Prediction of order parameters based on protein NMR structure ensemble and machine learning.

The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. The most used NMR approach to study fast protein dynamics is the model free method, which uses order parameter S2 to describe the amplitude of the internal motion of local group. However, to obtain order parameter through NMR experiments is quite complex and lengthy. In this paper, we present a machine learning approach for predicting backbone 1H-15N order parameters based on protein NMR structure ensemble. A random forest model is used to learn the relationship between order parameters and structural features. Our method achieves high accuracy in predicting backbone 1H-15N order parameters for a test dataset of 10 proteins, with a Pearson correlation coefficient of 0.817 and a root-mean-square error of 0.131.

Fraxin Ameliorates Ulcerative Colitis by Modulating Oxidative Stress, Inflammation and TLR4/NF-κB and MAPK Signaling Pathways.

Objective: UC is a chronic gastrointestinal disorder of uncertain etiology. However, effective therapeutic drug options for UC are relatively limited. Fraxin represents a principal active constituent within the traditional Chinese medicinal herb known as Cortex Fraxini or Qinpi. Nevertheless, the impact of Fraxin on UC remains uncharted. This study aims to explore the potential of Fraxin, a key component of Cortex Fraxini, in inhibiting DSS-induced intestinal inflammation in mice and to unravel the underlying mechanisms. Methods: In vitro experiment,the RAW264. 7 cells were induced by LPS as the model.In vivo experiment,the mice were induced by DSS as the animal model for a ten day experiment.The ELISA, western blots, measurement of oxidative stress markers and other relevant methods were used to discuss the effect of Fraxin on LPS-induced RAW264.7 cells and the inhibitory effect of Fraxin on intestinal inflammation induced by DSS in mice and underlying mechanisms. Results: Our findings indicated that Fraxin significantly reduced symptoms of UC, such as body weight loss, colonic length shortening, and histological damage. At the molecular level, it inhibited ROS generation, reduced pro-inflammatory cytokines, and regulated key pathways including TLR4/NF-κB and MAPK.The findings indicated that Fraxin diminished the expression of p-NF-κB and p-IκB, downregulated iNOS and COX-2 expression, and lessened p38, JNK and ERK phosphorylation. Conclusion: Taken together, Fraxin ameliorates UC by regulating oxidative stress, inflammation, and TLR4/NF-κB and MAPK pathways, and Fraxin may be a new treatment for UC. Our findings suggest that Fraxin could offer a novel therapeutic approach for UC, targeting oxidative stress and key inflammatory pathways.

New insights into evolution and functional diversification of Camellia sinensis LRR-RLKs.

Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subgroup of receptor-like kinases (RLKs) in plants. While some LRR-RLK members play a role in regulating various plant growth processes related to morphogenesis, disease resistance, and stress response, the functions of most LRR-RLK genes remain unclear. In this study, we identified 397 LRR-RLK genes from the genome of Camellia sinensis and categorized them into 16 subfamilies. Approximately 62% of CsLRR-RLK genes are situated in regions resulting from segmental duplications, suggesting that the expansion of CsLRR-RLK genes is due to segmental duplications. Analysis of gene expression patterns revealed differential expression of CsLRR-RLK genes across different tissues and in response to stress. Furthermore, we demonstrated that CssEMS1 localizes to the cell membrane and can complement Arabidopsis ems1 mutant. This study is the initial in-depth evolutionary examination of LRR-RLKs in tea and provides a basis for future investigations into their functionality. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-024-01458-1.

Gold and Palladium Relay Catalytic [4 + 4] Cycloadditions of Enynamides and γ-Methylene-δ-valerolactones: Diastereoselective Construction of Furan-Fused Azacyclooctanes.

We report a highly efficient and diastereoselective gold and palladium sequential relay catalysis system for the synthesis of furan-fused eight-membered heterocycles. Employing a one-pot procedure, easily accessible enynamides undergo cyclization to generate azadienes in situ, which subsequently participate in diastereoselective formal [4 + 4] cycloadditions with γ-methylene-δ-valerolactones. This strategy enables the rapid and efficient construction of a series of furan-fused azacyclooctanes with diverse substituents in good yields (63-97%) and a high level of diastereoselectivity (7:1 → 20:1 dr).

Silver-Catalyzed Tandem Cycloisomerization/[5 + 2] Cycloaddition of 3-Cyclopropylideneprop-2-en-1-ones with Oxidopyrylium Ylides to Form Bibridged Benzocycloheptanones.

Herein, we report a mild, one-pot method for silver-catalyzed tandem cycloisomerization/[5 + 2] cycloaddition reactions between readily accessible cyclopropyl-tethered allenyl ketones and benzopyranone-derived oxidopyrylium ylides. The reactions proceed via a cyclobutene-fused furan intermediate generated in situ by a cycloisomerization/1,2-carbene transfer/ring-expansion cascade. This method, which features an unprecedented formal [5 + 2] cycloaddition, delivers good to excellent yields of structurally complex bibridged benzocycloheptanones bearing a strained cyclobutane ring and an O-bridged ring.

Enhancement of oral bioavailability and anti-colitis effect of luteolin-loaded polymer micelles with RA (rosmarinic acid)-SS-mPEG as carrier.

OBJECTIVE: Polymer micelles were prepared (L-RSPMs) with luteolin and synthetic RA-SS-mPEG polymeric material before evaluation of their anti-inflammatory effect on 2, 4, 6-trinitro-benzene-sulfonic acid (TNBS)-induced ulcerative colitis (UC) model in rats. METHODS: The synthetic RA-SS-mPEG was characterized with NMR spectroscopy, before preparation of luteolin-coated RA-SS-mPEG polymer micelles. The in vitro characterization and evaluation of the formulation were accomplished, couple with its pharmacokinetic parameters. The levels of PEG2, MDA, CRP and GSH, as well as concentrations of TNF-α, IL1-ß, IL-6 and IL-10 in serum and colon tissue were detected via ELISA kit. The degree of colon injury and inflammation was evaluated via histopathologic examination. RESULTS: L-RSPMs displayed small average droplet size (133.40 ± 4.52 nm), uniformly dispersed (PDI: 0.163 ± 0.011), good stability, slow release and enhanced solubility. We observed 353.28% increase in the relative bioavailability of L-RSPMs compared to free luteolin, while the half-life of the micelle was extended by 6.16h. Compared to model (M) group, luteolin (low and high doses) and L-RSPMs (low and high doses) significantly reduced levels of MDA, PEG2, CRP, TNF-α, IL-6 and IL-1ß in colon tissue and serum of colitic rats but dose dependently increased IL-10 and SOD levels (p < 0.01). Histopathologic examination of colon showed that luteolin (low and high doses) and L-RSPMs (low and high doses) improved colonic inflammation in colitic rats to varying degrees compared to M group. CONCLUSION: L-RSPMs could improve TNBS-induced colon inflammation by enhancing bioavailability, promoting antioxidant effects and regulating cytokine release, which may become a potential agent for UC treatment in clinical settings.

CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts.

Protein secondary structure provides rich structural information, hence the description and understanding of protein structure relies heavily on it. Identification or prediction of secondary structures therefore plays an important role in protein research. In protein NMR studies, it is more convenient to predict secondary structures from chemical shifts as compared to the traditional determination methods based on inter-nuclear distances provided by NOESY experiment. In recent years, there was a significant improvement observed in deep neural networks, which had been applied in many research fields. Here we proposed a deep neural network based on bidirectional long short term memory (biLSTM) to predict protein 3-state secondary structure using NMR chemical shifts of backbone nuclei. While comparing with the existing methods the proposed method showed better prediction accuracy. Based on the proposed method, a web server has been built to provide protein secondary structure prediction service.

Diastereoselective Synthesis of Tetrabenzohydrofuran Spirooxindoles via Diethyl Phosphite-Mediated Coupling of Isatins with o-Quinone Methides.

Diethyl phosphite-initiated coupling of isatins with o-quinone methides (o-QMs) is reported. This reaction involves a cascade transformation initiated by base-promoted addition of phosphite to isatins, followed by [1,2]-phospha-Brook rearrangement. This generates α-phosphonyloxy enolates that are subsequently intercepted by o-QMs and finally intramolecular ring closure. This protocol was used to diastereoselectively synthesize a range of trans-tetrabenzohydrofuran spirooxindoles in moderate to good yields with moderate to excellent diastereoselectivities.

Improved oral bioavailability and anti-chronic renal failure activity of chrysophanol via mixed polymeric micelles.

AIMS: This study was designed to prepare chrysophanol-loaded micelles (CLM) to improve the oral bioavailability, targetability and anti-chronic renal failure (CRF) activity of chrysophanol (CH). METHODS: The preparation of CLM was achieved via thin-film dispersion technique. The in vitro release of CLM compared with free CH was measured in phosphate buffer solution (PBS) containing 0.5%w/v sodium dodecyl sulphate (pH 6.8) while the pharmacokinetic and anti-CRF activity study was also conducted in rats. Moreover, the tissue distribution of CLM was investigated in the mice. RESULTS: The CLM had particle size (PS) of 29.64 ± 0.71 nm, and encapsulation efficiency (EE) of 90.48 ± 1.22%w/w. The cumulative release rate of CH from the micellar system was significantly higher than that of the free CH (86%m/m vs. 15%m/m, p < 0.01). In vivo pharmacokinetic studies showed that the bioavailability of CLM after oral administration was substantially improved (about 3.4 times) compared with free drugs (p < 0.01). Also, it was observed that CLM accumulated well in the liver and brain. Moreover, in vitro renal podocytes study showed that CLM had better protection against renal podocyte damage than the free CH. In addition, CLM significantly (p < 0.01) reduced levels of blood urea nitrogen (BUN), kidney injury molecule-1 (Kim-1), and serum creatinine (SCr), which obviously improved kidney damage in rats with CRF. CONCLUSIONS: Collectively, these findings suggest that mixed micelles may be used as a promising drug delivery system for oral bioavailability improvement and concomitantly enhance the anti-CRF activity of CH, as well as provide a basis for the clinical application of CH.

Preparation of Fraxetin Long Circulating Liposome and Its Anti-enteritis Effect.

This study sought to improve the oral bioavailability and enhance the anti-enteritis effect of fraxetin by incorporating it into long circulating liposomes (F-LC-Lipo). The optimal formulation of F-LC-Lipo was obtained via orthogonal design. The particle size, morphology, encapsulation efficiency, stability, and anti-enteritis effect of F-LC-Lipo were evaluated. The particle size of F-LC-Lipo was 166.65 ± 8.75 nm with entrapment efficiency (EE) of 92.18 ± 0.17%. The release rate in different dissolution media (pH 1.2 HCl, DDW, and pH 7.4 PBS) was significantly higher than that of fraxetin solution. Compared with the free fraxetin solution, F-LC-Lipo increased oral bioavailability of fraxetin by 4.43 times (443%). More importantly, F-LC-Lipo could improve the levels of interleukin-1 beta (IL-1ß), IL-6, malondialdehyde (MDA), superoxide dismutase (SOD), tumor necrosis factor-alpha (TNF-α), C-reactive protein (CRP), prostaglandin E2 (PEG2), and IL-10 in rats with enteritis. Overall, these results suggested that LC-Lipo may serve as a potential carrier for improving the solubility and oral bioavailability of fraxetin as well as improving its enteritis effect.

A PPh3-catalyzed sequential annulation reaction to construct cyclopentane-fused dihydropyrazolone-pyrrolidinediones.

A PPh3-catalyzed sequential cycloaddition of maleimides with unsaturated pyrazolones has been developed. This protocol provides a simple and practical strategy for the construction of dispirocyclopentyl-[dihydropyrazolone-pyrrolidinedione] pyrrolidinedione skeletons containing five contiguous stereogenic centers, including two spiro-quaternary centers, with moderate yields (34-73%) and excellent diastereoselectivities (>20 : 1).

Synthesis of methylene cyclopropane-fused chromenes and dihydroquinolines by sequential [4 + 2]- and [1 + 2]-annulation.

A base promoted sequential [4 + 2]- and [1 + 2]-annulation of 2-hydroxychalcones or 2-tosylaminochalcones with prop-2-ynylsulfonium salts has been developed to give the corresponding methylene cyclopropane fused dihydroquinolines or chromenes in moderate to good yields. This transformation has advantage of wide substrate scope and functional group tolerance as well as excellent regioselectivity. Prop-2-ynylsulfonium salts act as both C2 and C1 synthons in the tandem processes.

[Network pharmacological analysis and preliminary validation of mechanisms of Baitouweng Decoction in treatment of ulcerative colitis].

The aim of this paper was to explore the pharmacological mechanism of Baitouweng Decoction in the treatment of ulcerative colitis(UC) by network pharmacology and to preliminarily verify the related targets by animal experiments. Cytoscape software was used to construct "ingredient-target-disease" network through TCMSP, GeneCards and Uniprot databases. The protein interaction network was constructed using STRING database, and the core targets were speculated. The GO and KEGG enrichment analysis was conducted using R software. Autodock Vina software was used for molecular docking of ingredients and core targets. UC mice induced by dextran sodium sulfate(DSS) were treated by Baitouweng Decoction. The pathological changes of colon tissues were observed by HE staining, and the expression levels of related genes were analyzed by immunohistochemistry.The results showed that 26 active ingre-dients and 30 core targets were found in Baitouweng Decoction through network pharmacology. GO enrichment analysis showed that these genes mainly affected nuclear receptor activity, transcription factor activity, steroid hormone receptor activity, ubiquitin-like protein ligase binding, protein heterodimerization activity, transcription cofactor binding and other biological processes. KEGG enrichment analysis showed that P53 signaling pathway, EGFR signaling pathway, TNF signaling pathway, PI3 K-AKT signaling pathway and some cancer-related pathways were enriched. Molecular docking showed that EGFR, PPARG, CASP3, NOS3, caspase-9, CCND1, ADH, IL6 and NFKB1 were better docked with active ingredients. The experiments verified that Baitouweng Decoction could improve the colon pathology of mice, and EGFR is one of the related targets. Our study suggested that Baitouweng Decoction could treat UC through multiple targets and pathways, which provided a theoretical basis for future research.

Lewis base catalyzed regioselective cyclization of allene ketones or α-methyl allene ketones with unsaturated pyrazolones.

A nitrogen-containing Lewis base catalyzed highly regioselective [4 + 2] cycloaddition of allene ketones or α-methyl allene ketones with unsaturated pyrazolones has been disclosed to give the corresponding tetrahydropyrano [2,3-c] pyrazoles in moderate to good yields under mild conditions. High regioselectivity, 100% atom-economy, broad substrate scope and good functional group tolerance are attractive features of this process and make it a practical and versatile transformation.

DBU-Promoted [4 + 4] Domino Cycloaddition of Ynones with Benzylidenepyrazolones To Access Eight-Membered Cyclic Ethers.

An efficient DBU-promoted [4 + 4] domino annulation reactions of ynones and benzylidenepyrazolones has been developed. This process resulted finally in the formation of eight-membered cyclic ethers in moderate to good yields. The easy availability of starting materials and the simple cyclization procedure make this approach suitable for the preparation of a wide range of useful oxocino [2,3- c] pyrazoles.

Bisphosphine catalyzed sequential [3 + 2] cycloaddition and Michael addition of ynones with benzylidenepyrazolones via dual α',α'-C(sp3)-H bifunctionalization to construct cyclopentanone-fused spiro-pyrazolones.

A bisphosphine-catalyzed sequential [3 + 2] cycloaddition and Michael addition reaction of ynones with benzylidenepyrazolones has been developed. Under the catalysis of DPPB [1,4-bis(diphenylphosphino)butane], the reaction proceeded smoothly to give spiro-[cyclopentanone] pyrazolone derivatives in moderate to good yields with good diastereoselectivities via sequential dual α',α'-C(sp3)-H bifunctionalization annulation. This strategy provides a novel route toward the synthesis of spiro-[cyclopentanone] pyrazolones containing three contiguous stereocenters which possess potential pharmaceutical activities.

TNF-α-308G/A polymorphism and the risk of colorectal cancer: A systematic review and an updated meta-analysis.

PURPOSE: This study aimed to explore the relationship between TNF-α-308G/A polymorphism (rs1800629) and the risk of colorectal cancer (CRC) by meta-analysis. METHODS: Articles on exploring the relationship between TNF-α-308G/A polymorphism and CRC risk were searched from PubMed, Web of Science and Embase. The timeliness and authority of the included articles were evaluated. 95% confidence interval (95% CI) and odds ratio (OR) were calculated using fixed effect model or random effect model. Subgroup analysis was performed based on the ethnicity, source of control and method of genotyping. Finally, meta-analysis was conducted using STATA 12.0 software. RESULTS: Sixteen articles were selected (all case-control studies) with 3391 CRC patients and 3995 normal individuals (controls). No significant correlation was found between TNF-α-308G/A polymorphism and CRC risk (dominant gene model, OR=0.96, 95%CI, 0.86-1.07, p>0.05; recessive gene model, OR=1.32, 95%CI, 0.99-1.76, p>0.05; homozygous model, OR=1.28, 95%CI, 0.95-1.72, p>0.05;heterozygous model, OR=0.92, 95%CI, 0.82-1.04, p>0.05; allele model, OR=0.96, 95%CI, 0.87-1.07, p>0.05). Besides, we did not observe remarkable correlation in subgroup analysis of Asian and Caucasian CRC patients. Subgroup analysis of source of control showed no significance in hospital-based subgroup. However, TNF-α-308G/A polymorphism could reduce CRC risk in population-based subgroup (dominant gene model, OR=0.80, 95%CI, 0.63-1.00, p<0.05; heterozygous model, OR=0.76, 95%CI, 0.60-0.97, p<0.05; allele model, OR=0.80, 95%CI, 0.66-0.98, p<0.05). On the contrary, TNF-α-308G/A polymorphism could increase CRC risk in subgroup analysis of method of genotype detected by PCR-RFLP (recessive gene model, OR=1.77, 95%CI, 1.10-2.86, p<0.05; homozygous model, OR=1.79, 95%CI, 1.10-2.89, p<0.05). CONCLUSIONS: Our analysis indicated no significant correlation between TNF-α-308G/A polymorphism (rs1800629) and CRC risk.

Regio- and Diastereoselective Construction of Spirocyclopenteneoxindoles through Phosphine-Catalyzed [3 + 2] Annulation of Methyleneindolinone with Alkynoate Derivatives.

A phosphine-catalyzed [3 + 2] annulation of isatin-derived α,ß-unsaturated ketones with alkynoates for the synthesis of cyclopentene spiro-oxindole skeletons has been developed. This reaction afforded the desired products in high to excellent yields (up to 99%) with high regioselectivity and moderate to high diastereoselectivities (up to 20:1). This strategy allows facile diastereoselective preparation of biologically important spiro-(cyclopentene) oxindoles containing three contiguous stereocenters, including the quaternary stereogenic center joining the two rings.

Diastereoselective Synthesis of Adjacent P,C-Stereogenic ß-N-Glycosidic Linked α-Aminophosphinates.

The diastereoselective formation of adjacent P,C-stereogenic ß-N-glycosidic linked α-aminophosphinates is developed in high yields via a phospha-Mannich reaction. The reaction was performed by employing (Rp)-O-(-)-menthyl H-phenylphosphinate and O-pivaloylated N-galactosylimine for double stereodifferentiation and BF3·Et2O as a promoter in THF. O-Pivaloylated N-galactosylphenyl imine 2 and (Rp)-O-(-)-menthyl H-phenylphosphinate 1 were converted to N-galactosyl α-aminoalkylphosphinate 3 with ratios of diastereomers up to 20:1. The synthetic method of the conversion provides a rapid access to adjacent P,C-stereogenic chiral α-aminophosphinates.

Injectable hydrogels as promising in situ therapeutic platform for cartilage tissue engineering.

Injectable hydrogels are gaining prominence as a biocompatible, minimally invasive, and adaptable platform for cartilage tissue engineering. Commencing with their synthesis, this review accentuates the tailored matrix formulations and cross-linking techniques essential for fostering three-dimensional cell culture and melding with complex tissue structures. Subsequently, it spotlights the hydrogels' enhanced properties, highlighting their augmented functionalities and broadened scope in cartilage tissue repair applications. Furthermore, future perspectives are advocated, urging continuous innovation and exploration to surmount existing challenges and harness the full clinical potential of hydrogels in regenerative medicine. Such advancements are crucial for validating the long-term efficacy and safety of hydrogels, positioning them as a promising direction in regenerative medicine to address cartilage-related ailments.