesis and to exploit systems biology to model their signaling cascades and physiological paths. Using current literature data on molecular interactions in early tendon development, species-specific data collections were created. Then, computational analysis was used to construct Tendon NETworks in which information flow and molecular links were traced, prioritized, and enriched. Species-specific Tendon NETworks generated a data-driven computational framework based on three operative levels and a stage-dependent set of molecules and interactions (embryo-fetal or prepubertal) responsible, respectively, for signaling differentiation and morphogenesis, shaping tendon transcriptional program and downstream modeling of its fibrillogenesis toward a mature tissue. The computational network enrichment unveiled a more complex hierarchical organization of molecule interactions assigning a central role to neuro and endocrine axes which are novel and only partially explored systems for tenogenesis. Overall, this study emphasizes the value of system biology in linking the currently available disjointed molecular data, by establishing the direction and priority of signaling flows. Simultaneously, computational enrichment was critical in revealing new nodes and pathways to watch out for in promoting biomedical advances in tendon healing and developing targeted therapeutic strategies to improve current clinical interventions.

Lowering levels of reelin in entorhinal cortex layer II-neurons results in lowered levels of intracellular amyloid-β

Projection neurons in the anteriolateral part of entorhinal cortex layer II are the predominant cortical site for hyper-phosphorylation of tau and formation of neurofibrillary tangles in prodromal Alzheimer's disease. A majority of layer II projection neurons in anteriolateral entorhinal cortex are unique among cortical excitatory neurons by expressing the protein reelin. In prodromal Alzheimer's disease, these reelin-expressing neurons are prone to accumulate intracellular amyloid-β, which is mimicked in a rat model that replicates the spatio-temporal cascade of the disease. Two important findings in relation to this are that reelin-signalling downregulates tau phosphorylation, and that oligomeric amyloid-β interferes with reelin-signalling. Taking advantage of this rat model, we used proximity ligation assay to assess whether reelin and intracellular amyloid-β directly interact during early, pre-plaque stages in anteriolateral entorhinal cortex layer II reelin-expressing neurons. We next made a viral vector delivering micro-RNA against reelin, along with a control vector, and infected reelin-expressing anteriolateral entorhinal cortex layer II-neurons to test whether reelin levels affect levels of intracellular amyloid-β and/or amyloid precursor protein. We analysed 25.548 neurons from 24 animals, which results in three important findings. First, in reelin-expressing anteriolateral entorhinal cortex layer II-neurons, reelin and intracellular amyloid-β engage in a direct protein-protein interaction. Second, injecting micro-RNA against reelin lowers reelin levels in these neurons, amounting to an effect size of 1.3-4.5 (Bayesian estimation of Cohen's d effect size, 95% credible interval). This causes a concomitant reduction of intracellular amyloid-β ranging across three levels of aggregation, including a reduction of Aβ42 monomers/dimers amounting to an effect size of 0.5-3.1, a reduction of Aβ prefibrils amounting to an effect size of 1.1-3.5 and a reduction of protofibrils amounting to an effect size of 0.05-2.1. Analysing these data using Bayesian estimation of mutual information furthermore reveals that levels of amyloid-β are dependent on levels of reelin. Third, the reduction of intracellular amyloid-β occurs without any substantial associated changes in levels of amyloid precursor protein. We conclude that reelin and amyloid-β directly interact at the intracellular level in the uniquely reelin-expressing projection neurons in anteriolateral entorhinal cortex layer II, where levels of amyloid-β are dependent on levels of reelin. Since amyloid-β is known to impair reelin-signalling causing upregulated phosphorylation of tau, our findings are likely relevant to the vulnerability for neurofibrillary tangle-formation of this entorhinal neuronal population.

Mycobacterium tuberculosis-macrophage interaction: Molecular updates

Mycobacterium tuberculosis (Mtb), the causative agent of Tuberculosis (TB), remains a pathogen of great interest on a global scale. This airborne pathogen affects the lungs, where it interacts with macrophages. Acidic pH, oxidative and nitrosative stressors, and food restrictions make the macrophage's internal milieu unfriendly to foreign bodies. Mtb subverts the host immune system and causes infection due to its genetic arsenal and secreted effector proteins. In vivo and in vitro research have examined Mtb-host macrophage interaction. This interaction is a crucial stage in Mtb infection because lung macrophages are the first immune cells Mtb encounters in the host. This review summarizes Mtb effectors that interact with macrophages. It also examines how macrophages control and eliminate Mtb and how Mtb manipulates macrophage defense mechanisms for its own survival. Understanding these mechanisms is crucial for TB prevention, diagnosis, and treatment.

Crystal structure of the sliding DNA clamp from the Gram-positive anaerobic bacterium Clostridioides difficile

The sliding DNA clamp is a ring-shaped protein that encircles DNA within its central channel. It binds to multiple proteins, such as DNA polymerases and DNA repair enzymes, and stimulates their enzymatic activities, thereby playing a crucial role in cell survival and proliferation. Accordingly, the bacterial clamp DnaN is considered to be a promising target for bacterial infection therapy. In this regard, 3D structures of DnaN from pathogenic bacteria are essential for the development of chemical compounds with antimicrobial activity. Here, the crystal structure of DnaN from a Gram-positive bacterium Clostridioides difficile, a human pathogen causing infectious diarrhoea, has been determined at 2.13 Å resolution. A comparison of the structures of DnaN from other bacteria indicates that the structural features of DnaN in terms of overall organization are essentially conserved within Gram-positive and Gram-negative bacteria. However, DnaN from C. difficile has structural differences in the potential binding pocket for partner proteins, implying a non-conventional interaction with its binding partners. Our findings will provide insight into the development of new therapies for C. difficile infection.

Size-dependent molecular interaction of nontraditional 2D antibiotics withStaphylococcus aureus

The application of nanomaterials for their antibacterial properties is the subject of many studies due to antibiotic resistance of pathogen bacteria and the necessity of omitting them from food and water resources. Graphene oxide (GO) is one of the most popular candidates for antibacterial application. However, the optimum condition for such an effect is not yet clear for practical purposes. To shed light on how GO and bacteria interaction depends on size, a wide range of GO flake sizes from hundreds of µm²going down to nano-scale as low as 10 N m²was produced. In anin-vitrosystematic study to inhibitStaphylococcus aureusgrowth, the correlation between GO flake size, thickness, functional group density, and antibacterial activity was investigated. The GO suspension with the average size of 0.05 µm², in the order of the size of the bacteria itself, had the best bacteriostatic effect onS. aureuswith the minimum inhibitory concentration value of 8 μg ml^-1, well within the acceptable range for practical use. The bacteriostatic effect was measured to be a 76.2% reduction of the colony count over 2 h of incubation and the mechanism of action was the wrapping and isolation of cells from the growth environment. Furthermore,in-vivoanimal studies revealed that 16 μg ml^-1of the optimum GO has efficient antibacterial performance against the methicillin-resistant strains of the bacteria with an enhanced wound healing rate and tensiometrial parameters which is important for realized targets.

Perilipin-2 promotes lipid droplet-plasma membrane interactions that facilitate apocrine lipid secretion in secretory epithelial cells of the mouse mammary gland

Secretory epithelial cells (sMEC) in mammary glands of lactating animals secrete lipids by a novel apocrine mechanism in which cytoplasmic lipid droplets (LD) contact and are enveloped by elements of the apical plasma membrane (APM) before being released into the lumen of the gland as membrane bound structures. The molecular properties of LD-APM contacts and the mechanisms regulating LD membrane envelopment and secretion are not fully understood. Perilipin-2 (Plin2) is a constitutive LD protein that has been proposed to tether LD to the APM through formation of a complex with the transmembrane protein, butyrophilin1a1 (BTN) and the redox enzyme, xanthine oxidoreductase (XOR). Using mice lacking Plin2 and physiological inhibition of apocrine lipid secretion, we demonstrate that LD-APM contact and envelopment are mechanistically distinct steps that they are differentially regulated by Plin2 and independent of LD secretion. We find that Plin2 is not required for formation of LD-APM contacts. However, it increases the percentage of LD that contact the APM and mediates enlargement of the LD-APM contact zone as LD undergo membrane envelopment. The effects of Plin2 LD-APM interactions are associated with increased abundances of BTN, XOR and Cidea, which are implicated as mediators of LD-APM contact formation, on membranes surrounding secreted LD, and with promotion of glycocalyx remodeling at LD-APM contact sites. We propose that Plin2 does not directly mediate contact between LD and the APM but acts by enhancing molecular interactions that stabilize LD-APM contacts and govern membrane envelopment of LD during apocrine lipid secretion. Plin2 does not appear to significantly affect the lipid content of milk in fully lactating animals, but it does increase lipid secretion at the onset of lactation in primaparous dams, which suggest a role in facilitating apocrine lipid secretion in sMEC during their initial transition to a secretory phenotype.

Influence of Water on Amorphous Lidocaine

Water is generally regarded as a universal plasticizer of amorphous drugs or amorphous drug-containing systems. A decrease in glass-transition temperature (T_g) is considered the general result of this plasticizing effect. A recent study exhibits that water can increase the T_g of amorphous prilocaine (PRL) and thus shows an anti-plasticizing effect. The structurally similar drug lidocaine (LID) might show similar interactions with water, and thus an anti-plasticizing effect of water is hypothesized to also occur in amorphous LID. However, the influence of water on the T_g of LID cannot be determined directly due to the very low stability of LID in the amorphous form. It is possible to predict the T_g of LID from a co-amorphous system of PRL-LID using the Gordon-Taylor equation. Interactions were observed between PRL and LID based on the deviations between the experimental T_gs and the T_gs calculated by the conventional use of the Gordon-Taylor equation. A modified use of the Gordon-Taylor equation was applied using the optimal co-amorphous system as a separate component and the excess drug as the other component. The predicted T_g of fully hydrated LID could thus be determined and was found to be increased by 0.9 ± 0.7 K compared with the T_g of water-free amorphous LID. It could be shown that water exhibited a small anti-plasticizing effect on LID.

The Molecular Mechanism of Propylene Glycol Monocaprylate on Skin Retention: Probing the Dual Roles on the Molecular Mobility and Collagen Connection in Roflumilast Cream

The present work was to construct a roflumilast (ROF) cream for the treatment of psoriasis and clarify the dual roles of propylene glycol monocaprylate (PGM) in both molecular mobility of the cream, and drug-skin miscibility via drug-PGM-ceramide and drug-PGM-collagen intermolecular interaction. The cream formulation was screened through the stability study and in vitro skin administration study, optimized by Plackett-Burman and Box-Behnken design, and finally verified by the in vivo tissue distribution study. PGM demonstrated a significant drug skin retention enhancement effect (R_{max in vivo} = 19.5 μg/g). It increased the molecular mobility of the oil phase of the cream by decreasing the molecular interaction of oil molecules proven by the rheology study (E_c = 3.73 × 10^-4 mJ·m^-3). More importantly, because of the good stratum corneum (SC) compatibility (∆H =  - 403.88 J/g), PGM promoted an orderly flow of SC lipids (X-ray scattering, ΔLPP = 1.18 nm) and entered the viable epidermis/dermis (VE/DE) in large quantities (R_PGM = 1186 μg/g), acting as a bridge to connect the drug to collagen through two H-bonds (Length_H-bond = 2.846 Å and 3.313 Å), thus increasing the miscibility of drug and VE/DE significantly (∆H =  - 310.10 J/g, E_mix = 21.66 kcal/mol). In this study, a ROF cream was developed successfully and the effect of PGM on the skin retention was clarified at molecular level.

Recombinant Antibody-Based and Computer-Aided Comprehensive Analysis of Antibody's Equivalent Recognition Mechanism of Alternariol and Alternariol Monomethyl Ether

Alternariol (AOH) and alternariol monomethyl ether (AME) are two main Alternaria mycotoxins that endanger human health. In this study, a single-chain antibody fragment (scFv) capable of equivalently and specifically recognizing AOH and AME was first expressed, and its equivalent recognition mechanism was discussed. According to molecular docking and dynamic simulation, the C9 site, which was always exposed outside the binding cavity, made the structural differences between AOH and AME negligible. Due to the high similarity of structures, AOH and AME interacted with almost the same amino acids on the scFv; thus, the same interaction mode and interaction force were produced. This was considered to be the most critical reason for the equivalent recognition. Thus, the exposure of common structures was considered a potential strategy to obtain the equivalent recognition antibodies, and C9 was considered the key site in the process of hapten modification. These results laid a theoretical foundation for further research on antibodies against Alternaria mycotoxins. It could promote the rapid detection of AOH and AME in food and provide a new idea for targeted preparation of antibodies that could recognize multiple hazards with similar structures.

Complex Crystal Structure Determination of Hsp90N-NVP-AUY922 and In Vitro Anti-NSCLC Activity of NVP-AUY922

New targeted chemotherapy agents greatly improved five-year survival in NSCLC patients, but which were susceptible to drug resistance. NVP-AUY922, terminated in phase II clinical trials, exhibited promising anti-NSCLC (non-small-cell lung cancer) activity targeting to Hsp90^N (heat shock protein), which demonstrated advantages in overcoming drug resistance as a broad-spectrum anti-cancer target. It was expected to develop novel anti-NSCLC drugs to overcome drug resistance by the structural optimization of NVP-AUY922. However, the absence of high-resolution complex crystal structure of Hsp90^N-NVP-AUY922 blocked the way. Herein, 1.59 Å-resolution complex crystal structure of Hsp90^N-NVP-AUY922 (PDB ID 6LTI) was successfully determined by X-ray diffraction. Meanwhile, there was a strong binding capability between NVP-AUY922 and its target Hsp90^N verified by TSA (ΔTm, -15.56 ± 1.78°C) and ITC (K _d, 5.10 ± 2.10 nM). Results by the complex crystal structure, TSA and ITC verified that NVP-AUY922 well accommodated in the ATP-binding pocket of Hsp90^N to disable the molecular chaperone activity of Hsp90. Therefore, NVP-AUY922 exhibited approving inhibitory activity on NSCLC cell line H1299 (IC₅₀, 2.85 ± 0.06 μM) by inhibiting cell proliferation, inducing cell cycle arrest and promoting cell apoptosis. At the basis of the complex crystal structure and molecular interaction analysis, thirty-two new NVP-AUY922 derivatives were further designed, and among which twenty-eight new ones display enhanced binding force with Hsp90^N by molecular docking evaluation. The results would promote anti-NSCLC new drug development to overcome drug resistance based on the lead compound NVP-AUY922.

Designing Ionic Liquids as the Solvent for Efficient and Stable Perovskite Solar Cells

As a green solvent, ionic liquids (ILs) are considered as a promising alternative to conventional polar aprotic solvents for the production of efficient and stable perovskite solar cells (PSCs). Moreover, with the use of IL solvents, perovskite films can be prepared without antisolvent treatments in an ambient environment instead of in a glovebox with inert gases, which simplifies the film manufacturing process and is favorable for industrialization production. However, the type of IL solvents that have been studied is limited, and the influence of IL molecular structures on the perovskite-film crystallization and device performance is not completely understood. In this work, four different ILs, methylammonium formate (MAF), methylammonium acetate (MAAc), methylammonium propionate (MAP), and mthylammonium isobutyrate (MAIB), are synthesized as the perovskite precursor solvents. The interaction between the functional groups of the synthesized solvents and Pb2+ in the precursor solution is studied, which has a direct impact on the morphology and crystallization of the deposited perovskite film. It is found that MAP solvent gives a high-quality perovskite film, which leads to the best photovoltaic performance with a champion PCE of 20.56% compared to the devices based on the other IL solvents. Moreover, the MAP-based device maintains 88% of its original PCE after 1000 h of storage in a N2 atmosphere, demonstrating excellent device stability. Therefore, it is concluded that MAP is the most suitable solvent for MAPbI3 films with respect to photovoltaic applications as compared to the other ILs.

Mannose-binding analysis and biological application of pradimicins

Pradimicins (PRMs) are an exceptional family of natural products that specifically bind d-mannose (Man). In the past decade, their scientific significance has increased greatly, with the emergence of biological roles of Man-containing glycans. However, research into the use of PRMs has been severely limited by their inherent tendency to form water-insoluble aggregates. Recently, we have established a derivatization strategy to suppress PRM aggregation, providing an opportunity for practical application of PRMs in glycobiological research. This article first outlines the challenges in studying Man-binding mechanisms and structural modifications of PRMs, and then describes our approach to address them. We also present our recent attempts toward the development of PRM-based research tools.

Biosynthesis of Silver Chloride Nanoparticles by Rhizospheric Bacteria and Their Antibacterial Activity against Phytopathogenic Bacterium Ralstonia solanacearum

Ralstonia solanacearum is the most destructive pathogen, causing bacterial wilt disease of eggplant. The present study aimed to develop green synthesis and characterization of silver chloride nanoparticles (AgCl-NPs) by using a native bacterial strain and subsequent evaluation of their antibacterial activity against R. solanacearum. Here, a total of 10 bacterial strains were selected for the biosynthesis of AgCl-NPs. Among them, the highest yield occurred in the synthesis of AgCl-NPs using a cell-free aqueous filtrate of strain IMA13. Ultrastructural observation revealed that the AgCl-NPs were spherical and oval with smooth surfaces and 5-35 nm sizes. XRD analysis studies revealed that these particles contained face-centered cubic crystallites of metallic Ag and AgCl. Moreover, FTIR analysis showed the presence of capping proteins, carbohydrates, lipids, and lipopeptide compounds and crystalline structure of AgCl-NPs. On the basis of phylogenetic analysis using a combination of six gene sequences (16S, gyrA, rpoB, purH, polC, and groEL), we identified strain IMA13 as Bacillus mojavensis. Three kinds of lipopeptide compounds, namely, bacillomycin D, iturin, and fengycin, forming cell-free supernatant produced by strain IAM13, were identified by MALDI-TOF mass spectrometry. Biogenic AgCl-NPs showed substantial antibacterial activity against R. solanacearum at a concentration of 20 µg/mL-1. Motility assays showed that the AgCl-NPs significantly inhibited the swarming and swimming motility (61.4 and 55.8%) against R. solanacearum. Moreover, SEM and TEM analysis showed that direct interaction of AgCl-NPs with bacterial cells caused rupture of cell wall and cytoplasmic membranes, as well as leakage of nucleic acid materials, which ultimately resulted in the death of R. solanacearum. Overall, these findings will help in developing a promising nanopesticide against phytopathogen plant disease management.

Kolaflavanone, a biflavonoid derived from medicinal plant Garcinia, is an inhibitor of mitotic kinesin Eg5

Mitotic kinesin Eg5 remains a validated target in antimitotic therapy because of its essential role in the formation and maintenance of bipolar mitotic spindles. Although numerous Eg5 inhibitors of synthetic origin are known, only a few inhibitors derived from natural products have been reported. In our study, we focused on identifying novel Eg5 inhibitors from medicinal plants, particularly Garcinia species. Herein, we report the inhibitory effect of kolaflavanone (KLF), a Garcinia biflavonoid, on the ATPase and microtubule-gliding activities of mitotic kinesin Eg5. Additionally, we showed the interaction mechanism between Eg5 and KLF via in vitro and in silico analyses. The results revealed that KLF inhibited both the basal and microtubule-activated ATPase activities of Eg5. The inhibitory mechanism is allosteric, without a direct competition with adenosine-5'-diphosphate for the nucleotide-binding site. KLF also suppressed the microtubule gliding of Eg5 in vitro. The Eg5-KLF model obtained from molecular docking showed that the biflavonoid exists within the α2/α3/L5 (α2: Lys111-Glu116 and Ile135-Asp149, α3: Asn206-Thr226; L5: Gly117-Gly134) pocket, with a binding pose comparable to known Eg5 inhibitors. Overall, our data suggest that KLF is a novel allosteric inhibitor of mitotic kinesin Eg5.

BLI-MS: Combining biolayer interferometry and mass spectrometry

Biolayer Interferometry (BLI) is a technology which allows to study the affinity between two interacting macro-molecules and to visualize their kinetic of interaction in real time. In this work we combine BLI interaction measurement with mass spectrometry in order to identify the proteins interacting with the bait. We provide for the first time the proof of concept of the feasibility of BLI-MS in complex biological mixtures. Data are available via ProteomeXchange with the identifier PXD019440. This article is protected by copyright. All rights reserved.

A Comprehensive Review on the Interaction of Milk Protein Concentrates with Plant-Based Polyphenolics

Functional properties and biological activities of plant-derived polyphenolic compounds have gained great interest due to their epidemiologically proven health benefits and diverse industrial applications in the food and pharmaceutical industry. Moreover, the food processing conditions and certain chemical reactions such as pigmentation, acylation, hydroxylation, and glycosylation can also cause alteration in the stability, antioxidant activity, and structural characteristics of the polyphenolic compounds. Since the (poly)phenols are highly reactive, to overcome these problems, the formulation of a complex of polyphenolic compounds with natural biopolymers is an effective approach. Besides, to increase the bioavailability and bioaccessibility of polyphenolic compounds, milk proteins such as whey protein concentrate, sodium caseinate, and milk protein concentrate act as natural vehicles, due to their specific structural and functional properties with high nutritional value. Therefore, milk proteins are suitable for the delivery of polyphenols to parts of the gastrointestinal tract. Therefore, this review reports on types of (poly)phenols, methods for the analysis of binding interactions between (poly)phenols-milk proteins, and structural changes that occur during the interaction.

Structural Equation Modeling of In silico Perturbations

Gene expression is controlled by multiple regulators and their interactions. Data from genome-wide gene expression assays can be used to estimate molecular activities of regulators within a model organism and extrapolate them to biological processes in humans. This approach is valuable in studies to better understand complex human biological systems which may be involved in diseases and hence, have potential clinical relevance. In order to achieve this, it is necessary to infer gene interactions that are not directly observed (i.e. latent or hidden) by way of structural equation modeling (SEM) on the expression levels or activities of the downstream targets of regulator genes. Here we developed an R Shiny application, termed “Structural Equation Modeling of In silico Perturbations (SEMIPs)” to compute a two-sided t-statistic (T-score) from analysis of gene expression data, as a surrogate to gene activity in a given human specimen. SEMIPs can be used in either correlational studies between outcome variables of interest or subsequent model fitting on multiple variables. This application implements a 3-node SEM model that consists of two upstream regulators as input variables and one downstream reporter as an outcome variable to examine the significance of interactions among these variables. SEMIPs enables scientists to investigate gene interactions among three variables through computational and mathematical modeling (i.e. in silico). In a case study using SEMIPs, we have shown that putative direct downstream genes of the GATA Binding Protein 2 (GATA2) transcription factor are sufficient to infer its activities in silico for the conserved progesterone receptor (PGR)-GATA2-SRY-box transcription factor 17 (SOX17) genetic network in the human uterine endometrium.

CBX7 is Dualistic in Cancer Progression Based on its Function and Molecular Interactions

Chromobox protein homolog 7 (CBX7) is a member of the Chromobox protein family and participates in the formation of the polycomb repressive complex 1(PRC1). In cells, CBX7 often acts as an epigenetic regulator to regulate gene expression. However, pathologically, abnormal expression of CBX7 can lead to an imbalance of gene expression, which is closely related to the occurrence and progression of cancers. In cancers, CBX7 plays a dual role; On the one hand, it contributes to cancer progression in some cancers by inhibiting oncosuppressor genes. On the other hand, it suppresses cancer progression by interacting with different molecules to regulate the synthesis of cell cycle-related proteins. In addition, CBX7 protein may interact with different RNAs (microRNAs, long noncoding RNAs, circular RNAs) in different cancer environments to participate in a variety of pathways, affecting the development of cancers. Furthermore, CBX7 is involved in cancer-related immune response and DNA repair. In conclusion, CBX7 expression is a key factor in the occurrence and progression of cancers.

Ochratoxin A-Induced Nephrotoxicity: Up-to-Date Evidence

Ochratoxin A (OTA) is a mycotoxin widely found in various foods and feeds that have a deleterious effect on humans and animals. It has been shown that OTA causes multiorgan toxicity, and the kidney is the main target of OTA among them. This present article aims to review recent and latest intracellular molecular interactions and signaling pathways of OTA-induced nephrotoxicity. Pyroptosis, lipotoxicity, organic anionic membrane transporter, autophagy, the ubiquitin-proteasome system, and histone acetyltransferase have been involved in the renal toxicity caused by OTA. Meanwhile, the literature reviewed the alternative or method against OTA toxicity by reducing ROS production, oxidative stress, activating the Nrf2 pathway, through using nanoparticles, a natural flavonoid, and metal supplement. The present review discloses the molecular mechanism of OTA-induced nephrotoxicity, providing opinions and strategies against OTA toxicity.

A Facile Strategy to Prepare Small Water Clusters via Interacting with Functional Molecules

Although small water clusters (SWCs) are important in many research fields, efficient methods of preparing SWCs are still rarely reported, which is mainly due to the lack of related materials and understanding of the molecular interaction mechanisms. In this study, a series of functional molecules were added in water to obtain small water cluster systems. The decreasing rate of the half-peak width in a sodium dodecyl sulfate (SDS)–water system reaches ≈20% at 0.05 mM from ¹⁷O nuclear magnetic resonance (NMR) results. Based on density functional theory (DFT) and molecular dynamics (MD) simulation calculation, it can be concluded that functional molecules with stronger negative electrostatic potential (ESP) and higher hydrophilicity have a stronger ability to destroy big water clusters. Notably, the concentrations of our selected molecule systems are one to two magnitudes lower than that of previous reports. This study provides a promising way to optimize aqueous systems in various fields such as oilfield development, protein stability, and metal anti-corrosion.

Understanding the Impact of Protein-Excipient Interactions on Physical Stability of Spray-Dried Protein Solids

Mannitol, leucine, and trehalose have been widely used in spray-dried formulations, especially for inhalation formulations. The individual contribution of these excipients on protein physical stability in spray-dried solids was studied here using bovine serum albumin (BSA) as a model protein. The spray-dried solids were characterized with scanning electron microscopy, powder X-ray diffraction, and solid-state Fourier-transform infrared spectroscopy to analyze particle morphology, crystallinity, and secondary structure change, respectively. Advanced solid-state characterizations were conducted with solid-state hydrogen-deuterium exchange (ssHDX) and solid-state nuclear magnetic resonance (ssNMR) to explore protein conformation and molecular interactions in the context of the system physical stability. Trehalose remained amorphous after spray-drying and was miscible with BSA, forming hydrogen bonds to maintain protein conformation, whereby this system showed the least monomer loss in the stability study. As indicated by ssNMR, both crystalline and amorphous forms of mannitol existed in the spray-dried BSA-mannitol solids, which explained its partial stabilizing effect on BSA. Leucine showed the strongest crystallization tendency after spray-drying and did not provide a stabilizing effect due to substantial immiscibility and phase separation with BSA as a result of crystal formation. This work showed novel applications of ssNMR in examining protein conformation and protein-excipient interaction in dry formulations. Overall, our results demonstrate the pivotal role of advanced solid-state characterization techniques in understanding the physical stability of spray-dried protein solids.

Effect of Cedrus deodara extract on the physiochemical and sensory properties of salted meat and its action mechanism

The effect of pine needle extract from Cedrus deodara (PNE) on the quality of salted meat was reported, and its action mechanism was further investigated. With the treatment of PNE, the physicochemical properties of salted meat were improved. The peroxide value decreased from 16.18 to 6.78 mmol O₂ /kg, while the thiobarbituric acid value decreased from 0.79 to 0.40 mg MDA/kg. Moreover, the salted meat with PNE also had the better texture, color, and volatile compositions. The 0.2% PNE group showed the highest ΔE value (63.16 ± 0.56), hardness (813.5 ± 48.7 g), and volatility (45.86 ± 0.39), while the control group showed the lowest ΔE value (43.92 ± 2.13), hardness (515.8 ± 17.3 g) and volatility (29.97 ± 0.56). In addition, with the analysis of fluorescence and circular dichroism spectroscopy, the spatial structures of myofibrillar protein (MP) in salted meat were obviously changed by PNE. Meanwhile, methylconiferin, 1-O-feruloyl-β-D-glucose, nortrachelogenin, secoxyloganin, 1-O-(4-coumaroyl)-β-D-glucose and pelargonidin-3-O-glucoside were identified from PNE. Furthermore, according to the analysis of molecular docking, hydrogen bond, hydrophobic force, and electrostatic force were obtained as the main molecular forces between MP and the phenolic compounds of PNE, while arginine, glutamic acid, and glycine residues were the main binding sites. All results suggested that PNE might be a potential candidate to improve the quality of salted meat in the food industry. PRACTICAL APPLICATION: The quality deterioration of meat may not only affect its further processing and consumption but also may lead to some food safety problems. In present study, PNE exhibited the fine capability to inhibit the oxidation of meat, while it could ameliorate the texture, color, and physicochemical properties of meat due to its tightly interaction with myofibrillar protein. All result suggested that PNE could be potentially utilized to improve the quality of meat in food industry.

Loss of immobilized water and intense protein aggregation responsible for quality deterioration of ready to eat firm tofu

The influence of high-temperature treatment (100-120°C, 15 min) on the texture, color, and water-holding capacity of tofu gels was investigated. As the temperature increasing, the hardness and chewiness as well as the values of redness a and yellowness b increased gradually, while the water content and the lightness L value reduced progressively, and these variations were more pronounced at 115 or 120°C. Low field nuclear magnetic resonance showed that the loss of T₂₂ water led to the decrease of the water content. Scanning electron microscope revealed that the micropore in gels decreased after heating, and almost entirely disappeared at 120°C. Further analysis by SDS-PAGE indicated the soy protein aggregation formed via disulfide linkage was observed in the thermal treated tofu gels, and nondisulfide linkage might also be occurred as temperature reached 110°C or higher. The quality deterioration may be attributed to immobilized water loss combined with the protein aggregation.

Fluorination Enables Tunable Molecular Interaction and Photovoltaic Performance in Non-Fullerene Solar Cells Based on Ester-Substituted Polythiophene

Owing to the advantages of low synthetic cost and high scalability of synthesis, polythiophene and its derivatives (PTs) have been of interest in the community of organic photovoltaics (OPVs). Nevertheless, the typical efficiency of PT based photovoltaic devices reported so far is much lower than those of the prevailing push-pull type conjugated polymer donors. Recent studies have underscored that the excessively low miscibility between PT and nonfullerene acceptor is the major reason accounting for the unfavorable active layer morphology and the inferior performance of OPVs based on a well-known PT, namely PDCBT-Cl and a non-halogenated nonfullerene acceptor IDIC. How to manipulate the miscibility between PT and acceptor molecule is important for further improving the device efficiency of this class of potentially low-cost blend systems. In this study, we introduced different numbers of F atoms to the end groups of IDIC to tune the intermolecular interaction of the hypo-miscible blend system (PDCBT-Cl:IDIC). Based on calorimetric, microscopic, and scattering characterizations, a clear relationship between the number of F atoms, miscibility, and device performance was established. With the increased number of F atoms in IDIC, the resulting acceptors exhibited enhanced miscibility with PDCBT-Cl, and the domain sizes of the blend films were reduced substantially. As a result, distinctively different photovoltaic performances were achieved for these blend systems. This study demonstrates that varying the number of F atoms in the acceptors is a feasible way to manipulate the molecular interaction and the film morphology toward high-performance polythiophene:nonfullerene based OPVs.

Role of Surfactant Micellization for Enhanced Dissolution of Poorly Water-Soluble Cilostazol Using Poloxamer 407-Based Solid Dispersion via the Anti-Solvent Method

This study aimed to investigate the role of micellization of sodium lauryl sulfate (SLS) in poloxamer 407 (POX)-based solid dispersions (POX-based SDs) using the anti-solvent method in enhancing the dissolution rate of practically water-insoluble cilostazol (CLT). Herein, SLS was incorporated into CLT-loaded SDs, at a weight ratio of 50:50:10 of CLT, POX, and SLS by three different methods: anti-solvent, fusion (60 °C), and solvent (ethanol) evaporation. The SDs containing micellar SLS in the anti-solvent method were superior in the transformation of the crystalline form of the drug into a partial amorphous state. It was notable that there was an existence of a hydrophobic interaction between the surfactant and the hydrophobic regions of polymer chain via non-covalent bonding and the adsorption of micellar SLS to the POX-based SDs matrix. Moreover, SLS micellization via the anti-solvent method was effectively interleaved in SDs and adhered by the dissolved CLT, which precluded drug particles from aggregation and recrystallization, resulting in improved SD wettability (lower contact angle) and reduced particle size and dissolution rate. In contrast, SDs without micellar SLS prepared by the solvent method exerted drug recrystallization and an increase of particle size, resulting in decreased dissolution. Incorporation of surfactant below or above critical micellar concentration (CMC) in SDs using the anti-solvent method should be considered in advance. Dissolution results showed that the pre-added incorporation of micellar SLS into POX-based SDs using the anti-solvent method could provide a way of a solubilization mechanism to enhance the dissolution rate of poorly water-soluble drugs.

Mutation Signatures and In Silico Docking of Novel SARS-CoV-2 Variants of Concern

One year since the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China, several variants of concern (VOC) have appeared around the world, with some variants seeming to pose a greater thread to public health due to enhanced transmissibility or infectivity. This study provides a framework for molecular characterization of novel VOC and investigates the effect of mutations on the binding affinity of the receptor-binding domain (RBD) to human angiotensin-converting enzyme 2 (hACE2) using in silico approach. Notable nonsynonymous mutations in RBD of VOC include the E484K and K417N/T that can be seen in South African and Brazilian variants, and N501Y and D614G that can be seen in all VOC. Phylogenetic analyses demonstrated that although the UK-VOC and the BR-VOC fell in the clade GR, they have different mutation signatures, implying an independent evolutionary pathway. The same is true about SA-VOC and COH-VOC felling in clade GH, but different mutation signatures. Combining molecular interaction modeling and the free energy of binding (FEB) calculations for VOC, it can be assumed that the mutation N501Y has the highest binding affinity in RBD for all VOC, followed by E484K (only for BR-VOC), which favors the formation of a stable complex. However, mutations at the residue K417N/T are shown to reduce the binding affinity. Once vaccination has started, there will be selective pressure that would be in favor of the emergence of novel variants capable of escaping the immune system. Therefore, genomic surveillance should be enhanced to find and monitor new emerging SARS-CoV-2 variants before they become a public health concern.

Label-free, mass-sensitive single-molecule imaging using interferometric scattering microscopy

Single-molecule imaging has mostly been restricted to the use of fluorescence labelling as a contrast mechanism due to its superior ability to visualise molecules of interest on top of an overwhelming background of other molecules. Recently, interferometric scattering (iSCAT) microscopy has demonstrated the detection and imaging of single biomolecules based on light scattering without the need for fluorescent labels. Significant improvements in measurement sensitivity combined with a dependence of scattering signal on object size have led to the development of mass photometry, a technique that measures the mass of individual molecules and thereby determines mass distributions of biomolecule samples in solution. The experimental simplicity of mass photometry makes it a powerful tool to analyse biomolecular equilibria quantitatively with low sample consumption within minutes. When used for label-free imaging of reconstituted or cellular systems, the strict size-dependence of the iSCAT signal enables quantitative measurements of processes at size scales reaching from single-molecule observations during complex assembly up to mesoscopic dynamics of cellular components and extracellular protrusions. In this review, I would like to introduce the principles of this emerging imaging technology and discuss examples that show how mass-sensitive iSCAT can be used as a strong complement to other routine techniques in biochemistry.

Enantioselective Mixed Matrix Membranes for Chiral Resolution

Most pharmaceuticals are stereoisomers that each enantiomer shows dramatically different biological activity. Therefore, the production of optically pure chemicals through sustainable and energy-efficient technology is one of the main objectives in the pharmaceutical industry. Membrane-based separation is a continuous process performed on a large scale that uses far less energy than the conventional thermal separation process. Enantioselective polymer membranes have been developed for chiral resolution of pharmaceuticals; however, it is difficult to generate sufficient enantiomeric excess (ee) with conventional polymers. This article describes a chiral resolution strategy using a composite structure of mixed matrix membrane that employs chiral fillers. We discuss several enantioselective fillers, including metal-organic frameworks (MOFs), covalent organic frameworks (COFs), zeolites, porous organic cages (POCs), and their potential use as chiral fillers in mixed matrix membranes. State-of-the-art enantioselective mixed matrix membranes (MMMs) and the future design consideration for highly efficient enantioselective MMMs are discussed.

Complex Crystal Structure Determination and in vitro Anti-non-small Cell Lung Cancer Activity of Hsp90 N Inhibitor SNX-2112

SNX-2112, as a promising anticancer lead compound targeting heat shock protein 90 (Hsp90), absence of complex crystal structure of Hsp90^N-SNX-2112 hindered further structural optimization and understanding on molecular interaction mechanism. Herein, a high-resolution complex crystal structure of Hsp90^N-SNX-2112 was successfully determined by X-ray diffraction, resolution limit, 2.14 Å, PDB ID 6LTK, and their molecular interaction was analyzed in detail, which suggested that SNX-2112 was well accommodated in the ATP-binding pocket to disable molecular chaperone activity of Hsp90, therefore exhibiting favorable inhibiting activity on three non–small cell lung cancer (NSCLC) cell lines (IC₅₀, 0.50 ± 0.01 μM for A549, 1.14 ± 1.11 μM for H1299, 2.36 ± 0.82 μM for H1975) by inhibited proliferation, induced cell cycle arrest, and aggravated cell apoptosis. SNX-2112 exhibited high affinity and beneficial thermodynamic changes during the binding process with its target Hsp90^N confirmed by thermal shift assay (TSA, ΔTm, and −9.51 ± 1.00°C) and isothermal titration calorimetry (K_d, 14.10 ± 1.60 nM). Based on the complex crystal structure and molecular interaction analysis, 32 novel SNX-2112 derivatives were designed, and 25 new ones displayed increased binding force with the target Hsp90^N verified by molecular docking evaluation. The results would provide new references and guides for anti-NSCLC new drug development based on the lead compound SNX-2112.

Screening ,development of Transglutaminase-2 Inhibitors and its derivative as anti-lung cancer agent by insilico and invitro approach

AIM

Screening and development of TG2 inhibitors as anti lung cancer agent.

BACKGROUND

Transglutaminase 2 (TG2) is multifunctional and ubiquitously expressed protein from transglutaminase family. It takes part in various cellular processes and plays an important role in the pathogenesis of autoimmune, neurodegerative and also cancer.

OBJECTIVE

The of proposed study is to focused on screening of potent inhibitors of TG2 by in-silico method and synthesis its derivative as well as analysis of its activity by invitro approach.

MATERIAL AND METHODS

Molecular docking studies have been carried on the different classes of TG2 inhibitors against the target protein. Nearly thirty TG2 inhibitors were selected from literature and docking was performed against transglutaminase 2. The computational ADME property screening was also carried out to check their pharmacokinetic properties. The compounds which exhibited positive ADME properties with good interaction with possessing least binding energy were further validated for their anti-lung cancer inhibition property against A549 cell lines by cytotoxicity studies.

RESULTS

The results of present study indicate that the docked complex formed by cystamine showed better binding affinity towards target protein so, this derivative of cystamine is formed using 2,5 dihydrobenzoic acid. Invitro results revealed that both molecule proved good cytotoxic agent against A549 lung cancer (875.10, 553.22 µg/ml) respectively. Further its activity should be validated on TG2 expressing lung cancer.

CONCLUSION

Cystamine and its derivative can be act as potential therapeutic target for lung cancer but further its activity should be validated on TG2 expressing lung cancer.

High-Efficiency Thickness-Insensitive Organic Solar Cells with an Insulating Polymer

Achieving high-efficiency thick-film bulk heterojunction (BHJ) organic solar cells (OSCs) with thickness-independent power conversion efficiencies (PCEs) in a wide thickness range is still a challenge for the roll-to-roll printing techniques. The concept of diluting the transport sites within BHJ films with insulating polymers can effectively eliminate charge trapping states and optimize the charge transport. Herein, we first adopted the concept with insulating polypropylene (PP) in the efficient non-fullerene system (PM6:Y6) and demonstrated its potential to fabricate thick-film OSCs. The PP can form an insulating matrix prior to PM6 and Y6 within the BHJ film, resulting in an enhanced molecular interaction and isolated charge transport by expelling Y6 molecules. We thus observed reduced trap state density and improved charge transport properties in the PP-blended device. At around 300 nm, the PM6:Y6:PP device enjoys a high PCE of 15.5% and achieves over 100% of the efficiency of the optimal thin-film device, which is significantly improved compared to the binary PM6:Y6 counterpart. This research promotes an effective strategy with insulating polymers and provides knowledge of commercial production with response to the roll-to-roll technique demands.