Interaction between polycyclic aromatic hydrocarbons and thymine (T)-base induces double-strand DNA distortion in different species

Polycyclic aromatic hydrocarbons (PAHs) are potent inhibitors of DNA that can induce genetic damage, abnormal gene expression, and metabolic disorders upon interfacing with biological macromolecules. However, the mechanism of their interactions with DNA remains elusive. Therefore, this study selected three representative PAHs, including phenanthrene (Phen), pyrene (Pyre), and benzo[a]pyrene (B[a]P), and explored their binding mechanisms with the double-strand DNA (dsDNA) from different species, including 1J1V (Escherichia coli), 6J5B (Arabidopsis thaliana), and 6Q1V (Homo sapiens). The results revealed that binding between PAHs and dsDNA occurred in the groove via van der Waals forces and π-π stacking, with the carboxyl oxygen atom of the thymine (T)-base within dsDNA being the key binding site. This result was further confirmed by the spectroscopic experiments, where significant changes in the peak of the T-base were observed after PAHs-dsDNA binding. More interestingly, the total binding energies of Pyre with the three dsDNA were -138.800 kJ/mol (Pyre-1J1V), -105.523 kJ/mol (Pyre-6J5B), and -127.567 kJ/mol (Pyre-6Q1V), respectively, all of which were higher than those of Phen and B[a]P. This suggests that that Pyre has the strongest dsDNA binding ability. Additionally, analysis of the thermodynamic parameters indicated that the interactions between the three PAHs and dsDNA were exothermic reactions. In contrast, the Pyre-dsDNA interaction predominantly involved van der Waals forces and hydrogen bonding due to the enthalpy change (∆H) < 0 and entropy change (∆S) < 0, while the Phen-dsDNA and B[a]P-dsDNA interactions predominantly involved hydrophobic forces due to ∆H > 0 and ∆S > 0. Furthermore, Pyre caused local distortion of dsDNA, which was more pronounced under atomic force microscopy (AFM). In summary, this study has unveiled a new phenomenon of binding between PAHs and dsDNA. This sheds light on the carcinogenic potential and environmental impacts of PAHs pollution.

CO2 hydrogenation to methanol over Pt functionalized Hf-UiO-67 versus Zr-UiO-67

Sustainable methanol formation from CO2/H2 is potentially a key process in the post-fossil chemical industry. In this study, Hf- and Zr-based metal-organic framework (MOF) materials with UiO-67 topology, functionalized with Pt nanoparticles, have been tested for CO2 hydrogenation at 30 bar and 170-240°C. The highest methanol formation rate, 14 molmethanol molPt-1 h-1, was obtained over a Hf-based catalyst, compared with the maximum of 6.2 molmethanol molPt-1 h-1 for the best Zr-based analogue. However, changing the node metal did not significantly affect product distribution or apparent activation energy for methanol formation (44-52 kJ mol-1), strongly indicating that the higher activity of the Hf-based analogues is associated with a higher number of active sites. Both catalysts showed stable catalytic performance during testing under kinetic conditions, but the addition of 2 vol% water to the feed induced catalyst deactivation, in particular the Hf-MOFs. Interestingly, mainly methanol and methane formation rates decreased, while CO formation rates were less affected by deactivation. No direct correlation was found between catalytic stability and framework stability (crystallinity, specific surface area). Experimental and computational studies suggest that water adsorption strength to the MOF node may affect the relative catalytic stability of Hf-UiO-67-Pt versus Zr-UiO-67-Pt methanol catalysts.This article is part of the discussion meeting issue 'Green carbon for the chemical industry of the future'.

Design, synthesis and biological evaluation of multitarget hybrid molecules containing NHC-Au(I) complexes and carbazole moieties

N-heterocyclic carbenes (NHCs) represent suitable ligands for rapid and efficient drug design, because they offer the advantage of being easily chemically modified and can bind several substituents, including transition metals as, for instance, gold derivatives. Gold-NHC complexes possess various biological activities and were demonstrated good candidates as anticancer drugs. Besides, carbazole derivatives are characterized by various pharmacological properties, such as anticancer, antibacterial, anti-inflammatory, and anti-psychotropic. Amongst the latter, N-thioalkyl carbazoles were proved to inhibit cancer cells damaging the nuclear DNA, through the inhibition of human topoisomerases. Herein, we report the design, synthesis and biological evaluation of nine new hybrid molecules in which NHC-Au(I) complexes and N-alkylthiolated carbazoles are linked together, in order to obtain novel biological multitarget agents. We demonstrated that the lead hybrid complexes possess anticancer, anti-inflammatory and antioxidant properties, with a high potential as useful tools for treating distinct aspects of several diseases, amongst them cancer.

Carbamic acid and its dimer: A computational study

A recent work by Marks et al. on the formation of carbamic acid in NH  3 -CO  2 interstellar ices pointed out its stability in the gas phase and the concomitant production of its dimer. Prompted by these results and the lack of information on these species, we have performed an accurate structural, energetic and spectroscopic investigation of carbamic acid and its dimer. For the former, the structural and spectroscopic characterization employed composite schemes based on coupled cluster (CC) calculations that account for the extrapolation to the complete basis set limit and core correlation effects. A first important outcome is the definitive confirmation of the nonplanarity of carbamic acid, then followed by an accurate estimate of its rotational and vibrational spectroscopy parameters. As far as the carbamic acid dimer is concerned, the investigation started from the identification of its most stable forms. For them, structure and vibrational properties have been evaluated using density functional theory, while a composite scheme rooted in CC theory has been employed for the energetic characterization. Our results allowed us to provide a better interpretation of the feature observed in the recent experiment mentioned above.

Targeting PERK and GRP78 in colorectal cancer: Genetic insights and novel therapeutic approaches

Colorectal cancer (CRC) ranks among the leading causes of cancer-related deaths worldwide. Enhancing CRC diagnosis and prognosis requires the development of improved biomarkers and therapeutic targets. Emerging evidence suggests that the unfolded protein response (UPR) plays a pivotal role in CRC progression, presenting new opportunities for diagnosis, treatment, and prevention. This study hypothesizes that genetic variants in endoplasmic reticulum (ER) stress response genes influence CRC susceptibility. We examined the frequencies of SNPs in PERK (rs13045) and GRP78/BiP (rs430397) within a South Iranian cohort. We mapped the cellular and molecular features of PERK and GRP78 genes in colorectal cancer, observing their differential expressions in tumor and metastatic tissues. We constructed co-expression and protein-protein interaction networks and performed gene set enrichment analysis, highlighting autophagy as a significant pathway through KEGG. Furthermore, the study included 64 CRC patients and 60 control subjects. DNA extraction and genotyping were conducted using high-resolution melting (HRM) analysis. Significant differences in PERK and GRP78 expressions were observed between CRC tissues and controls. Variations in PERK and GRP78 genotypes were significantly correlated with CRC risk. Utilizing a Multi-Target Directed Ligands approach, a dual PERK/GRP78 inhibitor was designed and subjected to molecular modeling studies. Docking experiments indicated high-affinity binding between the proposed inhibitor and both genes, PERK and GRP78, suggesting a novel therapy for CRC. These findings highlight the importance of understanding genetic backgrounds in different populations to assess CRC risk. Polymorphisms in UPR signaling pathway elements may serve as potential markers for predicting CRC susceptibility, paving the way for personalized therapeutic strategies.

Intermolecular interaction energies with AROFRAG-A systematic approach for fragmentation of aromatic molecules

Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.

Computational predictions of cocrystal formation: A benchmark study of 28 assemblies comparing five methods from high-throughput to advanced models

Cocrystals are assemblies of more than one type of molecule stabilized through noncovalent interactions. They are promising materials for improved drug formulation in which the stability, solubility, or biocompatibility of the active pharmaceutical ingredient (API) is improved by including a coformer. In this work, a range of density functional theory (DFT) and density functional tight binding (DFTB) models are systematically compared for their ability to predict the lattice enthalpy of a broad range of existing pharmaceutically relevant cocrystals. These range from cocrystals containing model compounds 4,4'-bipyridine and oxalic acid to those with the well benchmarked APIs of aspirin and paracetamol, all tested with a large set of alternative coformers. For simple cocrystals, there is a general consensus in lattice enthalpy calculated by the different DFT models. For the cocrystals with API coformers the cocrystals, enthalpy predictions depend strongly on the DFT model. The significantly lighter DFTB models predict unrealistic values of lattice enthalpy even for simple cocrystals.

Design and preparation of a multi-responsive Cd-based fluorescent coordination polymer for smart sensing of nitrobenzene and ornidazole

The improper utilization of nitrobenzene (NB) and ornidazole (ORN) has resulted in irreversible effects on the environment. By combining experimental investigation, density functional theory (DFT) calculations, and machine learning, an effective green strategy for detecting NB and ORN in aqueous solutions can be developed. In this study, a one-dimensional Cd-based coordination polymer (Cd-HCIA-3) was designed and synthesized using 5-((4-carboxybenzyl)oxy)isophthalic acid and rigid 2,2'-bipyridine under solvothermal reaction conditions. Cd-HCIA-3 exhibits excellent fluorescence properties and stability in aqueous solutions. DFT calculations were performed to predict the fluorescence sensing performance of Cd-HCIA-3, revealing that photoinduced electron transfer is the key mechanism for inducing fluorescence quenching in the presence of NB and ORN, with weak molecular interactions promoting electron transfer. Fluorescence sensing experiments were conducted to verify the DFT results, showing that Cd-HCIA-3 can selectively detect NB and ORN in aqueous solutions with limits of detection of 7.22 × 10-8 and 1.31 × 10-7 mol/L, respectively. This study's findings provide valuable insights into the design and synthesis of fluorescent coordination polymers for target analytes.

Phosphate ligand-mediated production of reactive oxygen species during oxygenation of Fe(II)-phosphate complexes

Reactive oxygen species (ROS) production upon the oxygenation of reduced iron minerals is of critical importance to redox cycles of Fe and the fate of refractory organic contaminants. The environmental impact factors during this process, however, have been underappreciated. In this study, prominently enhanced production of hydroxyl radicals (•OH) was observed by oxygenation of Fe(II) with 5-50 mM phosphate. The results of spin trap electron spin resonance (ESR) experiment showed that Fe(II)-phosphate complexes facilitated the generation of •OH. The degradation experiment of p-nitrophenol (PNP) confirmed that •OH formation was dominated by a consecutive one-electron O2 reduction (90.2-96.9 %), and the quantification of PNP degradation products revealed that Fe(II)/phosphate molar ratios regulated the O2 activation pathways for O2•- or •OH production. The further experimental and theoretical investigation demonstrated that the coordination of phosphate with Fe(II) plays a dual role in ROS generation that facilitated O2•- formation by lowering the energy barrier for Fe(II) oxidation and altered the reaction pathway of •OH formation due to its occupation of sites for electron transfer. The present work highlights an important role of natural oxyanions in O2 activation by Fe(II) and raises the possibility of in situ degradation of contaminants in subsurface environment.

Bacterial mercury methylation modulated by vitamin B9: An overlooked pathway leads to increased environmental risks

There has been a serious health and environmental concern in conversion of inorganic mercury (Hg) to the neurotoxin, methylmercury (MeHg) by anaerobic microbes, while very little is known about the potential role of vitamin B9 (VB9) regulator in the biochemical generation of MeHg. This study innovatively investigated bacterial Hg methylation by Geobacter sulfurreducens PCA in the presence of VB9 under two existing scenarios. In the low-complexing scenario, the bacterial MeHg yield reached 68 % higher than that without VB9 within 72 h, which was attributed to free VB9-protected PCA cells relieving oxidative stress, as manifested by the increased expression of Hg methylation gene (hgcAB cluster by 19-48 %). The high-complexing scenario emphasized the intracellular Hg accumulation (38-45 %) after 12 h, as indicated by the increased expression of outer membrane protein-related and mercuric reductase-encoding genes, indicating the inefficient bioavailability of Hg due to a gradual shift from Hg reduction toward Hg0 re-oxidation controlled by competitive ligand exchange. These results suggested that VB9 application significantly raised the potential for bacterial Hg methylation and cellular accumulation, thus proposing insights into the biochemical behaviors of hazardous Hg in farming environments where vulnerable organisms are more possibly co-exposed to higher levels of Hg and VB9.

Spectral-fluorescent study of substituted trimethine cyanine dyes in solutions and in complexes with DNA. Effects of aggregation, moderate heating, and decreasing pH

Trimethine cyanine dyes are widely used as probes for the detection, study and quantification of biomolecules. In particular, cationic trimethine cyanines noncovalently interact with DNA with growing fluorescence. However, their use is often limited by the tendency to self-association - to the formation of aggregates. Disubstituted trimethine cyanines with hydrophobic substituents are especially prone to aggregation. In this work, we studied the interaction of a number of substituted trimethine cyanines with DNA (in aqueous buffer solutions) and showed that their aggregation strongly interfered with their use as fluorescent probes for DNA. To eliminate this drawback, preliminary heating of dye solutions with DNA to 60-70 °C was used, followed by cooling to room temperature. Compared to the experiments without heating, an increase in the dye fluorescence intensity was observed due to the partial thermal decomposition of the aggregates and the interaction of the resulting monomers with DNA. To decompose aggregates, another method was also used - protonation of the dyes with amino substituents in buffer solutions with pH 5.0, which also led to growing the dye fluorescence intensity in the presence of DNA. Complexes of the dyes with DNA were modeled using molecular docking. Effective binding constants of the dyes to DNA and detection limits when using the dyes as probes for DNA (LOD and LOQ) were determined. It is shown that dye 3 with heating in neutral buffer and dye 1 in acidic buffer may be recommended as sensitive probes for DNA. It is concluded that the method of preliminary heating may be applied to dyes prone to aggregation, for improving their properties as biomolecular probes. Another possible means to reduce the interfering effects of dye aggregates is to use easily protonated dyes (with amino substituents) in slightly acidic media.

Indole-core inhibitors of influenza a neuraminidase: iterative medicinal chemistry and molecular modeling

Influenza viruses that cause seasonal and pandemic flu are a permanent health threat. The surface glycoprotein, neuraminidase, is crucial for the infectivity of the virus and therefore an attractive target for flu drug discovery campaigns. We have designed and synthesized more than 40 3-indolinone derivatives. We mainly investigated the role of substituents at the 2 position of the core as well as the introduction of substituents or a nitrogen atom in the fused phenyl ring of the core for inhibition of influenza virus neuraminidase activity and replication in vitro and in vivo. After evaluating the compounds for their ability to inhibit the viral neuraminidase, six potent inhibitors 3c, 3e, 7c, 12o, 12v, 18d were progressed to evaluate for cytotoxicity and inhibition of influenza virus A/PR/8/34 replication in in MDCK cells. Two hit compounds 3e and 12o were tested in an animal model of influenza virus infection. Molecular mechanism of the 3-indolinone derivatives interactions with the neuraminidase was revealed in molecular dynamic simulations. Proposed inhibitors bind to the 430-cavity that is different from the conventional binding site of commercial compounds. The most promising 3-indolinone inhibitors demonstrate stronger interactions with the neuraminidase in molecular models that supports proposed binding site.

Renewed spectroscopic and theoretical research of hydrogen bonding in ascorbic acid

The studies of two isomers of ascorbic acid and their deuteroanalogues, presented in the paper, have been accomplished by vibrational spectroscopy methods and quantum-chemical simulations. The spectroscopic research of L-ascorbic and D-isoascorbic acids have been carried out by the infrared (IR) and Raman (R) techniques. On the basis of the obtained results the spectral interpretation of the hydrogen bonded groups of ascorbic acids has been performed. Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT) have been employed to support spectroscopic experimental findings and shed light onto the bridged proton dynamics in the L- and D- isomers of ascorbic acids. The accurate assignments of the hydrogen bond modes have been accomplished with the application of deuterosubstitution, CPMD-solid state simulations and Potential Energy Distribution (PED) analysis. The spectral and structural results have shown that dependency ν(OH) = f(γ(OH)) is the most common for the OHO hydrogen bond, whereas dependency d(OO) = f(γ(OH)) differs as for the ionic and resonance assisted hydrogen bonds.

Ultrafast conformation-dependent charge transfer in N, N, N', N'-tetramethyl-1,3-propanediamine: Effect of flexible carbon skeleton on electron lone pair interactions

Flexible three-carbon skeleton makes N, N, N', N'-tetramethyl-1,3-propanediamine (TMPDA) an important diamine system to investigate the conformation-dependent electron lone pair interactions and charge delocalization. The charge transfer process linked to structural motions of the three-carbon skeleton has been monitored in real time by the Rydberg electron binding energy (BE) spectra of TMPDA coupled with quantum chemical calculations. Optical excitation to the 3p state with a 200 nm pump pulse initially generated a localized charge on one of the two nitrogen atoms that may partially transfer to the other one. Rapid internal conversion (IC) from the 3p to 3s state occurred within 430 fs, resulting in an initial charge delocalized 3s_h/3s_l population ratio of 23.6 %/76.4 %. A final 3s_h/3s_l (51.9 %/48.1 %) equilibrium proceeded within about 2.64 ps. The 3s_h (TTTT+, GG'TG+ and G'GG'G+) and 3s_l (GG'GG'+ and GG'G'G+) (see text for structure definitions) are identified as the extended and folded conformers, respectively. Two types of electron lone pair interactions, i.e., through-space interaction (TSI) and through-bond interaction (TBI), are found to coexist in TMPDA to drive charge transfer. The GG'GG'+ and GG'G'G+ structures exhibit TSI, while the TTTT+ structure shows TBI. The GG'TG+ and G'GG'G+ structures exhibit both TSI and TBI. Flexible three-carbon skeleton provide more opportunities for the two N-electron lone pairs to overlap in space (i.e., TSI), making TMPDA to be favorable for the most stably folded conformation.

Combination of oxidative and reductive effects of phenolic compounds on the degradation of aniline disinfection by-products by free radicals

In this study, we selected 13 phenolic compounds containing -COOH, -CHO, -OH, and -COCH3 functional groups as model compounds for dissolved organic matter (DOM), and explored the redox reactions during the co-degradation of phenolic compounds with aniline disinfection by-products (DBPs) at the molecular level. When phenolic compounds and aniline DBPs were degraded, phenoxy radicals and aniline radicals were the most important intermediates. Phenoxy radicals can degrade aniline DBPs via hydrogen atom abstraction (HAA) reactions, and the reaction rates were related to the reduction potentials of the compounds. Compounds containing electron-withdrawing groups were more likely to oxidize aniline DBPs. Aniline DBPs were more easily degraded by phenoxy radicals when they contained electron-donating groups, and the increase in the number of chlorine atoms inhibited the reaction rates of aniline DBPs degradation by phenoxy radicals. Although phenolic compounds can reduce aniline DBPs, there was no significant correlation between the reaction rates and the reduction potentials of the compounds. Considering the redox effects of phenolic compounds on aniline DBPs, co-degradation simulations showed that phenolics inhibited the degradation efficiency of aniline DBPs. This work provided new insights into the transformation mechanisms and degradation efficiencies of DOM and aniline DBPs when they were co-degraded.

Sustainable protein/polysaccharide aerogel for the simultaneous and efficient removal of multiple organic contaminants: Insights from DFT calculations and phenomenological mass-transfer modeling

Wastewater contains various organic contaminants that pose great hazards to human health and the environment. A protein/polysaccharide-derived aerogel, namely, ICMA, was developed as a high-performance adsorbent for the simultaneous and efficient removal of diverse contaminants from wastewater, including melanoidin (MLE), Congo red (CR), and diclofenac (DIC). Metal organic framework (UiO-66-NH2), as a regulatory factor, significantly improved the porosity and pore volume of the ICMA to enhance the capture performance of contaminants. The ICMA exhibited outstanding adsorption efficiency owing to the incorporation of ample polyamine functional groups and its well-developed pore structure, large porosity and pore volume, and remarkable heat resistance. The equilibrium capture capacities of the ICMA were 1364, 2031, and 539 mg/g for MLE, CR, and DIC, respectively, with corresponding removal efficiencies all exceeding 90%. Furthermore, the ICMA can capture cationic dyes through MLE/CR/DIC-bridging interactions. After five cycles, the used ICMA can still maintain a high contaminant removal rate/amount, demonstrating good reusability. The classic adsorption model showed that the capture of contaminants by the ICMA is a double-layered and heterogeneous adsorption orientation. A brand new LWAMTM model demonstrated that the adsorption mass-transfer process is jointly determined by the external mass conveyance, pore diffusion, and adsorption on the active site. Multiple characterizations indicated that the contaminant adsorption onto the ICMA was mainly facilitated by charge interactions, with H-bonds playing a secondary role. Quantum chemical theory simulations further provide insights into the atomic-level mechanisms involved in the capture of contaminants. Hirshfeld surface analysis revealed that the ICMA functions as both an H-bond acceptor and a donor during contaminant adsorption. Scale-up and upgrade adsorption were performed to treat actual/simulated wastewater, establishing the groundwork for the industrial implementation of the ICMA.

Hydrostatic pressure effect on excited state properties of room temperature phosphorescence molecules: A QM/MM study

Stimulus-responsive organic room temperature phosphorescence (RTP) materials exhibit variations in their luminescent characteristics (lifetime and efficiency) upon exposure to external stimuli, including force, heat, light and acid-base conditions, the development of stimulus-responsive RTP molecules becomes imperative. However, the inner responsive mechanism is unclear, theoretical investigations to reveal the relationship among hydrostatic pressures, molecular structures and photophysical properties are highly desired. Herein, taking the Se-containing RTP molecule (SeAN) as a model, based on the dispersion corrected density functional theory (DFT-D), the combined quantum mechanics and molecular dynamics (QM/MM) method and thermal vibration correlation function (TVCF) theory, the influences of hydrostatic pressure on molecular structures, transition properties as well as lifetimes and efficiencies of RTP molecule are theoretically studied. Results show that extended lifetime and enhanced efficiency are observed at 2 Gpa compared with molecule at normal pressure, and this is related with the small reorganization energy and large oscillator strength. Moreover, due to the small energy gap (0.34 eV) and remarkable spin-orbit coupling (SOC) constant (8.56 cm-1) between first singlet excited state and triplet state, fast intersystem crossing (ISC) process is determined for molecule at 6 Gpa. Furthermore, the intermolecular interactions are visualized using independent gradient model based on Hirshfeld partition (IGMH) and the changes of molecular packing modes, SOC values, lifetimes and efficiencies with pressures are detected. These results reveal the relationship between molecular structures and RTP properties. Our work provides theoretical insights into the hydrostatic pressure response mechanism and could promote the development new efficient stimulus-responsive molecules.

Phosphorylation site of L-alanyl-L-glutamine identified by Raman optical activity spectroscopy

Phosphorylated peptides are instrumental in studying protein phosphorylation events. In the present study, Raman optical activity (ROA) is employed to elucidate the structure of a dipeptide, L-alanyl-L-glutamine (L-Ala-L-Gln) and its two differently alkylated N-phosphorylated derivatives. Theoretical simulations were conducted to aid the interpretation of peptide conformation variations upon phosphorylation, and of the measured Raman and ROA spectra. Induced circularly polarized luminescence (CPL) was also recorded in solution, in the presence of a simple europium aqua ion. As the spectra are peptide specific, this type of stereochemical analysis is expected to aid identification of the phosphorylation sites also in other peptides and possibly proteins.

The molecular structure, vibrational spectra, solvation effect, non-covalent interactions investigations of psilocin

Psilocin, or 4-HO-DMT (or 3-(2-dimethylaminoethyl)-1H-indol-4-ol), is a psychoactive alkaloid substance from the tryptamine family, isolated from Psilocybe mushrooms. This substance is being studied by various research groups because it has a clear therapeutic effect in certain dosages. In this work, the study of the structure and properties of psilocin was carried using theoretical methods: the effects of polar solvents (acetonitrile, dimethylsulfoxide, water, and tetrahydrofuran) on the structural parameters, spectroscopic properties (Raman, IR, and UV-Vis), frontier molecular orbital (FMO), molecular electrostatic potential (MEP) surface, and nonlinear optical parameters (NLO). Theoretical calculations were performed at the B3LYP/6-311++G(d,p) level by the density functional theory (DFT) method. IEFPCM was used to account for solvent effects. The types and nature of non-covalent interactions (NCI) between psilocin and solvent molecules were determined using Atoms in Molecules (AIM), the reduced density gradient method (RDG), the electron localization function (ELF), and the localization orbital locator (LOL). Experimental and calculated FT-IR, FT-Raman, and UV-Vis spectra were compared and found to be in good agreement.

Discovery of pyrrolo[2,3-d]pyrimidin-4-one derivative YCH3124 as a potent USP7 inhibitor for cancer therapy

USP7 is one of the most studied deubiquitinating enzymes, which is involved in the regulation of multiple cell signaling pathways and has been shown to be associated with the occurrence and progression of a variety of cancers. Inhibitors targeting USP7 have been studied by several teams, but most of them lack selectivity and have low activities. Herein, we reported a serious of pyrrole[2,3-d]pyrimidin-4-one derivatives through scaffold hopping of recently reported 4-hydroxypiperidine compounds. The representative compound Z33 (YCH3124) exhibited highly potent USP7 inhibition activity as well as anti-proliferative activity against four kinds of cancer cell lines. Further study revealed that YCH3124 effectively inhibited the downstream USP7 pathway and resulted in the accumulation of both p53 and p21 in a dose-dependent manner. Notably, YCH3124 disrupted cell cycle progression through restricting G1 phase and induced significant apoptosis in CHP-212 cells. In summary, our efforts provided a series of novel pyrrole[2,3-d]pyrimidin-4-one analogs as potent USP7 inhibitors with excellent anti-cancer activity.

Combatting the antigenicity of common ragweed pollen and its primary allergen Amb a 1 with cold atmospheric pressure air plasma

Airborne allergens, especially those originating from various types of pollen, significantly compromise the health and well-being of individuals on a global scale. Here, cold atmospheric pressure plasma (CAP) created in ambient air was used to treat highly allergenic and invasive Ambrosia artemisiifolia pollen. Immunoassays were used to evaluate the impact of CAP on the principal A. artemisiifolia allergen Amb a 1, demonstrating that > 90 % reduction in antigenicity could be achieved. Chemical analyses using Fourier Transform infrared revealed that CAP induced significant alterations to proteins on the surface of pollen grains, resulting in a 43 % increase in the amide I peak area and a 57 % increase in the amide II peak area. These findings were corroborated by Raman and X-ray photoelectron spectroscopy, which indicated that the protein modifications induced by CAP were due to carbonylation and nitration/nitrosylation processes. Beyond protein transformations, CAP also induced notable oxidation and modification of lipid-like compounds, polysaccharides and sporopollenin. Evident transformations at the chemical level translated into morphological changes at the grain surface, manifesting as increased roughness via significant outer-layer etching. These findings underscore the potential of CAP technology as a viable approach for mitigating against the allergenicity of pollen, providing a deeper understanding into the underlying chemical mechanisms.

Unbiased MD simulations identify lipid binding sites in lipid transfer proteins

The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid binding to bridge LTPs of the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.

Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening

Acute lymphoblastic leukemia (ALL) is a disease of lymphocyte origin predominantly diagnosed in children. While its 5-year survival rate is high, resistance to chemotherapy drugs is still an obstacle. Our aim is to determine differentially expressed genes (DEGs) related to Asparaginase, Daunorubicin, Prednisolone, and Vincristine resistance and identify potential inhibitors via docking. Three datasets were accessed from the Gene Expression Omnibus database; GSE635, GSE19143, and GSE22529. The microarray data was analyzed using R4.2.0 and Bioconductor packages, and pathway and protein-protein interaction analysis were performed. We identified 1294 upregulated DEGs, with 12 genes consistently upregulated in all four resistant groups. KEGG analysis revealed an association with the PI3K-Akt pathway. Among DEGs, 33 hub genes including MDM2 and USP7 were pinpointed. Within common genes, CLDN9 and HS3ST3A1 were subjected to molecular docking against 3556 molecules. Following ADMET analysis, three drugs emerged as potential inhibitors: Flunarizine, Talniflumate, and Eltrombopag. Molecular dynamics analysis for HS3ST3A1 indicated all candidates had the potential to overcome drug resistance, Eltrombopag displaying particularly promising results. This study promotes a further understanding of drug resistance in ALL, introducing novel genes for consideration in diagnostic screening. It also presents potential inhibitor candidates to tackle drug resistance through repurposing.

Revealing miRNAs patterns by employing matrix representations and energy analysis

MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression. Despite their relatively short length (about 21 nucleotides), they can regulate thousands of transcripts within a cell. Due to their low complementarity to targets, studying their activity and binding region preferences (3'UTR, 5'UTR, or CDS) is challenging. In this paper, we analyzed a set of human miRNAs to uncover their general patterns. We began with a sequence logo to verify conservation at specific positions. To discover long-range correlations, we employed chaos game representation (CGR) and genomatrix, methods that enable both graphical and analytical analysis of sequence sets and are well-established in bioinformatics. Our results showed that miRNAs exhibit strongly non-random and characteristic patterns. To incorporate physicochemical properties into the analysis, we applied the electron-ion interaction potential (EIIP) parameter. An important part of our study was to validate the division of miRNAs into two parts-seed and puzzle. The seed region is responsible for target binding, while the puzzle region likely interacts with the RISC complex. We estimated duplex binding energy within the 3'UTR, 5'UTR, and CDS regions using the miRanda tool. Based on the median energy distribution, we divided the miRNAs into two subsets, reflecting different patterns in chaos game representation. Interestingly, one subset displayed significant similarity to conserved and highly confidential miRNAs. Our results confirm the low complementarity of miRNA/mRNA interactions and support the functional division of miRNA structure. Additionally, we present findings related to the localization of transcript target sites, which form the basis for further analyses.

Structure based computational RNA design towards MafA transcriptional repressor implicated in multiple myeloma

Multiple myeloma is recognized as the second most common hematological cancer. MafA transcriptional repressor is an established mediator of myelomagenesis. While there are multitude of drugs available for targeting various effectors in multiple myeloma, current literature lacks a candidate RNA based MafA modulator. Thus, using the structure of MafA homodimer-consensus target DNA, a computational effort was implemented to design a novel RNA based chemical modulator against MafA. First, available MafA-consensus DNA structure was employed to generate an RNA library. This library was further subjected to global docking to select the most plausible RNA candidates, preferring to bind DNA binding region of MafA. Following global docking, MD-ready complexes that were prepared via local docking program, were subjected to 500 ns of MD simulations. First, each of these MD simulations were analyzed for relative binding free energy through MM-PBSA method, which pointed towards a strong RNA based MafA binder, RNA1. Second, through a detailed MD analysis, RNA1 was shown to prefer binding to a single monomer of the dimeric DNA binding domain of MafA using higher number of hydrophobic interactions compared with positive control MafA-DNA complex. At the final phase, a principal component analyses was conducted, which led us to identify the actual interaction region of RNA1 and MafA monomer. Overall, to our knowledge, this is the first computational study that presents an RNA molecule capable of potentially targeting MafA protein. Furthermore, limitations of our study together with possible future implications of RNA1 in multiple myeloma were also discussed.

A robust amphiphilic ionic covalent organic framework intercalated into functionalized graphene oxide hybrid membranes for ultrafast extraction uranium from wastewater

The efficient capture of uranium from wastewater is crucial for environmental remediation and the sustainable development of nuclear energy, yet it poses considerable challenges. In this study, amphiphilic ionic covalent organic framework intercalated into graphene oxide (GO) nanosheets functionalized with polyethyleneimine (PEI) were used to construct hybrid membranes with ultrafast uranium adsorption. These hybrid membranes achieved equilibrium in just 10 min and the adsorption capacity was as high as 358.8 mg g-1 at pH = 6. X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT) analyses revealed that the strong interaction between sulfonic acid groups and uranyl ions was the primary reason for the high adsorption capacity and selectivity. The extended transition state and natural orbitals for chemical valence (ETS-NOCV) analysis revealed that the interaction between the 7 s and 5f orbitals of uranyl and the 2p orbitals of S and O in the sulfonate was the primary reason for the strong interaction between the sulfonate and the uranyl ion. This research presents an effective method for the rapid extraction of uranium from wastewater.

Bridging pyrimidine hemicurcumin and Cisplatin: Synthesis, coordination chemistry, and in vitro activity assessment of a novel Pt(II) complex

In the upcoming decades, the incidence and mortality rates of cancer are expected to rise globally, with colorectal and prostate cancers among the most prevalent types. Despite advancements in molecular targeted therapy, platinum-based chemotherapies remain the cornerstone of treatment, especially for colorectal and prostate cancer, with oxaliplatin and cisplatin being extremely effective due to their DNA-targeting capabilities. In our pursuit of new platinum-based chemotherapeutics that are potentially less toxic and more effective, we have explored the combination of the Pt-binding groups of the diaminocyclohexane ring used in oxaliplatin, with the stable amino-pyrimidine hemicurcumin moiety. This new derivative exhibit improved stability in physiological conditions and increased solubility in aqueous media, demonstrating promising effects on cell proliferation of both colorectal and prostate cells. We report herein the complete synthesis and chemical characterization in solution of the new derivative [(1R,2R)-N1-(3-(4-((E)-2-(2-Amino-6-methylpyrimidin-4-yl)vinyl)-2-methoxyphenoxy) propyl) cyclohexane-1,2-diamine] (MPYD). Our analysis includes an examination of its acid-base equilibria, speciation and stability in physiological conditions. The synthesis and in situ formation of Pt(II) complexes were investigated by nuclear magnetic resonance spectroscopy, while density functional theory calculations were employed to elucidate the chemical structure in solution. Results on the biological activity were obtained through cell viability assays on different colorectal and prostate cell lines (HCT116, HT29, PC3 and LNCaP).

Unraveling the synergism mechanistic insight of O-vacancy and interfacial charge transfer in WO3-x decorated on Ag2CO3/BiOBr for photocatalysis of water pollutants: Based on experimental and density functional theory (DFT) studies

Photocatalysis has been widely used as one of the most promising approaches to remove various pollutants in liquid or gas phases during the last decade. The main emphasis of the study is on the synergy of vacancy engineering and heterojunction formation, two widely used modifying approaches, to significantly alter photocatalytic performance. The vacancy-induced Ag2CO3/BiOBr/WO3-x heterojunction system has been fabricated using a co-precipitation technique to efficiently abate methylene blue (MB) dye and doxycycline (DC) antibiotic. The as-fabricated Ag2CO3/BiOBr/WO3-x heterojunction system displayed improved optoelectronic characteristic features because of the rational combination of dual charge transferal route and defect modulation. The Ag2CO3/BiOBr/WO3-x system possessed 97% and 74% photodegradation efficacy for MB and DC, respectively, with better charge isolation and migration efficacy. The ternary photocatalyst possessed a multi-fold increase in the reaction rate for both MB and DC, i.e., 0.021 and 0.0078 min-1, respectively, compared to pristine counterparts. Additionally, more insightful deductions about the photodegradation routes were made possible by the structural investigations of MB and DC using density functional theory (DFT) simulations. This study advances the understanding of the mechanisms forming visible light active dual Z-scheme heterojunction for effective environmental remediation.

Conserved sequence features in intracellular domains of viral spike proteins

Viral spike proteins mutate frequently, but conserved features within these proteins often have functional importance and can inform development of anti-viral therapies which circumvent the effects of viral sequence mutations. Through analysis of large numbers of viral spike protein sequences from several viral families, we found highly (>99%) conserved patterns within their intracellular domains. The patterns generally consist of one or more basic amino acids (arginine or lysine) adjacent to a cysteine, many of which are known to undergo acylation. These patterns were not enriched in cellular proteins in general. Molecular dynamics simulations show direct electrostatic and hydrophobic interactions between these conserved residues in hemagglutinin (HA) from influenza A and B and the phosphoinositide PIP2. Super-resolution microscopy shows nanoscale colocalization of PIP2 and several of the same viral proteins. We propose the hypothesis that these conserved viral spike protein features can interact with phosphoinositides such as PIP2.

New substituted benzenesulphonamoyl 'Cys-Gly' dipeptide carboxamide derivatives: Design, synthesis, characterization and pharmacological studies

Twelve new sulphonamide (Cys-Gly) dipeptide carboxamide derivatives 17a-17l were designed, prepared and characterized through spectroscopic techniques and their pharmacological properties investigated. The molecular docking analyses revealed good interactions of the derivatives with the desired amino residues active pockets. In vitro antimicrobial, in vivo antimalarial, haematological and other related tests (liver and kidney) were also conducted. Compounds 17b exhibited good minimum inhibitory concentration (MIC) results (0.9-11) mg/mL for the studied organisms when compared with ciprofloxacin and fluconazole. Derivatives 17a -17l showed parasitaemia inhibition in the range (31.11-67.78) % on the fourth day after treating the animals with 40 mg/kg of the compounds. Derivative 17b also displayed the highest parasitaemia inhibition (67.78 %) comparable with the standard (Lumenfantrine) 75.27 %. The prepared derivatives showed promising pharmacological properties with regards to hematological, liver and kidney function tests.

Discovery of novel thiazole derivatives containing pyrazole scaffold as PPAR-γ Agonists, α-Glucosidase, α-Amylase and COX-2 inhibitors; Design, synthesis and in silico study

A novel series of thiazole derivatives with pyrazole scaffold 16a-l as hybrid rosiglitazone/celecoxib analogs was designed, synthesized and tested for its PPAR-γ activation, α-glucosidase, α-amylase and COX-2 inhibitory activities. Regarding the anti-diabetic activity, all compounds were assessed in vitro against PPAR-γ activation, α-glucosidase and α-amylase inhibition in addition to in vivo hypoglycemic activity (one day and 15 days studies). Compounds 16b, 16c, 16e and 16 k showed good PPAR-γ activation (activation % ≈ 72-79 %) compared to that of the reference drug rosiglitazone (74 %). In addition, the same derivatives 16b, 16c, 16e and 16 k showed the highest inhibitory activities against α-glucosidase (IC50 = 0.158, 0.314, 0.305, 0.128 μM, respectively) and against α-amylase (IC50 = 32.46, 23.21, 7.74, 35.85 μM, respectively) compared to the reference drug acarbose (IC50 = 0.161 and 31.46 μM for α-glucosidase and α-amylase, respectively). The most active derivatives 16b, 16c, 16e and 16 k also revealed good in vivo hypoglycemic effect comparable to that of rosiglitazone. In addition, compounds 16b and 16c had the best COX-2 selectivity index (S.I. = 18.7, 31.7, respectively) compared to celecoxib (S.I. = 10.3). In vivo anti-inflammatory activity of the target derivatives 16b, 16c, 16e and 16 k supported the results of in vitro screening as the derivatives 16b and 16c (ED50 = 8.2 and 24 mg/kg, respectively) were more potent than celecoxib (ED50 = 30 mg/kg). In silico docking, ADME, toxicity, and molecular dynamic studies were carried out to explain the interactions of the most active anti-diabetic and anti-inflammatory compounds 16b, 16c, 16e and 16 k with the target enzymes in addition to their physiochemical parameters.

Patterned graphene: An effective platform for adsorption, immobilization, and destruction of SARS-CoV-2 Mpro

To address the ongoing challenges posed by the SARS-CoV-2 and potentially stronger viruses in the future, the development of effective methods to fabricate patterned graphene (PG) and other precisely functional products has become a new research frontier. Herein, we modeled the "checkerboard" graphene (CG) and stripped graphene (SG) as representatives of PG, and studied their interaction mechanism with the target protein (Mpro) by molecular dynamics simulation. The calculation results on the binding strength and the root mean square deviation values of the active pocket revealed that PG is an effective platform for adsorption, immobilization, and destruction of Mpro. Specifically, CG is found to promote disruption of the active pocket for Mpro, but the presence of "checkerboard" oxidized regions inhibits the adsorption of Mpro. Meanwhile, the SG can effectively confine Mpro within the non-oxidized strips and enhances their binding strength, but doesn't play well on disrupting the active pocket. Our work not only elucidates the biological effects of PGs, but also provides guidance for their targeted and precise utilization in combating the SARS-CoV-2.

Impact of surface-active ionic solutions on the structure and function of laccase from trametes versicolor: Insights from molecular dynamics simulations

Many protein-ionic liquid investigations have examined laccase interactions. Laccases are a class of poly-copper oxidoreductases that retain significant biotechnological relevance owing to their notable oxidative capabilities and their application in the elimination of synthetic dyes, phenolic compounds, insecticides, and various other substances. This study investigates the impact of surface active ionic liquids (SAILs), namely, decyltrimethylammonium bromide [N10111][Br] and 1-decyl-3-methylimidazolium chloride [C10mim][Cl] as cationic surfactant ionic liquids and cholinium decanoate [Chl][Dec], an anionic surfactant ionic liquid, on the structure and function of laccase from the fungus Trametes versicolor (TvL) by the molecular dynamics (MD) simulation method. In summary, this study showed that laccase solvent-accessible surface area increased in the ionic liquid [Chl][Dec] while it decreased in the other two ionic liquids. Interestingly, [Chl][Dec] ionic liquid components formed hydrogen bonds with laccase, while [N10111][Br] and [C10mim][Cl] components were unable to form hydrogen bonds with laccase. The quantity of hydrogen bonds formed between water molecules and the enzyme was also diminished in the presence of [Chl][Dec] in comparison to the other two ionic liquids. especially at a concentration of 250 mM. In 250 mM concentrations of [N10111][Br] and [C10mim][Cl], clusters of long-chain cations are likely to form near the copper T1 site. However, even at low [Chl][Dec] concentrations, long [Dec]- chains were observed to penetrate the enzyme near the copper T1 site, and at 250 mM [Chl][Dec], a large cluster of anions occupied the opening of the active site. The results of the analysis also show that the interaction between the [Dec]- anion and the enzyme is stronger than the interaction between [N10111]+ and [C10mim]+ with laccase; in addition, the [Dec]- anion, compared to [Br]- and [Cl]- has a much greater tendency to bind with the enzyme residues.

Uncovering substrate specificity determinants of class IIb aminoacyl-tRNA synthetases with machine learning

Specific amino acid (AA) binding by aminoacyl-tRNA synthetases (aaRSs) is necessary for correct translation of the genetic code. Sequence and structure analyses have revealed the main specificity determinants and allowed a partitioning of aaRSs into two classes and several subclasses. However, the information contributed by each determinant has not been precisely quantified, and other, minor determinants may still be unidentified. Growth of genomic data and development of machine learning classification methods allow us to revisit these questions. This work considered the subclass IIb, formed by the three enzymes aspartyl-, asparaginyl-, and lysyl-tRNA synthetase (LysRS). Over 35,000 sequences from the Pfam database were considered, and used to train a machine-learning model based on ensembles of decision trees. The model was trained to reproduce the existing classification of each sequence as AspRS, AsnRS, or LysRS, and to identify which sequence positions were most important for the classification. A few positions (5-8 depending on the AA substrate) sufficed for accurate classification. Most but not all of them were well-known specificity determinants. The machine learning models thus identified sets of mutations that distinguish the three subclass members, which might be targeted in engineering efforts to alter or swap the AA specificities for biotechnology applications.

Computational discovery of tripeptide inhibitors targeting monkeypox virus A42R profilin-like protein

Monkeypox is an infectious disease caused by the monkeypox virus (MPXV), a member of the Orthopoxvirus genus closely related to smallpox. The structure of the A42R profilin-like protein is the first and only available structure among MPXV proteins. Biochemical studies of A42R were conducted in the 1990s and later work also analyzed the protein's function in viral replication in cells. This study aims to screen tripeptides for their potential inhibition of the A42R profilin-like protein using computational methods, with implications for MPXV therapy. A total of 8000 tripeptides underwent molecular docking simulations, resulting in the identification of 20 compounds exhibiting strong binding affinity to A42R. To validate the docking results, molecular dynamics simulations and free energy perturbation calculations were performed. These analyses revealed two tripeptides with sequences TRP-THR-TRP and TRP-TRP-TRP, which displayed robust binding affinity to A42R. Markedly, electrostatic interactions predominated over van der Waals interactions in the binding process between tripeptides and A42R. Three A42R residues, namely Glu9, Ser12, and Arg38, appear to be pivotal in mediating the interaction between A42R and the tripeptide ligands. Notably, tripeptides containing two or three tryptophan residues demonstrate a pronounced binding affinity, with the tripeptide comprising three tryptophan amino acids showing the highest level of affinity. These findings offer valuable insights for the selection of compounds sharing a similar structure and possessing a high affinity for A42R, potentially capable of inhibiting its enzyme activity. The study highlights a structural advantage and paves the way for the development of targeted therapies against MPXV infections.

Investigating the cardiotoxicity of N-n-butyl haloperidol iodide: Inhibition mechanisms on hERG channels

The human Ether-à-go-go-Related Gene (hERG) encodes a protein responsible for forming the alpha subunit of the IKr channel, which plays a crucial role in cardiac repolarization. The proper functioning of hERG channels is paramount in maintaining a normal cardiac rhythm. Inhibition of these channels can result in the prolongation of the QT interval and potentially life-threatening arrhythmias. Cardiotoxicity is a primary concern in the field of drug development. N-n-Butyl haloperidol iodide (F2), a derivative of haloperidol, has been investigated for its therapeutic potential. However, the impact of this compound on cardiac toxicity, specifically on hERG channels, remains uncertain. This study employs computational and experimental methodologies to examine the inhibitory mechanisms of F2 on hERG channels. Molecular docking and molecular dynamics simulations commonly used techniques in computational biology to predict protein-ligand complexes' binding interactions and stability. In the context of the F2-hERG complex, these methods can provide valuable insights into the potential binding modes and strength of interaction between F2 and the hERG protein. On the other hand, electrophysiological assays are experimental techniques used to characterize the extent and nature of hERG channel inhibition caused by various compounds. By measuring the electrical activity of the hERG channel in response to different stimuli, these assays can provide important information about the functional effects of ligand binding to the channel. The study's key findings indicate that F2 interacts with the hERG channel by forming hydrogen bonding, π-cation interactions, and hydrophobic forces. This interaction leads to the inhibition of hERG currents in a concentration-dependent manner, with an IC50 of 3.75 μM. The results presented in this study demonstrate the potential cardiotoxicity of F2 and underscore the significance of considering hERG channel interactions during its clinical development. This study aims to provide comprehensive insights into the interaction between F2 and hERG, which will may guid us in the safe use of F2 and in the development of new derivatives with high efficiency while low toxicity.

The potential of Chlorella spp. as antiviral source against African swine fever virus through a virtual screening pipeline

African swine fever (ASF) causes high mortality in pigs and threatens global swine production. There is still a lack of therapeutics available, with two vaccines under scrutiny and no approved small-molecule drugs. Eleven (11) viral proteins were used to identify potential antivirals in in silico screening of secondary metabolites (127) from Chlorella spp. The metabolites were screened for affinity and binding selectivity. High-scoring compounds were assessed through in silico ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) predictions, compared to structurally similar drugs, and checked for off-target docking with prepared swine receptors. Molecular dynamics (MD) simulations determined binding stability while binding energy was measured in Molecular Mechanics - Generalized Born Surface Area (MMGBSA) or Poisson-Boltzmann Surface Area (MMPBSA). Only six (6) compounds passed until MD analyses, of which five (5) were stable after 100 ns of MD runs. Of these five compounds, only three had binding affinities that were comparable to or stronger than controls. Specifically, phytosterols 24,25-dihydrolanosterol and CID 4206521 that interact with the RNA capping enzyme (pNP868R), and ergosterol which bound to the Erv-like thioreductase (pB119L). The compounds identified in this study can be used as a theoretical basis for in vitro screening to develop potent antiviral drugs against ASFV.

In vitro and in silico studies of the inclusion complexation of 8-bromobaicalein with β-cyclodextrins

Baicalein, a flavone derived from Scutellaria baicalensis Georgi, exhibits potent anti-inflammatory, antiviral, and anticancer properties. Its derivative, known as 8-bromobaicalein (BB), has been found to have strong cytotoxic effect on MCF-7 human breast cancer cells. However, its limited solubility in water has hindered its potential for wider applications. To address this issue, we investigated the use of cyclodextrins specifically βCD, 2,6-di-O-methyl-β-cyclodextrin (DMβCD), and hydroxypropyl-β-cyclodextrin (HPβCD) to improve the solubility of BB through inclusion complexation. During 250 ns molecular dynamics simulations, it was found that BB can form inclusion complexes with all βCDs. These complexes exhibit two distinct orientations: chromone group insertion (C-form) and phenyl group insertion (P-form). The formation of these complexes is primarily driven by van der Waals interactions. DMβCD has the highest number of atom contacts with BB and the lowest solvent accessibility in the hydrophobic cavity. These results coincide with the highest binding affinity from the MM/GBSA-based free energy calculation method. Experimental phase solubility diagrams revealed a 1:1 stoichiometric ratio (AL type) between BB and βCDs, in which BB/DMβCD showed the highest stability. The formation of inclusion complexes was confirmed by differential scanning calorimetry and scanning electron microscope methods. Additionally, the BB/DMβCD inclusion complex demonstrated significantly higher anticancer activity against MCF-7 human breast cancer cells compared to BB alone. These findings underscore the potential of DMβCD for formulating BB in pharmaceutical and medical applications.

Central nervous system disturbances by thiamethoxam in Japanese quail (Coturnix japonica): In vivo, ex vivo, and in silico study

The neurotoxic effects of neonicotinoids (NEOs) have been widely reported in relation to the poisoning of wild birds, yet the underlying molecular mechanism has remained elusive. This study employed Japanese quails (Coturnix japonica) and primary quail embryonic neurons as in vivo and ex vivo models, respectively, to investigate the neurotoxic effects and mechanism of thiamethoxam (TMX), a representative neonicotinoid insecticide, at environmentally relevant concentrations. Following a 28-day exposure to TMX, metabolomic analysis of quail brain revealed TMX-induced changes in glutamatergic, GABA-ergic, and dopaminergic function. Subsequent ex vivo and in silico experimentation revealed that the activation of nicotinic acetylcholine receptors and calcium signaling, induced by clothianidin (CLO), the primary metabolite of TMX, served as upstream events for the alterations in neurotransmitter synthesis, metabolism, release, and uptake. Our findings propose that the disruption of the central nervous system, caused by environmentally significant concentrations of NEOs, may account for the avian poisoning events induced by NEOs.

Computational strategies in Klebsiella pneumoniae vaccine design: navigating the landscape of in silico insights

The emergence of multidrug-resistant Klebsiella pneumoniae poses a grave threat to global public health, necessitating urgent strategies for vaccine development. In this context, computational tools have emerged as indispensable assets, offering unprecedented insights into klebsiellal biology and facilitating the design of effective vaccines. Here, a review of the application of computational methods in the development of K. pneumoniae vaccines is presented, elucidating the transformative impact of in silico approaches. Through a systematic exploration of bioinformatics, structural biology, and immunoinformatics techniques, the complex landscape of K. pneumoniae pathogenesis and antigenicity was unravelled. Key insights into virulence factors, antigen discovery, and immune response mechanisms are discussed, highlighting the pivotal role of computational tools in accelerating vaccine development efforts. Advancements in epitope prediction, antigen selection, and vaccine design optimisation are examined, highlighting the potential of in silico approaches to update vaccine development pipelines. Furthermore, challenges and future directions in leveraging computational tools to combat K. pneumoniae are discussed, emphasizing the importance of multidisciplinary collaboration and data integration. This review provides a comprehensive overview of the current state of computational contributions to K. pneumoniae vaccine development, offering insights into innovative strategies for addressing this urgent global health challenge.

Simulating the anti-aggregative effect of fasudil in early dimerisation process of α-synuclein

The aggregation of the protein α-synuclein into amyloid deposits is associated with multiple neurological disorders, including Parkinson's disease. Soluble amyloid oligomers are reported to exhibit higher toxicity than insoluble amyloid fibrils, with dimers being the smallest toxic oligomer. Small molecule drugs, such as fasudil, have shown potential in targeting α-synuclein aggregation and reducing its toxicity. In this study, we use atomistic molecular dynamics simulations to demonstrate how fasudil affects the earliest stage of aggregation, namely dimerization. Our results show that the presence of fasudil reduces the propensity for intermolecular contact formation between protein chains. Consistent with previous reports, our analysis confirms that fasudil predominantly interacts with the negatively charged C-terminal region of α-synuclein. However, we also observe transient interactions with residues in the charged N-terminal and hydrophobic NAC regions. Our simulations indicate that while fasudil prominently interacts with the C-terminal region, it is the transient interactions with residues in the N-terminal and NAC regions that effectively block the formation of intermolecular contacts between protein chains and prevent early dimerization of this disordered protein.

Molecular insights reveal how the glycolipids in cell membrane mitigates nanomaterial's invasion

Nanomaterial-cellular membrane interaction is crucial for the cytotoxicity of such materials in theoretical investigations. However, previous research often used cellular membrane models with one or few lipid types, which deviates significantly from realistic membrane compositions. Here, employing molecular dynamics (MD) simulations, we investigate the impact of a typical nanomaterial, boron nitride (BN), on a cellular membrane model based on the realistic small intestinal epithelial cell (SIEC) membrane. This membrane contains a complex composition, including abundant glycolipids. Our MD simulations reveal that BN nanosheet can partially insert into the SIEC membrane, maintaining a stable binding conformation without causing obvious structural changes. Dynamic analyses suggest that van der Waals (vdW) interactions drive the binding process between BN and the SIEC membrane. Further simulation of the interaction between BN nanosheet and deglycosylated SIEC membrane confirms that BN nanosheet cause significant structural damage to deglycosylated SIEC membranes, completely inserting into the membrane, extracting lipids, and burying some lipid hydrophilic heads within the membrane interior. Quantitative analyses of mean squared displacements (MSD) of membranes, membrane thicknesses, area per lipid, and order parameters indicate that BN nanosheet causes more substantial damage to deglycosylated SIEC membrane than to intact SIEC membrane. This comparison suggests the molecular mechanism involved in mitigating BN invasion by SIEC membrane that the polysaccharide heads of glycolipids in the SIEC membrane form a significant steric hindrance on membrane surface, not only hindering the insertion of BN, but also resisting the lipid extraction by BN. Free energy calculations further support this conclusion. Overall, our MD simulations not only shed new light into the reduced impact of BN nanosheet on the realistic SIEC membrane but also highlight the importance of glycolipids in protecting cell membranes from nanomaterial invasion, contributing to a deeper understanding of nanomaterial-realistic cell membrane interactions.

A vitamin D-based strategy overcomes chemoresistance in prostate cancer

BACKGROUND AND PURPOSE

Castration-resistant prostate cancer (CRPC) is a common male malignancy that requires new therapeutic strategies due to acquired resistance to its first-line treatment, docetaxel. The benefits of vitamin D on prostate cancer (PCa) progression have been previously reported. This study aimed to investigate the effects of vitamin D on chemoresistance in CRPC.

EXPERIMENTAL APPROACH

Structure function relationships of potent vitamin D analogues were determined. The combination of the most potent analogue and docetaxel was explored in chemoresistant primary PCa spheroids and in a xenograft mouse model derived from a patient with a chemoresistant CRPC.

KEY RESULTS

Here, we show that Xe4MeCF3 is more potent than the natural ligand to induce vitamin D receptor (VDR) transcriptional activities and that it has a larger therapeutic window. Moreover, we demonstrate that VDR agonists restore docetaxel sensitivity in PCa spheroids. Importantly, Xe4MeCF3 reduces tumour growth in a chemoresistant CRPC patient-derived xenograft. In addition, this treatment targets signalling pathways associated with cancer progression in the remaining cells.

CONCLUSION AND IMPLICATIONS

Taken together, these results unravel the potency of VDR agonists to overcome chemoresistance in CRPC and open new avenues for the clinical management of PCa.

Insights into the catalytic effect of atmospheric organic trace species on the hydration of Criegee intermediates

The bimolecular reactions between Criegee intermediates (CIs) and atmospheric trace species have been extensively investigated, with a particular focus on the reaction with water, while the catalytic role of atmospheric organic compounds in hydration reactions was often neglected. In this study, we employed quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations to investigate the catalytic effects of atmospheric organic amines, organic acids, and alcohols on the hydration reactions of CIs in the gas phase and at the gas-liquid interface. The catalytic reactions were found to follow a cyclic catalytic structure and a stepwise reaction mechanism. Gas-phase studies revealed that organic acids exhibited stronger catalytic effects compared to amines and alcohols, and the catalytic efficiency of amines and alcohols was similar to those of single water molecule. In addition, the catalytic reaction barriers of organic acids and alcohols were positively correlated with their gas-phase acidity (R2 = 0.94 to 0.97). A negative correlation was observed between the catalytic reaction barrier of amines and their gas-phase basicity (R2 = 0.84 to 0.90) and proton affinity (R2 = 0.84 to 0.92). At the gas-liquid interface, organic acids promoted the formation of hydroxyethyl hydroperoxide (HEHP, CH3CH(OH)(OOH)), organic acid ions, and H3O+, whereas the catalytic hydration of CIs by organic amines resulted in the formation of CH3CH(OH)OO and amine ions. Both HEHP and CH3CH(OH)OO can be further decomposed to form OH and HO2, or participate in new particles formation as precursors. This study complements the research gap on the reaction of CIs with water, providing valuable insights into the atmospheric sources of HEHP and HOx as well as the formation of secondary organic aerosols (SOAs).

Mitigating the resistance of MCF-7 cancer cells to Doxorubicin under hypoxic conditions with novel coumarin based carbonic anhydrase IX and XII inhibitors

In the present study, the design and synthesis of novel coumarin derivatives 8a-h, 11a-d and 16a-c as potential selective inhibitors for the tumor associated human carbonic anhydrase isoforms (hCA IX and XII) was reported. All the newly synthesized derivatives showed potent to mild activity against the targeted CA IX (KI = 0.08-9.57 µM), with selectivity indices over CA I (SI = 2.0-21.9) and over CA II (SI = 1.1-15.7). They showed similar activities against CA XII (KI = 0.06-9.48 µM) with selectivity indices over CA I (SI = 1.4-21.2) and CA II (SI = 0.9-15.5). Compound 16b featuring sulfonamide function possessed promising inhibitory activities against the targeted isoforms CA IX and XII with KI values of 0.08 and 0.06 µM, respectively. Interestingly, it was found that using compound 16b at a nontoxic concentration as an adjuvant with Doxorubicin against MCF-7 cells enhanced the cytotoxicity under hypoxia by almost 3.5 folds; IC50 decreased from 25.74 to 7.43 µM. Therefore, compound 16b restored the cytotoxicity of Doxorubicin against MCF-7 cells under hypoxia, almost as normoxia. Furthermore, flow cytometry analysis of a combination treatment of compound 16b and Doxorubicin to the MCF7 cell line revealed an increase in cell cycle arrest at the G2/M phase and a more efficient apoptotic effect than Doxorubicin alone. Furthermore, compound 16b showed no cytotoxicity against normal breast MCF-10A cell line (IC50 = 296.25 µM).

Contribution of chemical permeation enhancers to the process of transdermal drug delivery: Adsorption, microscopic interactions, and mechanism

Transdermal drug delivery (TDD) has attracted widespread attention because of the advantage of its non-invasive nature, easy self-administration, and low side effects. The key to this pathway of drug delivery is how to overcome the barrier of the lipid matrix in the stratum corneum (SC). In this work, molecular dynamics (MD) were employed to investigate the adsorption of thyrotropin-releasing hormone (TRH) on the SC, and the effects of three different chemical permeation enhancers (ethanol (ETOH), carveol (CAV), and borneol (BOR)) on the SC were analyzed. The results showed that ETOH hardly altered the order of lipids in the SC, while CAV and BOR disrupted the morphology of the SC. The primary target of CAV was the CHOL in SC, which not only disrupted the ordered arrangement of CHOL, but also "extracted" CHOL from SC. The thickness distribution of SC became more inhomogeneous in the presence of CAV and BOR, which facilitated the penetration of drug molecules. Compared to no chemical permeation enhancers, the free energy of permeation in the presence of chemical permeation enhancers was less than 4-10 kcal mol-1, which suggested that chemical permeation enhancers were more favorable for the permeation of drugs from viewpoints of thermodynamics. All the results provided theoretical insights into the effect of chemical permeation enhancers on the transdermal permeation of drugs.

Anthraquinones-based photocatalysis: A comprehensive review

In recent years, there has been significant interest in photocatalytic technologies utilizing semiconductors and photosensitizers responsive to solar light, owing to their potential for energy and environmental applications. Current efforts are focused on enhancing existing photocatalysts and developing new ones tailored for environmental uses. Anthraquinones (AQs) serve as redox-active electron transfer mediators and photochemically active organic photosensitizers, effectively addressing common issues such as low light utilization and carrier separation efficiency found in conventional semiconductors. AQs offer advantages such as abundant raw materials, controlled preparation, excellent electron transfer capabilities, and photosensitivity, with applications spanning the energy, medical, and environmental sectors. Despite their utility, comprehensive reviews on AQs-based photocatalytic systems in environmental contexts are lacking. In this review, we thoroughly describe the photochemical properties of AQs and their potential applications in photocatalysis, particularly in addressing key environmental challenges like clean energy production, antibacterial action, and pollutant degradation. However, AQs face limitations in practical photocatalytic applications due to their low electrical conductivity and solubility-related secondary contamination. To mitigate these issues, the design and synthesis of graphene-immobilized AQs are highlighted as a solution to enhance practical photocatalytic applications. Additionally, future research directions are proposed to deepen the understanding of AQs' theoretical mechanisms and to provide practical applications for wastewater treatment. This review aims to facilitate mechanistic studies and practical applications of AQs-based photocatalytic technologies and to improve understanding of these technologies.

SLC2A1 boosts the resistance of non-small cell lung cancer to taxanes by stimulating the formation of EPCAM+ cancer stem-like cells via glycolysis

BACKGROUND

The mechanisms by which SLC2A1 enhances chemo-resistance of taxanes to non-small cell lung cancer (NSCLC) remains enigmatic.

METHODS

An investigation into the SLC2A1 expression pattern and prognosis across diverse datasets, as well as our internally collected samples, was undertaken. Additionally, the biological function of SLC2A1 was further delved into through in vitro experiments. The study also examined the chemo-resistance of NSCLC to taxanes using CCK-8, Annexin-V, and caspase-3 assays. Furthermore, the impact of taxanes on SLC2A1 expression was determined via western blot analysis. The effects of SLC2A1 on the formation of CSCs was examined via flow cytometry and metabolomics techniques. Finally, the impact of SLC2A1 on the tumor microenvironment was analyzed using single-cell sequencing and cellchat.

RESULTS

In the present investigation, it was observed that there was an elevated expression of SLC2A1 in NSCLC tumor tissues, which exhibited a significant association with a poorer prognosis. SLC2A1 overexpression in vitro promoted NSCLC cell proliferation, invasion, migration, chemo-resistance, and the formation of CD90+ and EpCAM+ CSCs. NSCLC cells were categorized based on SLC2A1 and EpCAM expression. SLC2A1highEpCAM+ CSCs were more chemo-resistance to taxanes. NSCLC patients with high SLC2A1 and EpCAM expression had poorer prognosis. Mechanically, SLC2A1 promoted the formation of CD90+ and EpCAM+ CSCs via activating glycolysis. Finally, SLC2A1low tumor cells promoted CD8+T cell function via HLA-A, B, C, and suppressed NK cell function via HLA-E.

CONCLUSION

Together, SLC2A1 plays an important role in enhancing chemo-resistance of taxanes to NSCLC.

Role of non-redox innocent ligand units in the oxidation of alcohols with H2O2 catalyzed by μ-oxido-diiron(III) bis-phenolato polypyridyl complexes

Redox non-innocent ligands hold the potential to expand the redox chemistry and activity of transition metal catalysts. The impact of the additional redox chemistry of phenol ligands in oxidation catalysis is explored here in the complex μ-oxido-diiron(III) polypyridyl (1) [(L)Fe(III)(μ-O)Fe(III)(L)](ClO4)2 (where HL is 2-(((di(pyridin-2-yl)methyl) (pyridin-2-ylmethyl) amino)methyl)phenol) and its tert-butyl substituted analog 2, in which each of the Fe(III) centers is coordinated to a phenolato moiety of the ligand. Complex 1 was shown earlier to catalyse the oxidation of benzyl alcohols to aldehydes with H2O2. In particular acid was found to accelerate the reactions by removal of a lag period before catalysis initiated. Here, we use reaction monitoring with resonance Raman, UV/vis absorption and EPR spectroscopy to show that under catalytic conditions, i.e. with excess H2O2, rapid (< 5 s) loss of the phenolato moiety occurs, resulting in the formation of an N4 ligated Fe(III) complex. This N4 coordinated complex forms a Fe(III)-OOH species, which is responsible for alcohol oxidation and over time a relatively stable oxido-bridged dinuclear Fe(III) complex forms as a resting state in the catalytic system. The main role of acid in the catalysis is shown to be to facilitate the initial coordination of H2O2 by driving the formation of mononuclear complexes from 1 and 2. The data show that although the phenolato moiety imparts interesting redox properties on complex 1, it does not contribute directly to the oxidation catalysis observed with H2O2.

Direct measurements of neurosteroid binding to specific sites on GABAA receptors

BACKGROUND AND PURPOSE

Neurosteroids are allosteric modulators of GABAA currents, acting through several functional binding sites although their affinity and specificity for each site are unknown. The goal of this study was to measure steady-state binding affinities of various neurosteroids for specific sites on the GABAA receptor.

EXPERIMENTAL APPROACH

Two methods were developed to measure neurosteroid binding affinity: (1) quenching of specific tryptophan residues in neurosteroid binding sites by the neurosteroid 17-methylketone group, and (2) FRET between MQ290 (an intrinsically fluorescent neurosteroid) and tryptophan residues in the binding sites. The assays were developed using ELIC-α1GABAAR, a chimeric receptor containing transmembrane domains of the α1-GABAA receptor. Tryptophan mutagenesis was used to identify specific interactions.

KEY RESULTS

Allopregnanolone (3α-OH neurosteroid) was shown to bind at intersubunit and intrasubunit sites with equal affinity, whereas epi-allopregnanolone (3β-OH neurosteroid) binds at the intrasubunit site. MQ290 formed a strong FRET pair with W246, acting as a site-specific probe for the intersubunit site. The affinity and site-specificity of several neurosteroid agonists and inverse agonists was measured using the MQ290 binding assay. The FRET assay distinguishes between competitive and allosteric inhibition of MQ290 binding and demonstrated an allosteric interaction between the two neurosteroid binding sites.

CONCLUSIONS AND IMPLICATIONS

The affinity and specificity of neurosteroid binding to two sites in the ELIC-α1GABAAR were directly measured and an allosteric interaction between the sites was revealed. Adaptation of the MQ290 FRET assay to a plate-reader format will enable screening for high affinity agonists and antagonists for neurosteroid binding sites.