Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Immunostimulatory effects of isomalto/malto-polysaccharides via TLR2 and TLR4 in preventing doxycycline-induced cytokine loss

Isomalto/malto-polysaccharides (IMMPs) are α-glucans with prebiotic potential used as food ingredients. However, their ability to exert direct cellular effects remains unknown. IMMPs may enhance immunity by activating toll-like receptors (TLRs), key for defense against pathogens. Doxycycline is an antibiotic that requires an effective immune function but paradoxically has immune-attenuating effects by reducing TLR2 activity, potentially increasing antibiotic needs. We hypothesize that IMMPs are recognized by various cell surface TLRs, leading to the activation of the NF-κB signaling pathway. Furthermore, IMMPs' immune-stimulating effect could prevent the doxycycline-induced reduction of TLR2 activity in immune cells. IMMPs activated TLR2, increasing NF-κB signaling by 3.42- and 6.37-fold at 1 and 2 mg/mL, respectively. TLR4 activation increased 5.47-, 7.39-, and 8.34-fold at 0.5, 1, and 2 mg/mL. IMMPs enhanced IL-8, TNFα, and IL1-RA production in THP-1 monocytes. Additionally, preincubation of macrophages with IMMPs enhanced cytokine production and partially prevented doxycycline-induced cytokine reduction in response to TLR2 activation. Molecular docking analyses support IMMPs and doxycycline binding to these TLRs. These findings suggest that IMMPs stimulate immunity via TLR2 and TLR4, partially mitigating doxycycline's adverse effects. This provides a dietary strategy to enhance pathogen clearance, reduce antibiotic needs, and support immune health.

Influence of terminal moiety on PCE of DSSCs: An In Silico study based on triazatruxene-benzothiadiazole dye

Our study utilized an experimentally synthesized dye as a reference molecule, employing a donor-π linker-acceptor (D-π-A) framework for organic solar cells. The molecule featured a triazatruxene group linked with alkyl branches as the donor and ethynyl benzoic acid as the acceptor, connected through a derivative of benzothiadiazole as the π linker. To improve optoelectronic and photovoltaic properties, ten theoretically designed dyes (ZA1-ZA10) are proposed, differing from the reference (R) by modifying the terminal acceptor moiety. Various quantum analyses, including frontier molecular orbitals, optical properties, reorganization energies, binding energies, transition density matrices (TDM), molecular electrostatic potential (MEP), dipole moment, and density of states were carried out at DFT/B3LYP/6-31G(d,p). Ground state geometries revealed a co-planar morphology in ZA1-ZA10, facilitating efficient charge transportation. TDM and MEP illustrated improved electronic transitions in the excited states. Computational analyses revealed superior photovoltaic properties of ZA1-ZA10. Notably, ZA5 exhibited the most significant redshift (1021 nm) in absorption, lowest bandgap (1.44 eV), smallest transition energy (1.21 eV), least binding energy (0.23 eV), and improved charge mobilities. Results from the adsorption of ZA1-ZA10 on the TiO2 layer confirmed their anchoring potential and effective injection of electrons to anatase (TiO2)9. These significant outcomes promise the potential and novelty of our designed dyes for higher power conversion efficiencies (PCE) in dye-sensitized solar cells (DSSCs).

Experimental and computational insights into starch pasting as influenced by amino acids with different R-groups

The effects of amino acids with different R-groups, namely glutamic acid (GLU), glutamine (GLN), and theanine (THE), on the pasting and structure properties of corn starch (CS) were investigated. During gelatinization, GLU decreased viscosity of CS. GLN and THE increased pasting enthalpy of CS from 7.62 to 8.72 and 9.50 J/g, respectively. All starch-amino acid systems had higher storage and loss modulus. Amino acids could adhere to starch granule surface. After co-gelatinization, GLU increased short-range order degree of starch, while GLN and THE decreased. Both infrared spectroscopy and quantum computation showed that non-covalent interaction occurred between amino acids and starch. Molecular dynamics revealed that the interaction between GLU and starch weakened hydrogen bonding between starch and water, promoting cross-linking between starch chains. GLN and THE changed dihedral angle torsion of glycoside bonds, and mainly interacted with starch by electrostatic interaction (50.06 kJ/mol) and van der Waals force (50.30 kJ/mol), respectively.

Highly cost-effective wheat starch-stearic acid complexes enabled by microwave processing: Structural properties, anti-digestion, and molecular dynamics simulation

Microwave (MW) heating shows higher efficiency in preparing wheat starch-stearic acid (WS-SA) complexes than the traditional water bath (WB) heating method, while the detailed "time-energy-quality" evaluations and the potential anti-digestion mechanism of the MW-processed WS-SA remain further exploration. In this study, 95 % time cost and 73 % energy consumption were saved when using MW processing WS-SA, and the MW-processed complexes were verified to show significantly higher relative crystallinity, short-range ordered structure degree, thermal stability, complex index, and resistant starch content. Molecular dynamics (MD) simulation demonstrated that MW treatment notably facilitated the binding rate of amylose and SA molecules, generating a tight and stable helical structure through hydrogen bonds and van der Waals forces. Analyses of solvent-accessible surface area and water status cross-verified that the denser structure could endow the MW-processed complexes with higher resistance to water solvation effects and correspondingly reduce the water mobility for enzymatic hydrolysis reactions, ultimately making the MW-processed complexes more undigestible. This study provides a further understanding of the anti-digestion mechanisms of the MW-processed WS-SA from the molecular level, and it is expected that the current work could attract more concerns to the highly cost-effective MW heating method for processing starchy food.

A promising class of antiprotozoal agents, design and synthesis of novel Pyrimidine-Cinnamoyl hybrids

Malaria, caused by parasitic protozoans of the Plasmodium genus, continues to be one of the greatest global health crises, especially in Africa. The emergence of antimalarial drug resistance continues to be a health problem necessitating an urgent need for alternative and cost-effective antimalarials. Using a molecular hybridization approach, we report the design and synthesis of an efficacious novel class of antiprotozoal agents; (E)-1-(4-(4,6-diphenylpyrimidin-2-yl)piperazin-1-yl)-3-phenyl prop-2-en-1-one derivatives (8a-r). The in vitro inhibitory activity of the synthesized compounds was evaluated against the NF54 chloroquine-sensitive strain of Plasmodium falciparum. From the antiprotozoal screening, three compounds displayed propitious activity with IC50 values (0.18-0.21 μM), using quinine and chloroquine as standard antimalarials. Compounds 8o and 8l emerged as the most potent candidates with IC50 values of 0.18 ± 0.02 μM and 0.21 ± 0.001 μM with an associated good safety index of 18.59 and 16.75 to human kidney epithelial (HEK293) cells, respectively. The synthesized analogues present a new chemical architecture structurally unrelated to the current regime of antimalarial drugs, representing a valid strategy to combat resistance in P. falciparum species to current commercial drugs. We further investigated the binding affinities of the compounds against recombinant forms of two P. falciparum heat shock protein 70 homologues; PfHsp70-1 and PfHsp70-z, both of which are essential and promising druggable candidates. Compound 8l exhibited the highest binding affinity for PfHsp70-1 and PfHsp70-z. Furthermore, molecular docking revealed that compounds 8k, 8l, 8m, and 8o exhibited better fitness to PfHsp70-1, with compounds 8l and 8o showing the highest binding affinity of -10.5 kcal/mol and -10.1 kcal/mol, respectively. Therefore, it can be speculated that PfHsp70-1 may be a possible target of some of the inhibitors tested in this study. The presence of electron-donating groups on the phenyl ring of 4,6-pyrimidine moiety and cinnamoyl group demonstrated a positive correlation between the observed computational data and the biological activity. Taken together, this paper demonstrates the importance of using the molecular hybridization approach in the development of newer cinnamoyl clubbed with 4,6-diphenyl pyrimidine hybrids as potential antiprotozoal agents.

Database, prediction, and antibacterial research of astringency based on large language models

Astringency, a sensory experience causing mouth dryness, significantly impacts the taste of foods such as wine and tea, and astringent molecules may exhibit antibacterial properties. Traditional methods for predicting astringency are costly, and the connection between astringency and antibacterial activity remains largely unexplored. In this study, we present a pioneering computational approach that includes: (1) the creation of the first comprehensive astringency database comprising 238 molecules; (2) the development of a Ligand-Based Prediction (LBP) framework that combines large language models, deep learning, and traditional machine learning for enhanced molecular and peptide prediction; (3) an astringency predictor achieving 0.95 accuracy and 0.90 AUC, validated through electronic tongue measurements; (4) antibacterial predictors for molecules and peptides with accuracies of 0.92 and 0.88, respectively, revealing that 51 % of astringent molecules possess antibacterial properties; (5) accessibility of these predictors via the AstringentPD and ABPD web servers. This work not only enhances the understanding of taste-related molecules but also elucidates the relationship between astringency and antibacterial properties, setting the stage for future explorations in food science and medicinal applications.

Atomistic Simulations and Analysis of Peripheral Membrane Proteins with Model Lipid Bilayers

All-atom molecular dynamics (AAMD) is a computational technique that predicts the movement of particles based on the intermolecular forces acting on the system. It enables the study of biological systems at atomic detail, complements observations from experiments, and can help the selection of experimental targets. Here, we describe the applications of MD simulations to study the interaction between peripheral membrane proteins and lipid bilayers. Specifically, we provide step-by-step instructions to set up MD simulations to study the binding and interaction of ALPS, the amphipathic helix of the lipid transport protein Osh4, and Thanatin, an antimicrobial peptide with model membranes. We describe examples of systems built with fully atomistic lipid tails and those truncated with the highly-mobile-membrane-mimetic method to enhance conformational sampling. We also comment on the importance of lipid diversity, molecular resolution, and best practices for constructing, running, and analyzing protein-lipid simulation systems. In this second edition, we include a brief discussion on alternative approaches and software to construct protein-membrane coordinate systems, as well as analysis tools and practices that have become relevant to examining protein-lipid interactions since the first edition of this chapter.

Gene silencing of Histidyl-tRNA synthetase in Leishmania donovani promastigotes inhibits parasite growth and reduces virulence: A comprehensive computational and in vitro study

The majority of anti-leishmanial drugs used for treating trypanosomatid parasites help to reduce human morbidity and mortality. However, parasites have developed drug resistance, which has made it challenging to treat leishmaniasis. Therefore, new drugs and drug targets need to be identified. Protein synthesis is a crucial anabolic mechanism necessary for parasite survival. Histidyl-tRNA synthetase (HisRS) is an essential enzyme that is required for histidine incorporation into proteins. Recent studies on HisRS have shown differences between trypanosomatid HisRS and human HisRS, which could lead to the development of trypanosomatid HisRS structure-based inhibitors. This study aims to determine the role of L. donovani HisRS (LdHisRS) in parasite growth and virulence in vitro using RNAi. The silencing effect of LdHisRS expression was determined using qPCR. The results showed that after 24 and 48 h of incubation with 90 ng siRNAs, LdHisRS mRNA expression levels were significantly reduced by ∼3.14-fold and ∼3.90-fold, respectively. SiRNA-treated parasites also exhibited ∼46.6 % delayed growth and ∼47 % reduced virulence. Additionally, homology modeling, virtual screening, and molecular docking studies were performed with potential inhibitors that have significant suppressive activity in bacteria, fungi, and viruses. Halofuginone was found to have the best binding affinity of -9.09 kcal/mol as a potent inhibitor against LdHisRS. The molecular dynamics (MD) results showed that halofuginone could interact with the various active site segments, potentially blocking substrate access. The data on gene silencing through siRNA suggests that LdHisRS is essential for the parasite's growth and survival. The computational findings could lead to the development of a potent ligand (halofuginone) as a future anti-leishmanial drug, paving the way for an effective therapeutic treatment.

Photoaging effects on polyethylene microplastics: Structural changes and chlorpyrifos adsorption

Microplastics (MP) are a global concern due to their small size, insolubility in water, and non-degradable nature, and long-term environmental persistence. Weathering processes, such as ultraviolet (UV) radiation, can alter their properties, enhancing their ability to absorb pollutants or release harmful substances, such as pesticides, which is also an environmental concern, thereby complicating their environmental impact and mitigation efforts. This study investigates the impact of UVB-induced photoaging on polyethylene (PE) microplastics and their sorption behavior towards the pesticide chlorpyrifos (CP). PE microplastics were exposed to varying UVB aging durations, leading to significant changes in their physicochemical and morphological properties. The sorption experiments revealed that aged microplastics exhibited increased affinity for CP, with adsorption capacity rising by 17.9% compared to pristine PE. This enhanced adsorption was attributed to the (1) introduction of oxygen-containing functional groups, facilitating the formation of hydrogen bonds between the microplastic surface and surrounding water molecules, thereby contributing to the adsorption of CP; (2) formation of irregular micropores and surface roughness, potentially providing ample sites for pesticide adsorption and (3) reduction in crystallinity from 35% to 30%, which favors the sorption of hydrophobic organic pollutants. Density Functional Theory (DFT) calculations supported these findings by showing changes in the electronic structure of PE that facilitate interactions with CP. These results provide critical insights into the environmental behavior of aged microplastics and their potential to adsorb hazardous chemicals, underscoring the need for further research on the environmental impact of microplastic aging.

Cysteines in β-lactoglobulin affects its interfacial adsorption and protein film stabilization

HYPOTHESIS

Disulfide bonds in proteins are strong chemical bonds forming the secondary and tertiary structure like in the dairy protein β-lactoglobulin. We hypothesize that the partial or complete removal of disulfide bonds affects the structural rearrangement of proteins caused by intra- and intermolecular interactions that in turn define the interfacial activity of proteins at oil/water interfaces. The experimental and numerical investigations contribute to the mechanistic understanding of the structure-function relationship, especially for the interfacial adsorption behavior of proteins.

EXPERIMENTAL AND NUMERICAL

Systematically, the 5 cysteines of β-lactoglobulin were recombinantly exchanged by alanine. First, the protein structure of the variants in bulk was analyzed with Fourier-transform-infrared-spectroscopy and molecular dynamic simulations. Second, the structural changes after adsorption to the interface have been also analyzed by molecular dynamic simulations. The adsorption behavior was investigated by pendant drop analysis and the interfacial film properties by dilatational rheology.

FINDINGS

The structural flexibility of β-lactoglobulin with no cysteines encourages its unfolding at the interface, and accelerates the interfacial protein film formation that results in more visco-elastic films in comparison to the reference.

Piperine solubility enhancement via DES formation: Elucidation of intermolecular interactions and impact of counterpart structure via computational and spectroscopic approaches

The development of new forms of existing APIs with enhanced physicochemical properties is critical for improving their therapeutic potential. In this context, ionic liquids (ILs) and deep eutectic solvents (DESs) have gained significant attention in recent years due to their unique properties and potential for solubility enhancement. In this study, we explore the role of different counterparts in the formation of IL/DESs with piperine (PI), a poorly water-soluble drug. After screening a library of fourteen counterpart molecules, ten liquid PI-counterpart systems were developed and investigated. Thermal analysis confirmed the formation of IL/DES, while computational and spectroscopic studies revealed that hydrogen bonding played a crucial role in the interaction between PI and the counterparts, confirming DES formation. The solubility enhancement of PI in these systems ranged from ∼ 36 % to 294 %, with PI-Oxalic acid (OA) exhibiting the highest saturation solubility (49.71 μg/mL) and PI-Ibuprofen (IB) the lowest (17.23 μg/mL). The presence of hydrogen bonding groups in counterparts was key to successful DES formation. A negative correlation was observed between solubility and logP (r =  - 0.75, p* = 0.0129), while a positive correlation was found between solubility and normalized polar surface area (PSA) (r = 0.68, p* = 0.029). PI-OA and PI-IB were located at the extreme ends of these regression lines, further validating the relationship between these properties and solubility enhancement. These findings highlight essential aspects of rational IL/DES design, optimizing their properties for broader applications.

Coamorphous systems of rebamipide: Selection of amino acid coformers based on protein-ligand docking, in vitro assessment and study of interactions by computational and multivariate analysis

Three coamorphous systems of Rebamipide (REB) with the amino acids namely, Tryptophan (TRP), Phenylalanine (PHE) and Arginine (ARG) are reported. A unique approach for the virtual screening of amino acid coformers is presented by employing molecular docking studies based on interactions of the drug molecule with various amino acid fragments in the drug-receptor cocrystal structure. Successful formation of stable coamorphous systems with ARG, TRP and PHE served as the proof-of-concept along with negative benchmarking standards Histidine and Aspartic acid, wherein coamorphous systems could not be obtained despite multiple trials which resulted in crystalline physical mixtures. The coamorphous systems were characterized by a halo pattern in Powder XRD and a single glass transition temperature (Tg) in modulated DSC. Physical stability assessments of the coamorphous systems showed direct correlation of Tg with the observed stability of the amorphous phase which was found in the order ARGREB > TRPREB ≥ PHEREB. To determine the specific functional groups engaged in the interactions, multivariate analysis was performed on the FTIR spectra. These interactions were further validated by DFT and QTAIM analysis, which revealed key noncovalent interactions in the three coamorphous systems. All three coamorphous systems showed excellent release profiles of the API as demonstrated by the f2 and DE parameters in the order ARGREB ≥ TRPREB > PHEREB ≥ amorphous drug, far exceeding that of the crystalline drug. The interplay of multivariate analysis and QTAIM can be useful in estimating the interactions within the coamorphous systems which can further contribute to stability and physicochemical properties of the systems.

Bioprospecting hydroxylated chalcones in in vitro model of ischemia-reoxygenation and probing NOX4 interactions via molecular docking

Ischemia/reperfusion injury (I/R) is a leading cause of acute kidney injury (AKI) in conditions like kidney transplants, cardiac surgeries, and nephrectomy, contributing to high global mortality and morbidity. This study aimed to analyze the protective effects of 2'-hydroxychalcones in treating I/R-induced AKI by targeting key pathological pathways. Considering strong antioxidant action along with other pharmacological roles of chalcone derivatives, six 2'-hydroxychalcones were synthesized via Claisen-Schmidt condensation and analyzed for their protective effects in an I/R induced AKI model using HK-2 cells. Among six 2'-hydroxychalcones, chalcone A4 significantly increased the HK-2 cells viability compared to I/R group. Chalcone A4 reduced the cell death events by reducing generation of cytoplasmic ROS and mitochondrial transmembrane potential. It also increased GSH and SOD activity while reducing TBARS levels, indicating strong antioxidant action. Scanning electron microscope images showed that chalcone A4 reversed I/R-induced morphological changes in HK-2 cells, including apoptotic blebbing and cytoplasmic fragmentation. Furthermore, in silico studies revealed interactions with NADPH oxidase 4, further supporting its protective role in I/R-induced AKI. These results showed that chalcone A4 possess potential protective action against I/R induced cellular damage possibly due to its strong antioxidant action and potential interaction with NOX4 subunit of NADPH oxidase.

Atomistic insights into liquid crystals of board-like molecules via molecular dynamics simulation

As the temperature decreases, rigid anisotropic molecules that usually incorporate polar groups, aromatic rings or multiple bonds, orient along a common direction, eventually forming liquid-crystalline phases under specific thermodynamic conditions. This study explores the phase behavior and dynamics of board-shaped mesogens with a 1,4,5,8-tetraphenyl-anthraquinone core and four lateral arms forming an oligo(phenyleneethynylene) scaffold. These molecules are promising candidates for forming the elusive biaxial nematic phase. Through atomistic molecular dynamics simulations, we observe the formation of nematic and smectic liquid crystals, in qualitative agreement with experimental observations. To characterize the structure, we compute pair correlation functions along relevant symmetry directions and the nematic order parameter, which indicate a dominant uniaxial ordering with very weak biaxiality. In addition, we analyze the dynamics of our board-shaped mesogens along and perpendicular to the nematic director, revealing an intriguing non-Gaussian behavior and dynamical heterogeneities, with coexisting slow and fast molecules. Building on our recent simulations at the colloidal scale, which demonstrated that monodisperse board-like particles are unable to form biaxial nematics while polydisperse particles can, we hypothesize that a similar behavior may occur at the molecular scale in mixtures of molecules. Although pure-component molecular systems reveal weak biaxiality, our findings suggest that investigating mixtures of the most promising candidates, those molecules that form nematic or smectic phases, could uncover conditions conducive to the formation of biaxial nematic liquid crystals.

Identification of novel inhibitors of cancer target telomerase using a dual structure-based pharmacophore approach to virtually screen libraries, molecular docking and validation by molecular dynamics simulations

In about 85% of cancer malignancies, replicative immortality caused by increased telomerase activity makes it an attractive target for developing anticancer therapeutics. However, the lack of approved small-molecule inhibitors rooted in the structural ambiguity of telomerase has impeded drug development for decades. In this study, we have exploited the FVYL pocket in the thumb domain, which plays a key role in the enzyme's processivity. Due to the unavailability of a co-crystalized structure of BIBR1532 with the catalytic hTERT thumb domain, we utilized the molecular dynamics method to identify the precise binding site of the inhibitor. Two pharmacophore models were generated and validated for the putative (Site-I) and newly identified (Site-II) binding pockets which were screened virtually through the ChemDiv anticancer library, Otava drug-like green collection to identify novel lead compounds, and Binding database to screen out thumb domain-specific telomerase inhibitors. The top hits obtained were filtered using drug-likeliness parameters followed by redocking using a three-level screening strategy into their binding site. The structural investigation, molecular docking studies, and confirmatory molecular dynamics revealed that the exact binding site of BIBR1532 is away from the reported FVYL pocket with characteristic interactions conserved. Subsequently, the lead compounds with the highest docking scores and significant interactions in the newly discovered extended FVYL pocket were validated using 100 ns MD simulations. Additionally, cross-validated binding free energy calculations were performed using MM-PB(GB)SA methods followed by PCA and FEL characterization. The identified top lead compounds can be validated in vitro and taken forward for anticancer drug development.

Exploring the GSTP1 inhibition potential of photosensitizer compounds for enhanced cancer treatment in photodynamic therapy

Photodynamic therapy (PDT) has gained considerable attention in cancer treatment due to its non-invasive nature and the ability of photosensitizers to generate reactive oxygen species upon light activation, leading to tumor destruction. Glutathione S-transferase P1 (GSTP1) is a key enzyme in chemotherapy resistance, often overexpressed in various cancers, and its inhibition of GSTP1 presents a promising strategy to enhance cancer treatment. This study is aimed at assessing the potential of prominent photosensitizers as GSTP1 inhibitors through molecular docking analysis to strengthen the efficacy of PDT. The photosensitizers were docked into the active site of GSTP1, and their binding affinities, inhibition constants (Ki), and molecular interactions were assessed. Among the tested photosensitizers, zinc phthalocyanine, hypericin, and temoporfin emerged as the top candidates, exhibiting binding energies of - 10.8, - 10.2, and - 9.8 kcal/mol, along with Ki values of 0.012, 0.033, and 0.064 µM, respectively. These compounds outperformed the reference inhibitor ethacrynic acid, which had a binding energy of - 6.6 kcal/mol and a Ki of 14.35 µM. These findings suggest that the dual action of these photosensitizers provides a promising strategy for combating cancer and overcoming treatment resistance.

Impact of Intracellular Proteins on μ-Opioid Receptor Structure and Ligand Binding

Chronic pain is a prevalent problem affecting approximately one out of every five adults in the U.S. The most effective way to treat chronic pain is with opioids, but they cause dangerous side effects such as tolerance, addiction, and respiratory depression, which makes them quite deadly. Opioids, such as fentanyl, target the μ-opioid receptor (MOR), which can then bind to the intracellular Gi protein or the β-arrestin protein. The Gi pathway is primarily responsible for pain relief and potential side effects, but the β-arrestin pathway is chiefly responsible for the unwanted side effects. Ideally, an effective pain medication without side effects would bind to MOR, which would bias signaling solely through the Gi pathway. We used the Bio3D library to conduct principal component analysis to compare the cryo-electron microscopy MOR structures in complex with the Gi versus an X-ray crystallography MOR structure with a nanobody acting as a Gi mimic. Our results agree with a previous study by Munro, which concluded that nanobody-bound MOR is structurally different than Gi-bound MOR. Furthermore, we investigated the structural diversity of opioids that can bind to MOR. Quantum mechanical calculations show that the low energy solution structures of fentanyl differ from the one bound to MOR in the experimental structure, and pKa calculations reveal that fentanyl is protonated in aqueous solution. Glide docking studies show that higher energy structures of fentanyl in solution form favorable docking complexes with MOR. Our calculations show the relative abundance of each fentanyl conformation in solution as well as the energetic barriers that need to be overcome to bind to MOR. Docking studies confirm that multiple fentanyl conformations can bind to the receptor. Perhaps a variety of conformations of fentanyl can stabilize multiple conformations of the MOR, which can explain why fentanyl can induce different intracellular signaling and multiple physiological effects.

PSMA-Targeting Imprinted Nanogels for Prostate Tumor Localization and Imaging

Prostate-specific membrane antigen (PSMA) is overexpressed in prostate cancer cells and tumor vasculature, making it an important biomarker. However, conventional PSMA-targeting agents like antibodies and small molecules have limitations. Antibodies exhibit instability and complex production, while small molecules show lower specificity and higher toxicity. Herein, this work develops a novel PSMA-targeting synthetic antibody to address prior limitations. This work synthesizes fluorescently labelled, N-isopropylacrylamide-based epitope imprinted nanogels (MIP-M) using a dispersion of magnetic nanoparticles as template carriers with a linear epitope from PSMA's extracellular apical domain as the template. MIP-M demonstrates high binding affinities for both the epitope template (apparent KD = 6 × 10-10 м) and PSMA (apparent KD = 2.5 × 10-9 м). Compared to reference peptides and human serum albumin, MIP-M indicates high specificity. Flow cytometry and confocal laser scanning microscopy comparing cell lines displaying normal (PC3) and enhanced (LNCaP) PSMA expression levels, revealed that MIP-M and a PSMA antibody exhibits comparable binding preferences for the latter cell line. Moreover, MIP-M demonstrates selectivity on par with the PSMA antibody for targeting PSMA-positive prostate tumor over normal tissue, enabling discrimination. This MIP-M addresses stability, production, specificity and toxicity limitations of prior targeting agents and offer a promising alternative for PSMA-directed cancer diagnosis and treatment.

Molecular Dynamics Simulations of Structurally Nanoengineered Antimicrobial Peptide Polymers Interacting with Bacterial Cell Membranes

Multidrug resistance (MDR) to conventional antibiotics is one of the most urgent global health threats, necessitating the development of effective and biocompatible antimicrobial agents that are less inclined to provoke resistance. Structurally nanoengineered antimicrobial peptide polymers (SNAPPs) are a novel and promising class of such alternatives. These star-shaped polymers are made of a dendritic core with multiple arms made of copeptides with varying amino acid sequences. Through a comprehensive set of in vivo experiments, we previously showed that SNAPPs with arms made of random blocks of lysine (K) and valine (V) residues exhibit sub-μM efficacy against Gram-negative and Gram-positive bacteria tested. Cryo-TEM images suggested pore formation by a SNAPP with random block copeptide arms as one of their modes of actions. However, the molecular mechanisms responsible for this mode of action of SNAPPs are not fully understood. To address this gap, we employed an atomistic molecular dynamics simulation technique to investigate the influence of three different sequences of amino acids, namely (1) alt-block KKV, (2) ran-block, and (3) diblock motifs on the secondary structure of their arms and SNAPP's overall configuration as well as their interactions with lipid bilayer. We, for the first time, identified a step-by-step mechanism through which alt-block and random SNAPPs interact with lipid bilayer and lead to "pore formation", hence, cell death. These insights provide a strong foundation for further optimization of the chemical structure of SNAPPs for maximum performance against MDR bacteria, therefore offering a promising avenue for addressing antibiotic resistance and the development of effective antibacterial agents.

Bactericidal and antibiofilm activities of Piper betle extract against Burkholderia pseudomallei: in vitro and in silico approaches

Burkholderia pseudomallei biofilm is a significant virulence factor in infection. This study aimed to investigate antibacterial and antibiofilm activities of Piper betle extract against B. pseudomallei. The MIC and MBC values of the extract against the isolates were 0.5-1.0 mg/mL. At 2 × MIC, the cells showed cell shrinkage and abnormalities. At 1/2 × MIC, the extract displayed 40-71% inhibition of biofilm formation. At 8 × MIC, the extract reduced the viability of mature biofilms by 60-86%. Hydroxychavicol and eugenol, the main compounds in the extract, showed binding activity to CdpA, an enzyme implicated in biofilms as observed by in silico studies. Hydroxychavicol exhibited the highest affinity for CdpA, with a distance of 2.27 Å. Molecular dynamics simulations revealed that hydroxychavicol forms a stable complex with cyclic di-GMP phosphodiesterase, maintaining protein structural integrity with minimal conformational changes. The results suggested that Piper betle may have medicinal benefits by inhibiting biofilm-related infections.

Targeted anticancer pre-vinylsulfone covalent inhibitors of carbonic anhydrase IX

We designed novel pre-drug compounds that transform into an active form that covalently modifies particular His residue in the active site, a difficult task to achieve, and applied to carbonic anhydrase (CAIX), a transmembrane protein, highly overexpressed in hypoxic solid tumors, important for cancer cell survival and proliferation because it acidifies tumor microenvironment helping invasion and metastases processes. The designed compounds have several functionalities: (1) primary sulfonamide group recognizing carbonic anhydrases (CA), (2) high-affinity moieties specifically recognizing CAIX among all CA isozymes, and (3) forming a covalent bond with the His64 residue. Such targeted covalent compounds possess both high initial affinity and selectivity for the disease target protein followed by complete irreversible inactivation of the protein via covalent modification. Our designed prodrug candidates bearing moderately active pre-vinylsulfone esters or weakly active carbamates optimized for mild covalent modification activity to avoid toxic non-specific modifications and selectively target CAIX. The lead inhibitors reached 2 pM affinity, the highest among known CAIX inhibitors. The strategy could be used for any disease drug target protein bearing a His residue in the vicinity of the active site.

Enzymatic modification of dihydromyricetin by glucosylation and acylation, and its effect on the solubility and antioxidant activity

Although dihydromyricetin exhibits strong potential for pharmaceutical applications, its limited aqueous solubility, permeability and stability restrict its use. In this work, we have synthesized a series of glucosides and acyl-glucosides of dihydromyricetin that could increase the bioavailability of this molecule. First, the R134A variant of sucrose phosphorylase from Thermoanaerobacterium thermosaccharolyticum catalyzed the formation of three monoglucosides, and the major one was identified as dihydromyricetin 4'-O-α-D-glucopyranoside (>75% conversion yield). The molecular features that define this specificity for the 4'-OH phenolic group were investigated through induced-fit docking analysis of each potential derivative. Furthermore, the acylation of the 4'-monoglucoside with fatty acid vinyl esters (C8, C12, and C16) was performed with high efficiency using the lipase from Thermomyces lanuginosus. Three novel acyl derivatives of dihydromyricetin were characterized. Furthermore, the water solubility and antioxidant activity (ABTS, DPPH) of the synthesized compounds were measured, concluding that the location of the glucosyl moiety may affect their physicochemical properties and, as a result, their bioactivity.

Assessing the interaction between the N-terminal region of the membrane protein magnesium transporter A and a lipid bilayer

This study investigates the interaction of KEIF, the intrinsically disordered N-terminal region of the magnesium transporter MgtA, with lipid bilayers mimicking cell membranes. Combining experimental techniques such as neutron reflectometry (NR), quartz-crystal microbalance with dissipation monitoring (QCM-D), synchrotron radiation circular dichroism (SRCD), and oriented circular dichroism (OCD), with molecular dynamics (MD) simulations, we characterized KEIF's adsorption behavior.

HYPOTHESIS

KEIF undergoes conformational changes upon interacting with lipid bilayers, potentially influencing MgtA's function within the plasma membrane.

EXPERIMENTS

The study assessed KEIF's structural transitions and position within lipid bilayers under various conditions, including zwitterionic versus anionic bilayers and different salt concentrations. The techniques analyzed adsorption-induced structural shifts and peptide localization within the bilayer.

FINDINGS

KEIF transitions from a disordered to a more structured state, notably increasing α-helical content upon adsorption to lipid bilayers. The peptide resides primarily in the hydrophobic tail region of the bilayer, where it may displace lipids. Electrostatic interactions, modulated by bilayer charge and ionic strength, play a critical role. These results suggest that KEIF's conformational changes and bilayer interactions can be integral to its potential modulatory role in MgtA function within the plasma membrane. This research highlights the importance of surface-induced structural transitions in intrinsically disordered proteins and their implications for membrane protein modulation.

Order-Disorder Balance in Silk-Elastin-like Polypeptides Determines Their Self-Assembly into Hydrogel Networks

The biofabrication of recombinant structural proteins with a range of mechanical or structural features usually relies on the generation of protein libraries displaying variations in terms of amino acid composition, block structure, molecular weight, or physical/chemical cross-linking sites. This approach, while highly successful in generating a wealth of knowledge regarding the links between design features and material properties, has some inherent limitations related to its low throughput. This slows down the pace of the development of de novo recombinant structural proteins. Here, we propose an approach to tune the viscoelastic properties of temperature-responsive hydrogels made of silk-elastin-like polypeptides (SELPs) without modifying their sequence. To do so, we subject purified SELPs to two different postprocessing methods─water annealing or EtOH annealing─that alter the topology of highly disordered SELP networks via the formation of ordered intermolecular β-sheet physical cross-links. Combining different analytical techniques, we connect the order/disorder balance in SELPs with their gelling behavior. Furthermore, we show that introducing a functional block (in this case, a biomineralizing peptide) in the sequence of SELPs can disrupt its self-assembly and that such disruption can only be overcome by EtOH annealing. Our results suggest that postprocessing of as-purified SELPs might be a simple approach to tune the self-assembly of SELPs into biomaterials with bespoke viscoelastic properties beyond the traditional approach of developing SELP libraries via genetic engineering.

Tuning the nanostructure and tribological properties of a non-ionic deep eutectic solvent with water addition

HYPOTHESIS

The addition of water to a non-ionic N-oxide deep eutectic solvent(DES) composed of phenylacetic acid (PhAA) and N-dodecylmorpholine-N-oxide(MO-12) in a 1:1 M ratio(PhAA/MO-12) will promote interfacial nanostructure formation due to increased proton transfer and solvophobic interactions, leading to reduced friction.

EXPERIMENTS

The interfacial structure and friction of PhAA/MO-12 with water content up to 41.9 wt% were investigated at mica surfaces. Atomic force microscopy(AFM) was used to measure normal force-separation profiles, lateral images, and nanoscale friction.

FINDINGS

Conductivity increases over twentyfold with the addition of 23.6 wt% water. AFM force curves reveal that increasing water content in PhAA/MO-12 leads to a more pronounced interfacial structure with steps extending further into the bulk. High-resolution near-surface images show a well-defined sponge-like nanostructure at 23.6 wt% water, which is absent in the neat DES. The enhanced nanostructure is attributed to increased proton transfer from PhAA to MO-12 and segregation of polar and apolar domains driven by water-strengthened solvophobic interactions. Friction reduces up to 72 % for ≥7.0 wt% water compared to the neat DES, due to a more robust boundary layer facilitated by water.

Steric Selection of Anion Binding Sites by Organoantimony(V) Pnictogen Bond Donors: An Experimental and Computational Study

Catecholatostiboranes have emerged as useful Lewis acids in several applications. To better understand the factors that control the properties of these species, we examined the Lewis acidities of (o-C6Cl4O2)Sb(o-Tol)3 (2, Tol = tolyl) and (o-C6Cl4O2)Sb(p-Tol)3 (3), two triarylcatecholatostiboranes that differ by the nature of the aryl substituent. Fluoride anion binding studies indicate that 3 is more Lewis acidic than 2, a factor readily assigned to the steric crowding around antimony in the case of the o-tolyl derivative. But, while 3 binds F- trans to a Sb-Caryl bond as is typical of catecholatostiboranes, 2 prefers binding trans to a Sb-O bond. Computational analyses of 2 and 3 reveal the existence of several σ holes, and an activation strain analysis is employed to elucidate the origin of these stiboranes' anion-binding geometry preferences.

Exploring the Impact of Protein Chain Selection in Binding Energy Calculations with DFT

Calculation of binding free energies between a protein and a ligand are highly desired for computer-aided drug design. Here we approximate the binding energies of ABL1, an enzyme which is the target for drugs used in the treatment of chronic myeloid leukaemia, with minimal models and density functional theory (DFT). Starting from the crystal structures of protein-drug complexes, we estimated the binding free energies having used all available individual molecules (protein chains) within each structure, not only a single one as commonly used, in order to see if the choice of the protein chain is important in such calculations. Differences were observed between chains in the same file. Energy decomposition analysis (EDA) revealed that the most important factors for binding were exchange, repulsion and electrostatics. The desolvation term varied dramatically between the inhibitors (between 4.2 and 92.3 kcal/mol). All functionals showed similar patterns in the EDA and in discriminating between the ligands. Non-covalent interactions (NCI) analysis was used to further explain the differences between protein chains and functionals. Overall, it is shown that small minimal models of a drug binding site can be useful to infer on the suitability of an initial crystal structure for further analysis such as EDA.

Dizocilpine derivatives as neuroprotective NMDA receptor antagonists without psychomimetic side effects

We aimed to prepare novel dibenzo [a,d][7]annulen derivatives that act on N-methyl-d-aspartate (NMDA) receptors with potential neuroprotective effects. Our approach involved modifying the tropane moiety of MK-801, a potent open-channel blocker known for its psychomimetic side effects, by introducing a seven-membered ring with substituted base moieties specifically to alleviate these undesirable effects. Our in silico analyses showed that these derivatives should have high gastrointestinal absorption and cross the blood-brain barrier (BBB). Our pharmacokinetic studies in rats supported this conclusion and confirmed the ability of leading compounds 3l and 6f to penetrate the BBB. Electrophysiological experiments showed that all compounds exhibited different inhibitory activity towards the two major NMDA receptor subtypes, GluN1/GluN2A and GluN1/GluN2B. Of the selected compounds intentionally differing in the inhibitory efficacy, 6f showed high relative inhibition (∼90 % for GluN1/GluN2A), while 3l showed moderate inhibition (∼50 %). An in vivo toxicity study determined that compounds 3l and 6f were safe at 10 mg/kg doses with no adverse effects. Behavioral studies demonstrated that these compounds did not induce hyperlocomotion or impair prepulse inhibition of startle response in rats. Neuroprotective assays using a model of NMDA-induced hippocampal neurodegeneration showed that compound 3l at a concentration of 30 μM significantly reduced hippocampal damage in rats. These results suggest that these novel dibenzo [a,d][7]annulen derivatives are promising candidates for developing NMDA receptor-targeted therapies with minimal psychotomimetic side effects.

Exploring the potential of beta-cyclodextrin-based MIL-101(Cr) for pharmaceutical removal from wastewater: A combined density functional theory and molecular simulations study

Pharmaceutical contaminants pose significant risks to ecosystems and human health, necessitating effective removal strategies. This research focuses on developing advanced adsorbents for removing pharmaceutical pollutants from the environment. Metal-organic frameworks (MOFs), specifically MIL-101(Cr) functionalized with biodegradable beta-cyclodextrin (β-CDex), were investigated as potential nanocomposite adsorbents for the removal of ketorolac (KTRK), naproxen (NPXN), and tramadol (TRML). The study employed molecular simulations and density functional theory (DFT) calculations to explore the interactions between the pollutants and adsorbents. Analyses of DFT results, including electrostatic potential, ionization energy, density of states, and molecular orbital analysis, provided insights into the reactivity of pollutants and adsorbents. Additionally, the structural properties of the adsorbents, such as fractional free volume, radius of gyration, and system energies, were thoroughly examined. Molecular dynamics (MD) and Monte Carlo (MC) simulations were used to evaluate the adsorption capacities of MIL-101(Cr) for the target pharmaceutical pollutants. The results demonstrated the superior adsorption performance of the nanocomposite adsorbent, particularly for KTRK, with an adsorption energy of -1934 kcal/mol, compared to the pristine MIL-101(Cr), which had an adsorption energy of -1916 kcal/mol. This enhanced adsorption is attributed to the optimal molecular fit, guest-host solid interactions, and the selective encapsulation capabilities of β-CDex. This research highlights the potential of MOF-based nanocomposites as effective and sustainable solutions for pharmaceutical pollution. By advancing the understanding of molecular interactions through simulations, this study contributes to developing innovative adsorbents for wastewater treatment and the protection of water resources.

Hypershifted spin spectroscopy with dynamic nuclear polarization at 1.4 K

Dynamic nuclear polarization (DNP) enhances nuclear magnetic resonance (NMR) sensitivity by transferring polarization from unpaired electrons to nuclei, but nearby nuclear spins are difficult to detect or "hidden" due to strong electron-nuclear couplings that hypershift their NMR resonances. Here, we detect these hypershifted spins in a frozen glycerol-water mixture doped with TEMPOL at ~1.4 K using spin diffusion enhanced saturation transfer (SPIDEST), which indirectly reveals their spectrum. Additionally, we directly observe 1H NMR lines spanning 10 MHz. The spectrum is confirmed by simulations and density functional theory (DFT) calculations, which verify that the signals originate from intramolecular protons on TEMPOL. Using two-dimensional NMR, we demonstrate polarization transfer from hypershifted to bulk nuclei across a spin diffusion barrier. This methodology provides new insights into the structures of radicals and could aid in designing more efficient DNP polarizing agents. It also complements information on hyperfine interaction accessible by electron paramagnetic resonance (EPR).

Structure-function analysis of 2-sulfamoylacetic acid synthase in altemicidin biosynthesis

Altemicidin and its analogs are valuable sulfonamide antibiotics with valuable antitumor and antibacterial activities. Structures of altemicidin and congeners feature an unusual sulfonamide side chain. In the biosynthesis of altemicidin, the aldehyde dehydrogenase SbzJ catalyzes the conversion of 2-sulfamoylacetic aldehyde into 2-sulfamoylacetic acid, a key step in producing the sulfonamide side chain. Here, we conducted the biochemical characterization and structure-function analysis of SbzJ. In vitro assays revealed that SbzJ exhibits substrate promiscuity, accepting various aldehyde substrates and cofactors. The crystal structure of SbzJ in complex with NAD+, along with subsequent mutagenesis studies, provided insights into how SbzJ recognizes the sulfonamide group of the substrate. Notably, His431 and Glu240 were identified as key residues serving as catalytic bases to activate the catalytic Cys273 and a water molecule. These findings provide structural and mechanistic understanding of SbzJ, offering potential for enzyme engineering to generate novel bioactive compounds.

Molecular and Biochemical Characterization of Olive 4-Hydroxyphenyl Pyruvate Dioxygenase Involved in the Biosynthesis of Tocopherols Present in Virgin Olive Oil

Olive (Olea europaea) fruit contains high amounts of tocopherols that are responsible, along with secoiridoid phenolic compounds, for most of the antioxidant and anti-inflammatory properties of virgin olive oil. This study focuses on the molecular and biochemical characterization of olive 4-hydroxyphenyl pyruvate dioxygenase (OeHPPD) catalyzing the biosynthesis of homogentisic acid, which constitutes the phenolic residue in the tocopherol molecule. OeHPPD is a cytoplasmic enzyme with a molecular weight of 49.8 kDa and a predicted tertiary structure very similar to the Arabidopsis enzyme that suggests similar catalytic mechanisms. OeHPPD has an estimated Kcat of 75.26 s-1 and catalytic efficiency (Km/Kcat) of 0.145 μM-1 s-1 with 4-hydroxyphenyl pyruvate as the substrate. The expression analysis in fruits from selected olive cultivars harvested at different ripening stages indicates that the OeHPPD gene is temporally regulated and cultivar-dependent. Moreover, the analysis of OeHPPD expression in fruits affected by drought stress suggests that HPPD is involved in olive environmental adaptation.

In silico exploration of potent flavonoids for dengue therapeutics

Dengue poses a persistent and widespread threat with no effective antiviral drug available till now. Several inhibitors have been developed by targeting the viral non-structural proteins including methyl transferase (NS5) of the dengue virus with possible therapeutic values. In this work, virtual screening, molecular docking, molecular dynamics simulations (200 ns), and assessments of free energy changes have been carried out to identify potential candidates from a database of flavonoids (ca. 2000) that may have good curative potential from the disease. The binding affinity of flavonoids, namely Genistein-7-glucoside (FLD1), 6'-O-Acetylgenistin (FLD2), 5,6-dihydroxy-2-(4-hydroxyphenyl)-7-[3,4,5-trihydroxy-6-(hydroxymethyl)oxane-2-yl]oxychromen-4-one (FLD3), Glucoliquiritigenin (FLD4), and Chrysin-7-O-glucoronide (FLD5) showed the binding affinities of -10.2, -10.2, -10.1, -10.1, -9.9 kcal/mol, respectively, and possessed better values than that of the native ligand (-7.6 kcal/mol) and diclofenac sodium (-7.3 kcal/mol). Drug-likeness of the top five flavonoids were acceptable and no end-point toxicity was hinted by ADMET predictions. The stability of the protein-ligand complexes was accessed from 200 ns molecular dynamics simulations in terms of various geometrical parameters; RMSD, RMSF of residues, Rg, SASA, H-bond, and RPDF. The binding free energy changes of these adducts were calculated by the MM/PBSA solvation model with negative values (from -38.01±7.53 to -17.75±11.03 kcal/mol) indicating the sustained spontaneity of the forward reaction and favorability of the product formation. The geometrical and thermodynamic parameters inferred that the flavonoids could bind at the orthosteric site of the target protein of DENV-2 and could inhibit its functioning, possibly, resulting in the prevention of the disease. Overall, this study highlights the anti-DENV activity of five flavonoids, positioning them as promising candidates for further development as antiviral agents against dengue infection.

Two Isomeric Thienoacenes in Thin Films: Unveiling the Influence of Molecular Structure and Intermolecular Packing on Electronic Properties

Isomerism of molecular structures is often encountered in the field of organic semiconductors, but little is known about how it can impact electronic and charge transport properties in thin films. This study reveals the molecular orientation, electronic structure, and intermolecular interactions of two isomeric thienoacenes (DN4T and isoDN4T) in thin films, in relation to their charge transport properties. Utilizing scanning tunneling microscopy (STM), angle-resolved photoemission spectroscopy (ARUPS), and near-edge X-ray absorption fine structure measurements (NEXAFS), we systematically analyze the behavior of these isomers from submonolayer to multilayer coverage on highly ordered pyrolytic graphite (HOPG) as substrates. We find that at submonolayer coverage both DN4T and isoDN4T molecules predominantly adopt a nearly flat-lying orientation on the surface, minimizing intermolecular interactions. The distinct emission features of the highest occupied molecular orbital (HOMO) level in ARUPS enables the determination of molecular reorganization energies. These are found to be in good agreement with theoretical predictions, suggesting superior charge transport in DN4T compared to isoDN4T. Notably, thickness-dependent photoemission measurements reveal a significant splitting (approximately 450 meV) of the HOMO level of isoDN4T, attributed to polarization-induced effects rather than wave function overlap, indicating a nuanced interplay between molecular packing and electronic properties. Our results underscore the importance of molecular packing and substrate interactions in determining the electronic structure and transport properties of organic semiconductor thin films. Substrate-induced polymorphism and the crucial role of polarization-induced effects influencing charge transport are highlighted. These insights are pivotal for future engineering of molecular and thin film structures, aiming to enhance the performance of organic semiconductor-based devices.

Coumarin-based fluorescent probes for the detection of copper (II) and imaging in mice of Wilson's disease

Copper is an essential redox-active metal nutrient, with tightly regulated homeostasis. Copper homeostasis is closely linked to various diseases, making it a critical area of study. Fluorescent probes serve as powerful tools for investigating these conditions. In this study, a fluorescent probe, Con-Cu400 for detecting Cu2+ was developed. Con-Cu400 exhibited a strong "turn-on" fluorescence signal in response to Cu2+, demonstrating high selectivity and sensitivity. Con-Cu400 also exhibited good biocompatibility and was successfully employed for fluorescence sensing of Cu2+ in both cellular and mouse models under conditions of normal, copper-depleted, and copper-overloaded. This probe effectively detected elevated Cu2+ levels in the livers of mice with Wilson's disease. This work may contribute to the broader application of fluorescent probes in studying Cu2+ dysregulation-related diseases in cellular and animal models.

Utilizing High X-ray Energy Photon-In Photon-Out Spectroscopies and X-ray Scattering to Experimentally Assess the Emergence of Electronic and Atomic Structure of ZnS Nanorods

The key to controlling the fabrication process of transition metal sulfide nanocrystals is to understand the reaction mechanism, especially the coordination of ligands and solvents during their synthesis. We utilize in situ high-energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD-XAS) as well as in situ valence-to-core X-ray emission spectroscopy (vtc-XES) combined with density functional theory (DFT) calculations to identify the formation of a tetrahedral [Zn(OA)4]2+ and an octahedral [Zn(OA)6]2+ complex, and the ligand exchange to a tetrahedral [Zn(SOA)4]2+ complex (OA = oleylamine, OAS = oleylthioamide), during the synthesis of ZnS nanorods in oleylamine. We observe in situ the transition of the electronic structure of [Zn(SOA)4]2+ with a HOMO/LUMO gap of 5.0 eV toward an electronic band gap of 4.3 and 3.8 eV for 1.9 nm large ZnS wurtzite nanospheres and 2 × 7 nm sphalerite nanorods, respectively. Thus, we demonstrate how in situ multimodal X-ray spectroscopy and scattering studies can not only resolve structure, size, and shape during the growth and synthesis of NPs in organic solvents and at high temperature but also give direct information about their electronic structure, which is not readily accessible through other techniques.

Identification of novel fructose 1,6-bisphosphate aldolase inhibitors against tuberculosis: QSAR, molecular docking, and molecular dynamics simulation-based analysis of DrugBank compounds

Global initiatives aim to curb tuberculosis (TB) by developing efficient vaccines and drugs against Mycobacterium tuberculosis (M. tb). The pressing need for innovative and swift anti-TB drug screening methods, due to the drawbacks of traditional approaches, is met by employing Structure-based virtual screening (SBVS) and machine learning (ML) in drug discovery. The present study utilizes these methods to repurpose compounds from the DrugBank database (DBD) as anti-TB drugs, explicitly targeting the enzyme fructose-1,6-bisphosphate aldolase (FBA) in glycolysis and gluconeogenesis pathways.Five classifiers, including REPTree, Decision Stump, Random Tree, Random Forest, and J48evaluate training data against M. tbFBA. AdmetSAR 2.0 assesses drug-like properties and toxicity of ML-identified compounds using four filters. Out of 9213 DBD compounds, 5280 were predicted as TB-active. REPTree, chosen for further screening, led to the identification of four promising preclinical anti-TB drug candidates from DrugBank-Serdemetan, Parecoxib, N, N-Diethyl-2-[(2-Thienylcarbonyl) amino], and Visnadine.All screened ligands show stable binding behaviour during a 200-ns molecular dynamics simulation. Density functional theory (DFT) analysis was also employed for the analysis HOMO (highest occupied molecular orbital)/LUMO (lowest unoccupied molecular orbital) gap, and both screened hits showed efficient results. This study presents a potential avenue for effective TB therapeutics development from compounds with proven druggability in other contexts.

A putative mycobacterial GDP-mannose dependent α-mannosyltransferase Rv0225 acts as PimC: an in-silico study

The complex cell envelope of pathogenic mycobacteria provides a strong barrier against the host immune system and various antibiotics. Phosphatidyl-myo-inositol mannosides (PIMs), lipomannan (LM), and lipoarabinomannan (LAM) are structurally important elements of mycobacterial cell envelope and also play crucial roles in modulating the host immune functions. At the cytoplasmic side of the mycobacterial inner membrane, phosphatidyl-myo-inositol (PI) is mannosylated by α-mannosyltransferases PimA and PimB' to synthesize PIM2 using GDP-mannose (GDPM) as the mannose donor. This PIM2 compound is acylated to synthesize Ac1/2PIM2, which is further mannosylated by an unknown enzyme PimC to produce Ac1/2PIM3. Synthesis of LM/LAM or higher PIM compounds (Ac1/2PIM4 / Ac1/2PIM5 / Ac1/2PIM6) requires polyprenol-phosphate-mannose (PPM) as the mannose donor and takes place at the periplasmic side of the mycobacterial inner membrane. Previously, a GDPM-dependent α-mannosyltransferase RvD2-ORF1 was identified as the PimC in Mycobacterium tuberculosis CDC1551 (Mtb CDC1551). However, its counterpart was missing in most other mycobacterial strains. Bioinformatic analyses, molecular docking, and molecular dynamics (MD) simulations in this study indicate that Rv0225, an essential protein of Mycobacterium tuberculosis H37Rv, is a GDPM-binding α-mannosyltransferase. The predicted structure of Rv0225 showed similarities with mycobacterial proteins PimA, PimB', and PimC of Mtb CDC1551. Further molecular docking and MD simulations also suggest that Ac1/2PIM2 can bind to Rv0225 and showed similar dynamic patterns as the glycolipid substrates of PimA and PimB'. The binding of Ac1PIM3 caused opening and closing motions of Rv0225, a phenomenon also observed in the case of PimA. Overall, the computational analyses suggest that Rv0225 may play the role of PimC in mycobacteria.

Tuning emissive color of trivalent terbium ion through environmental factors: optoelectronic insights from theoretical, spectral and computational studies

The combination of 4,4,4-trifluoro-1-phenyl-1,3-butanedione (TFPB) and pyrazine (pyz) with Tb3+ ions forms two distinct types of complexes, represented by the formulas [Tb(TFPB)3(L)2], where L is either H2O or pyz, and [(Tb(TFPB)3)2pyz]. A detailed examination of the impact of the surrounding environment on the photophysical properties of these synthesized complexes was conducted. Photoluminescence (PL) analysis indicated that the magnetic dipole transition (5D4 → 7F5) is dominant in Tb(iii)-based systems. The prepared complexes exhibit visible luminescence in both solid and solution media. Remarkably, the luminescence intensity of the mononuclear complex is significantly higher than that of its dinuclear counterpart, highlighting the impact of efficient energy transfer on emission intensity. The CIE color coordinates of these complexes in solution closely align with NTSC standard values. Additionally, modulation of emissive color is evident when the surrounding media (from solid to solution) and solvent nature are altered. Density Functional Theory (DFT) calculations were performed to elucidate the electronic density distribution in the synthesized complexes. Additionally, a comprehensive analysis, including IR, UV, NMR, thermogravimetry and cyclic voltammetry, was conducted, along with theoretical calculations using Judd-Ofelt analysis.

Correlating Mechanical Properties and Sequence Motifs in Artificial Spider Silk by Targeted Motif Substitution

The major ampullate silk of orb-weaving spiders is renowned for its exceptional mechanical properties, including high tensile strength and extensibility. The development of artificial spider silk presents a promising alternative to traditional fibers with significant environmental impacts. This study aims to elucidate the relationship between sequence motifs of natural spider silk and the mechanical properties of artificial spider silk. Using the Spider Silkome Database, we identified motifs correlated with specific physical properties and substituted them into MaSp2-based mini-spidroin BP1. We then measured the mechanical properties of the resulting recombinant artificial spider silk through tensile tests, observed structural properties via birefringence measurement and wide-angle X-ray scattering, and evaluated the water response through boiled water shrinkage tests. Introducing a positively correlated motif increased the tensile strength by 9.3%, while a negatively correlated motif decreased it by 5.1%, confirming the sequence-property relationship. These findings demonstrate that targeted motif substitution can effectively control the physical properties of artificial spider silk, facilitating the development of sustainable biomaterials with tailored mechanical properties for diverse industrial applications.

Delving into Macrolide Binding Affinities and Associated Structural Modulations in Erythromycin Esterase C: Insights into the Venus Flytrap Mechanism

Since their inception in antibacterial therapy, macrolide-based antibiotics have significantly shaped the evolutionary pathways of pathogenic bacteria, driving them to develop diverse antimicrobial resistance (AMR) mechanisms. Among these, macrolide esterase, commonly referred to as erythromycin esterase, emerged as a critical defense mechanism, enabling bacteria to detoxify macrolides by hydrolyzing the macrolactone ring within the bacterial cell. In this study, we delve into the intricate interactions and conformational dynamics of erythromycin esterase C (EreC), a key member of the Ere enzyme family. We have focused on three FDA-approved and widely prescribed macrolides─erythromycin, clarithromycin, and azithromycin─by employing classical molecular dynamics, absolute binding free energy calculations, and 2D well-tempered metadynamics simulations to explore their interactions with EreC. To estimate the absolute binding free energies, we have used the recently developed and robust "Streamlined Alchemical Free Energy Perturbation (SAFEP)" protocol. The results from our molecular dynamics simulations and advanced analyses portrayed the crucial role of hydrophobic interactions within the macrolide binding cleft of EreC, along with the significant influence of the minor lobe in facilitating overall structural fluctuation. In silico alanine scanning identified top three hydrophobic residues, i.e., PHE248, MET333, and PHE344, responsible for macrolide binding inside that cleft. According to the free energy calculations, azithromycin and clarithromycin showed greater binding affinities toward EreC than the parent macrolide erythromycin. Moreover, 2D metadynamics simulations along with graph theory-based eigenvector centrality analyses revealed a metastable "semiopen" state during the hypothesized "active loop closure" of the EreC protein triggered by subtle conformational changes of an important histidine residue, HIS289, upon macrolide capture, drawing a fascinating parallel to the renowned "Venus flytrap" mechanism.

The potential role of alkaline diets in prevention of calcium oxalate kidney stone formation

Formation of kidney stones is considered a major global problem. Diet plays an important role in the management of kidney stone formation. The main goal of the present research was to evaluate the protective role of fruit and vegetable mixtures as models of an alkaline diet on formation of kidney stones in rats and to conduct molecular docking study. The chemical compositions, phenolic compound profile, β-carotene content, vitamin C and antioxidant activity of both mixtures were assessed. Fruit (-42.419 ) and vegetable (-11.13) mixtures recorded a negative potential renal acid load in the presence of macro-/micro-nutrients, β-carotene and phenolic compounds; chlorogenic acid was the major content in both mixtures. Both mixtures exhibited high antioxidant activity. Molecular docking study proved that rutin displayed the highest binding affinities for glycolate oxidase (-11.8 kcal mol-1) and lactate dehydrogenase (-10.1 kcal mol-1). The kidney stone model in rats exhibited metabolic acidosis in the urinary profile through reduction of citrate; Ca, Mg and K excretion and elevation of oxalate, creatinine, creatinine clearance, uric acid, urea and protein. Additionally, there was a significant reduction in plasma Ca, Mg and K levels, while liver and kidney function parameters improved significantly. Fruit and vegetable mixtures as models of an alkaline diet proved improvement in all the parameters. Histopathological examination of kidney sections of the kidney stone model showed crystal deposition, inflammation, and severe necrosis. Kidney sections of alkaline diet models indicated mild and moderate changes. Conclusion: The results of this study proved that both alkaline diet models were effective in protecting against kidney stone formation in vivo and in molecular docking studies.

Addressing the Evolution of Cardenolide Formation in Iridoid-Synthesizing Plants: Site-Directed Mutagenesis of PRISEs (Progesterone-5β-Reductase/Iridoid Synthase-like Enzymes) of Plantago Species

Enzymes capable of processing a variety of compounds enable plants to adapt to diverse environmental conditions. PRISEs (progesterone-5β-reductase/iridoid synthase-like enzymes), examples of such substrate-promiscuous enzymes, are involved in iridoid and cardenolide pathways and demonstrate notable substrate promiscuity by reducing the activated C=C double bonds of plant-borne and exogenous 1,4-enones. In this study, we identified PRISE genes in Plantago media (PmdP5βR1) and Plantago lanceolata (PlP5βR1), and the corresponding enzymes were determined to share a sequence identity of 95%. Despite the high sequence identity, recombinant expressed PmdP5βR1 was 70 times more efficient than PlP5βR1 for converting progesterone. In order to investigate the underlying reasons for this significant discrepancy, we focused on specific residues located near the substrate-binding pocket and adjacent to the conserved phenylalanine "clamp". This clamp describes two phenylalanines influencing substrate preferences by facilitating the binding of smaller substrates, such as 2-cyclohexen-1-one, while hindering larger ones, such as progesterone. Using structural analysis based on templates PDB ID: 5MLH and 6GSD from PRISE of Plantago major, along with in silico docking, we identified positions 156 and 346 as hot spots. In PlP5βR1 amino acid residues, A156 and F346 seem to be responsible for the diminished ability to reduce progesterone. Moreover, the double mutant PlP5βR_F156L_A346L, which contains the corresponding amino acids from PmdP5βR1, showed a 15-fold increase in progesterone 5β-reduction. Notably, this modification did not significantly alter the enzyme's ability to convert other substrates, such as 8-oxogeranial, 2-cyclohexen-1-one, and methyl vinyl ketone. Hence, a rational enzyme design by reducing the number of hotspots selectively, specifically improved the substrate preference of PlP5βR1 for progesterone.

MXene-encapsulated ZIF-8@Liposomes for NIR-enhanced photothermal therapy in hepatocellular carcinoma treatment: In vitro, in vivo, and in silico study

Photothermal therapy (PTT) utilizes near-infrared (NIR) light to enhance localized, non-invasive cancer treatments and drug delivery systems (DDS). Combination chemotherapy with PTT (chemo-PTT) offers multiple therapeutic advantages, involving synergistic effects, reduced side effects, and decreased drug toxicity. In this study, 2D titanium carbide (Ti3C2Tx) MXene nanosheets were encapsulated in a zeolitic imidazolate framework-8 (ZIF-8) to form (MX-ZIF-8) nanoparticles (NPs) for PTT applications. Sorafenib (SB), an anticancer drug was loaded onto MX-ZIF-8 and further modified with a liposomes (LPs) lipid bilayer to create (SB-MX-ZIF-8@LPs) nanocomposites. TEM imaging revealed that SB-MX-ZIF-8@LPs had a lamellar structure and spherical shape, with an average diameter of 75.2 nm and a zeta potential (ZP) of -8.4 ± 4.5 mV. Additionally, the PT stability, drug encapsulation, and in-vitro release kinetics of SB-MX-ZIF-8@LPs were assessed. These nanocomposites exhibited an impressive PT conversion efficiency of 55 % at 50 μg/mL under NIR irradiation. The cumulative release of SB from SB-MX-ZIF-8@LPs reached 86.15 % at pH 7.4 and 89.3 % at pH 4.8 under NIR over a period of 72 h, with an encapsulation efficiency of 87.34 %. MTT assays revealed strong cytotoxicity against HepG2 cells, with SB-MX-ZIF-8@LPs showing an IC50 value of 2.7 μg/mL and inducing approximately 96 % total apoptosis. The SB-MX-ZIF-8@lip nanocomposite demonstrated excellent biological stability in a serum environment, retaining over 98 % of sorafenib and maintaining consistent particle size (∼347 nm) over 30 days. An in vivo xenograft study in BALB/c mice further demonstrated the efficacy of SB-MX-ZIF-8@LPs, with this treatment group showing the smallest tumor volume compared to other groups and a significantly higher tumor volume reduction than SB alone. Molecular docking studies indicated that SB exhibited strong binding affinities particularly with ABL1 (-8.7 kcal/mol) and EGFR (-9.3 kcal/mol). Docking interactions between MXene and SB, conducted using the Hdock Server, resulted in a docking score of -10.53, with one bond forming at a distance of 4 Å. These findings were consistent with experimental results, highlighting the favorable interaction between MXene and SB. ADMET analysis confirmed that MX-ZIF-8@LPs possessed favorable drug carrier properties, including high intestinal absorption (96.6 %), and low toxicity supporting its potential as an effective DDS for cancer therapy.

Neutral Adducts of Molybdenum Hexafluoride: Structure and Bonding in MoF6(NC5H5) and MoF6(NC5H5)2

The first Lewis acid base adducts of MoF6 and an organic base have been synthesized, i. e., MoF6(NC5H5) and MoF6(NC5H5)2. These adducts are structurally characterized with X-ray crystallography, showing that both adducts adopt capped trigonal prismatic structures. The MoF6(NC5H5) and MoF6(NC5H5)2 adducts are fluxional on the NMR time scale at room temperature. Two different fluorine environments could be resolved by 19F NMR spectroscopy at -80 °C for the 1 : 2 adduct, MoF6(NC5H5)2, whereas MoF6(NC5H5) remains fluxional at that temperature. Density functional theory (DFT) calculations aide the assignment of the infrared and Raman spectra. Natural Bond Order and Molecular Electrostatic Potential analyses elucidate the structures and properties of the MoF6 pyridine adducts. Regions of significantly higher molecular electrostatic potential, i. e., σ-holes, in trigonal prismatic compared to octahedral MoF6 rationalize the capped trigonal prismatic geometry of the adducts. Whereas MoF6(NC5H5) is stable at room temperature under exclusion of moisture, MoF6(NC5H5)2 decomposes at 60 °C in pyridine solvent, and the solid slowly decomposes at room temperature after 24 h.

Fluorescent polymers for environmental monitoring: Targeting pathogens and metal contaminants with naphthalimide derivatives

Monitoring Hg2+ levels in aqueous environments is crucial to assess the potential methylmercury contamination via bacterial conversion, however, existing methods often require extensive sample treatment and expensive equipment. To mitigate this issue, this study examines the synthesis and application of three naphthalimide-based compounds, with significant fluorescent and solvatochromic behavior (C1, C2, and C3). Compounds C1 and C2 demonstrated a strong affinity for Hg2+ metal ions, with C2 showing selectivity and a strong antibacterial profile, particularly against S. aureus (MIC50 (C2) = 0.01 µg/mL). Moreover, these compounds were incorporated into three polymeric matrices, namely polyvinyl chloride (PVC), poly (methyl methacrylate-co-methacrylic acid) (PMMMA), and Starch, allowing for the development of solid-support sensors/surfaces with a strong antibacterial profile, highlighting the inherent dual-functionality of the compounds. Interestingly, the C2-doped Starch biopolymer detected low concentrations of Hg2+ ions, such as 23 nM in tap water (value within the WHO standards for drinking water), through a rapid spectroscopic evaluation without sample treatment. This biopolymer was generated via a sustainable, green-chemistry-oriented, temperature-dependent water/Starch synthetic route, without the addition of plasticizers and any associated ecotoxicity. The study used sustainable methods for environmental monitoring and antibacterial applications, advancing material science to offer effective, accessible, and eco-friendly solutions for detecting and mitigating mercury pollution and bacterial contaminations, enhancing environmental and health safety.

A free radical interlocking co-deposition strategy based on the oxidative pyrolysis mechanism of polyethylene terephthalate to achieve green energy recovery

Accidental combustion and energy recovery of polyethylene terephthalate (PET) result in the formation of harmful organic substances and excessive emissions of CO2 and CO. This paper presents our recent efforts to unravel the formation mechanism of these harmful substances during the PET combustion process using thermal analysis and simulation calculations (DFT, CDFT, and ReaxFF). Our findings reveal that PET oxidative pyrolysis produces free radicals, harmful small molecule gases, and CO2. The interaction between aromatic free radicals and oxygen initiates unstable peroxy bonds, triggering uncontrollable chain exothermic reactions and producing oxygenated polycyclic aromatic hydrocarbon (OPAH) precursors. We propose a straightforward and eco-friendly free radical interlocking co-deposition inhibition strategy for PET by incorporating polycarbonate (PC). This strategy aims to facilitate green energy recovery by curbing OPAH formation and reducing CO2 and CO emissions during PET waste combustion. Our investigation into the oxidative pyrolysis of PET challenges conventional wisdom dominated by C-H bond fracture, paving the way for efficient, low-pollution green energy recovery.

Complexes of a Frustrated Lewis Pair-Supported P(-1) Ligand

Several complexes of the intramolecular frustrated Lewis pair (FLP)-supported P(-1) ligand [iPr2P(C6H4)BCy2{P}]- are presented (Cy=cyclohexyl). Chief among these is the first example of a monomeric zinc bis(phosphido) complex, which was synthesized as a potential precursor for the solution-phase deposition of Zn3P2. While this goal was ultimately unsuccessful, the Zn(II) complex acts as a convenient springboard to other metal phosphide species via transmetallation: affording a tellurium bis(phosphido) complex and a formal adduct of the phosphorus subhalide PPCl2. Trapping experiments show that the PPCl2 adduct can also be prepared directly through the in situ reduction of PCl3 in the presence of an intramolecular FLP ligand. Lastly, we report a formal η2-phosphaborene complex of cobalt(-1) which is isoelectronic to olefin complexes, and explore its bonding via density functional theory (DFT) computations.

Multi-spectral and docking assessments to explore the combination of an antiviral drug, entecavir with bovine serum albumin

Molecular interaction of entecavir (ETV) with the transport protein, albumin from bovine serum (BSA) was explored through multispectral and molecular docking approaches. The BSA fluorescence was appreciably quenched upon ETV binding and the quenching nature was static. The ETV-BSA complexation and the static quenching process were further reiterated using UV-visible absorption spectra. The binding constant (Ka) values of the complex were found as 1.47 × 104-4.0 × 103 M-1, which depicting a modarate binding strength in the ETV-BSA complexation. The experimental outcomes verified that the stable complexation was primarily influenced by hydrophobic interactions, hydrogen bonds and van der Waals forces. Synchronous and 3-D fluorescence spectral results demonstrated that ETV had significant impact on the hydrophobicity and polarity of the molecular environment near Tyr and Trp residues. Competitive site-markers displacement (with warfarin and ketoprofen) results discovered the suitable binding locus of ETV at site I in BSA. The molecular docking assessments also revealed that ETV formed hydrogen bonds and hydrophobic interactions with BSA, predominantly binding to site I (sub-domain IIA) of BSA.

Identification of Coumarin-Chalcone and Coumarin-Pyrazoline Derivatives as Novel Anti-Toxoplasma gondii Agents

Introduction

Toxoplasmosis, a zoonotic infection caused by the apicomplexan parasite Toxoplasma gondii, affects a significant portion of the global human population. This condition, particularly dangerous for pregnant women and immunocompromised individuals, currently lacks effective treatment options.

Methods

 Eighteen coumarin-based derivatives were synthesized, comprising coumarin-chalcone hybrids (5a-i) and coumarin-pyrazoline hybrids (6a-i). Cytotoxicity was evaluated using L929 mouse fibroblasts and Hs27 human fibroblasts. Anti-T. gondii activity was assessed, and molecular docking studies were performed to predict binding modes with TgCDPK1.

Results

 Pyrazoline hybrids (6a-i) showed lower toxicity than chalcone-bearing coumarins (5a-i), with CC30 values exceeding the highest tested concentration (500 µg/mL) for most compounds. The synthesized molecules demonstrated strong anti-T. gondii activity, with IC50 values ranging from 0.66 µg/mL to 9.05 µg/mL. Molecular docking studies provided insights into potential binding mechanisms.

Conclusion

 This study highlights the potential of coumarin-based hybrids as anti-T. gondii agents. The findings should contribute to the growing arsenal of small molecules against T. gondii and underscore the value of molecular hybridization in drug design. Further studies to elucidate these compounds' mechanism of action and in vivo efficacy are warranted to fully realize their potential as anti-parasitic agents.