Classification models for predicting the bioactivity of pan-TRK inhibitors and SAR analysis.

Tropomyosin receptor kinases (TRKs) are important broad-spectrum anticancer targets. The oncogenic rearrangement of the NTRK gene disrupts the extracellular structural domain and epitopes for therapeutic antibodies, making small-molecule inhibitors essential for treating NTRK fusion-driven tumors. In this work, several algorithms were used to construct descriptor-based and nondescriptor-based models, and the models were evaluated by outer 10-fold cross-validation. To find a model with good generalization ability, the dataset was partitioned by random and cluster-splitting methods to construct in- and cross-domain models, respectively. Among the 48 models built, the model with the combination of the deep neural network (DNN) algorithm and extended connectivity fingerprints 4 (ECFP4) descriptors achieved excellent performance in both dataset divisions. The results indicate that the DNN algorithm has a strong generalization prediction ability, and the richness of features plays a vital role in predicting unknown spatial molecules. Additionally, we combined the clustering results and decision tree models of fingerprint descriptors to perform structure-activity relationship analysis. It was found that nitrogen-containing aromatic heterocyclic and benzo heterocyclic structures play a crucial role in enhancing the activity of TRK inhibitors. Workflow for generating predictive models for TRK inhibitors.

Advances in Biosynthesis of Non-Canonical Amino Acids (ncAAs) and the Methods of ncAAs Incorporation into Proteins.

The functional pool of canonical amino acids (cAAs) has been enriched through the emergence of non-canonical amino acids (ncAAs). NcAAs play a crucial role in the production of various pharmaceuticals. The biosynthesis of ncAAs has emerged as an alternative to traditional chemical synthesis due to its environmental friendliness and high efficiency. The breakthrough genetic code expansion (GCE) technique developed in recent years has allowed the incorporation of ncAAs into target proteins, giving them special functions and biological activities. The biosynthesis of ncAAs and their incorporation into target proteins within a single microbe has become an enticing application of such molecules. Based on that, in this study, we first review the biosynthesis methods for ncAAs and analyze the difficulties related to biosynthesis. We then summarize the GCE methods and analyze their advantages and disadvantages. Further, we review the application progress of ncAAs and anticipate the challenges and future development directions of ncAAs.

Endoplasmic Reticulum-Targeting Two-Photon Fluorescent Probe for CYP1A Activity and Its Imaging Application in Endoplasmic Reticulum Stress.

Cytochrome P450 1A is one of the vital subfamilies of heme-containing cytochrome P450 enzymes belonging to an important exogenous metabolizing CYP in human. The abnormal of endoplasmic reticulum (ER) may directly affect the functional activity of ER-located CYP1A and be associated with the occurrence and development of various diseases. In the present study, we constructed a selective two-photon fluorescent probe ERNM for rapid and visual detection of endogenous CYP1A that was localized in the ER. ERNM could target the ER and detect the enzymatically active CYP1A in living cells and tissues. The monitoring ability of ERNM for the fluctuations in functionality level of CYP1A was confirmed using ER stressed A549 cell. Based on the ER-targeting two-photon probe for CYP1A, the close association of ER state and the functional activity of ER-locating CYP1A was confirmed, which would promote the deep understanding of the biofunction of CYP1A in various ER-related diseases.

[Application of high-speed counter current chromatography in extraction and separation of alkaloids in natural products].

Alkaloids, widespread in plants, have a series of pharmacological activities and have been widely used to treat various diseases. Because alkaloids are usually presented in multicomponent mixtures and are deeply low in content, they are very difficult to extract and separate by traditional methods. High-speed counter current chromatography(HSCCC) is a kind of liquid-liquid chromatography without solid support phase, which has the advantages of large injection volume, low cost, and no irreversible adsorption. Compared with the traditional methods of extraction and separation of alkaloids, HSCCC can ensure the separation of many different alkaloids at one time, with a high recovery and large amount. In this paper, the advantages and disadvantages of HSCCC compared with traditional separation methods were discussed and the solvent system and elution mode of HSCCC used to separate alkaloids in recent years were summarized by referring to the relevant literature to provide some references for the separation of alkaloids by HSCCC.

Self-Assembled pH-Responsive Metal-Organic Frameworks for Enhancing the Encapsulation and Anti-Oxidation and Melanogenesis Inhibition Activities of Glabridin.

Metal organic frameworks (MOFs) are formed by self-assembly of metal ions and organic ligands. A special type of MOF called ZIF-8, which is formed by self-assembly of zinc ions and 2-methylimidazole, shows excellent stability in aqueous solutions and disintegrates under acidic conditions. These properties make ZIF-8 a suitable carrier material for pH-stimulated drug delivery systems. Glabridin is an isoflavane compound that is widely present in the roots of licorice. Because of its outstanding skin whitening properties, glabridin is widely used as a whitener in the cosmetics industry. In this study, ZIF-8 was employed to encapsulate glabridin. Glabridin-loaded ZIF-8 was successfully prepared with a drug encapsulation efficiency of 98.67%. The prepared sample showed a fusiform or cruciate flower-like structure, and its size was about 3 µm. ZIF-8 enabled pH-controlled release of glabridin. Moreover, ZIF-8 encapsulation significantly enhanced the intracellular anti-oxidant activity and melanogenesis inhibitory activity of glabridin. This study provides a new approach that shows great potential to improve the biological application of glabridin.

A novel vector-based RNAi method using mouse U6 promoter-driven shRNA expression in the filamentous fungus Blakeslea trispora.

PURPOSE: There are several studies on the use of RNA interference (RNAi) for gene function analysis in fungi. However, most studies on filamentous fungi are based on in vitro-transcribed or -synthesized small interfering RNA (siRNA), and only a few have reported the use of vector-based RNAi. Here we want to develop and evaluate a new vector-based RNAi method using the mouse U6 promoter to drive short hairpin RNA (shRNA) expression in the filamentous fungi. METHODS: Molecular techniques were employed to develop and evaluate a new vector-based RNAi method using the mouse U6 promoter to drive short hairpin RNA (shRNA) expression in the filamentous fungus Blakeslea trispora. RESULTS: We characterized the mouse U6 promoter and utilized it for the expression of shRNA in B. trispora. Using real-time polymerase chain reaction and western blotting analyses, we confirmed the decrease in the mRNA and protein expression of carRA, respectively, in cells transformed with the mouse U6 promoter-driven shRNA expression vector. This indicated that the shRNA was transcribed from the mouse U6 promoter and correctly processed into siRNA and that the mouse U6 promoter exhibited transcription ability in the filamentous fungi. CONCLUSIONS: The results suggest that the mouse U6 promoter that drives the expression of shRNA vectors may serve as a novel tool for RNAi induction in filamentous fungi.

Study on the interaction of hyperoside and human serum albumin in VC and VC -free environments by spectroscopic and molecular docking techniques.

The interaction between hyperoside and human serum albumin was studied in vitamin C (VC ) and VC -free environments using ultraviolet (UV)-vis absorption, fluorescence, circular dichroism spectra, and molecular docking techniques under simulated physiological conditions. The two environments had different influences on the secondary structure of human serum albumin (HSA). The α-helix content was slightly increased from 50% to 51% in the VC environment and increased from 50% to 55% in the VC -free environment. The thermodynamic parameters were ΔH° = -30.7 kJ⋅mol-1 and ΔS° = -23.4 mol-1 ⋅K-1 in the VC environment and ΔH° = -25.4 kJ⋅mol-1 and ΔS° = -11.4 J⋅mol-1 ⋅K-1 in the VC -free environment. Through thermodynamics parameters, hydrophobic force played a dominant role in the whole environment. The binding constants were calculated to be 7.25 × 105 mol⋅L-1 and 9.76 × 105 mol⋅L-1 at 298 K and they declined with the rise in temperature. The two binding distances were 2.6 nm and 2.5 nm respectively at 298 K, indicating that fluorescence energy transfer occurred. The UV-vis spectra indicated that fluorescence quenching of the HSA-hyperoside complex was a static quenching process. Hyperoside could spontaneously bind to HSA at site I (subdomain IIA). Molecular docking elucidated the way to binding basically through hydrophobic and van der Waals force interactions. Moreover, molecular docking showed that the VC environment could influence binding of HSA and hyperoside by more H-binding and less hydrophobic forces.

Isolation and Identification of Anthocyanin Component in the Fruits of Acanthopanax Sessiliflorus (Rupr. & Maxim.) Seem. by Means of High Speed Counter Current Chromatography and Evaluation of Its Antioxidant Activity.

Acanthopanax sessiliflorus (Rupr. & Maxim.) Seem. (Araliaceae) is one of the most abundant species of genus Acanthopanax. The fruits of A. sessiliflorus are used in traditional medical protocols as an analgesic, tonic, antidiabetic, antihypertensive, anti-inflammatory, antitumor, and immune-stimulating agent. In this work, we carried out a comprehensive investigation into the anthocyanin components in the fruits of A. sessiliflorus. The anthocyanin content in the fresh fruits of A. sessiliflorus was determined by high performance liquid chromatography-diode array detection (HPLC/DAD), and the anthocyanin component was isolated from these using high-speed counter-current chromatography (HSCCC) and elucidated by electro-spray ionization-mass spectrometry (ESI/MS), 1H- and 13C-NMR. Its antioxidant activity was evaluated by ferric-reducing antioxidant power (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH). We found that A. sessiliflorus contained a gross anthocyanin content of 121.35 mg/100 g. HSCCC was successfully used for separation and purification of the primary anthocyanin component, cyanidin 3-xylosyl-galactoside. The antioxidant and radical scavenging tests indicated that cyanidin 3-xylosyl-galactoside is a potent antioxidant.

Biotransformation of furanocoumarins by fungi: preparation of imperation analogs.

Imperation analogs have the furanocoumarin skeleton, with the isopentenyl group, which displayed significant bioactivities. The biotransformation of furanocoumarins imperation, isoimperation and phellopterin (1-3) by fungi has been proved to be an efficient method for the structural modification. Ten transformed furanocoumarin analogs were obtained by fungal biotransformation, including one new highly oxygenated furanocoumarin (4c). Aspergillus niger AS 3.739 displayed selectively transformed capability toward furanocouamrins (1-3) with one or two major products. So, seven hydroxylation and hydrolysis derivatives have been prepared efficiently. Additionally, the biotransformation of phellopterin gave multiple products (4a, 4b, 4c) by Cunninghamella blakesleana AS 3.970. The biotransformation time-courses of furanocoumarins have been established, which suggested the preferred incubation time. The bioactivities of furanocoumarin analogs have been investigated in an in vitro bioassay. And, furanocoumarins 1-3, 2a, and 2c displayed moderate anti-osteoporosis activities using MCET3-E1 cell line at the concentrations of 1, 10, and 100 µM.

Identification of the hydroxylated derivatives of bufalin: phase I metabolites in rats.

Bufalin was a typical bioactive bufadienolide, existed in the traditional Chinese medicine Chan Su with the high content of 1-5%. The in vivo metabolites (1-5) of bufalin were prepared by various chromatographic techniques from the bile samples of SD rats, which were administrated with bufalin orally. Their structures were determined on the basis of the widely spectroscopic data, including HRESIMS, 1D-, and 2D NMR. And 1-3, 5 were new compounds. In the in vitro cytotoxicity assay, metabolites (1-5) showed weaker cytotoxic effects than bufalin against human cancer cell lines A549 and H1299, which indicated that the metabolism was a significant pathway for the detoxification of bufalin. Structures analyses indicated that metabolites 1-5 were hydroxylated derivatives of bufalin. This study suggested that Phase I metabolism catalyzed by CYP450 enzymes was one of the metabolic ways of bufalin, which may promote the excretion of bufalin.

Biotransformation of resibufogenin by Actinomucor elegans.

Resibufogenin (RB), a major bioactive bufadienolide, has the potential anticancer activity. In the present work, biotransformation of RB by Actinomucor elegans AS 3.2778 yielded five products, namely 3-oxo-resibufogenin (1), 3-epi-resibufogenin (2), 3-epi-12-oxo-hydroxylresibufogenin (3), 3α-acetoxy-15α-hydroxylbufalin (4), and 3-epi-12α-hydroxylresibufogenin (5), respectively. Among them, metabolites 3 and 4 are previously unreported. The chemical structures of metabolites 1-5 were fully elucidated on the basis of 2D NMR and HR-MS. The highly stereo- and regio-specific isomerization, hydroxylation, and esterification reactions were observed in the biotransformation process of RB by A. elegans. Their cytotoxicities against A549 and H1299 cells were evaluated.

Microbial transformation of resibufogenin by Curvularia lunata AS 3.4381.

In this paper, the microbial transformation of resibufogenin by Curvularia lunata AS 3.4381 was investigated, and four transformed products were isolated and characterized as 3-epi-resibufogenin (2), 12α-hydroxy-3-epi-resibufogenin (3), 12-oxo-16ß-hydroxy-3-epi-resibufogenin (4), and 12ß,15-epoxy-3-epi-bufalin-14,15-ene (5). Among them, 4 and 5 are new compounds, and isomerization, hydroxylation, and oxidation reactions in microbial transformation process were observed. Additionally, the cytotoxicities of transformed products (2-5) were also investigated.

Phytochemical properties and antioxidant capacities of various colored berries.

BACKGROUND: Berries are known to be rich in anthocyanins. These compounds give berries their distinctive colors and, more importantly, have several health benefits, such as contributing to the prevention of heart disease, cancer and inflammatory disease. In this study, anthocyanin-rich extracts from 12 colored berries found in northern China were analyzed by high-performance liquid chromatography coupled with diode array detection and electrospray ionization mass spectrometry (HPLC-DAD/ESI-MS). Total polyphenol content (TPC), total flavonoid content (TFC), total anthocyanin content (TAC) and antioxidant capacity (AOC) of the berries were assayed. The contribution of anthocyanins in the berries to their antioxidant capacity and bioactivity was also investigated. RESULTS: The 12 berries analyzed had typical profiles with different anthocyanin compositions, which can be considered as an indicator for differentiating berries. Cyanidin-3-xylosyl-galactoside and cyanidin-3-xylosyl-rutinoside were identified for the first time in Acanthopanax S. and Chinese dwarf cherry respectively. All berry extracts showed potent antioxidant activity, and TPC correlated well with AOC. Blue honeysuckle, blackcurrant and blueberry had higher TAC/TPC ratio, with anthocyanins contributing more to AOC. The higher flavonoid content in yellow raspberry and sea buckthorn might increase their antioxidant activity. In addition, wild raspberry had higher antioxidant activity than cultivated raspberries, but they all had lower anthocyanin content with less contribution to AOC. CONCLUSION: There is great potential to improve human health through consumption of these colored berries, especially those high in AOC.

Microbial transformation of acetyl-11-keto-boswellic acid by Cunninghamella elegans.

Microbial biotransformation of acetyl-11-keto-boswellic acid by Cunninghamella elegans AS 3.1207 was carried out, and totally four transformed products were isolated. On the basis of the extensive spectral data, their structures were characterized as 7ß-hydroxy-11-keto-boswellic acid (1), 7ß,30-dihydroxy-11-keto-boswellic acid (2), 7ß,16α-dihydroxy-3-acetyl-11-keto-boswellic acid (3), and 7ß,15α,21ß-trihydroxy-3-acetyl-11-keto-boswellic acid (4), respectively. Among them, products 1 and 2 are the new compounds.

Biotransformation of osthole by Alternaria longipes.

The biotransformation of osthole (1) by Alternaria longipes was carried out, and five transformed products were obtained in the present research work. Based on their extensive spectral data, the structures of these metabolites were characterized as 4'-hydroxyl-osthole (2), 4'-hydroxyl-2',3'-dihydroosthole (3), 2',3'-dihydroxylosthole (4), osthole-4'-oic acid methyl ester (5), and osthole-4'-oic acid glucuron-1-yl ester (6), respectively. Among them, products 5 and 6 were new compounds.

Effect of resveratrol in gestational diabetes mellitus and its complications.

The incidence rate of diabetes in pregnancy is about 20%, and diabetes in pregnancy will have a long-term impact on the metabolic health of mothers and their offspring. Mothers may have elevated blood glucose, which may lead to blood pressure disease, kidney disease, decreased resistance and secondary infection during pregnancy. The offspring may suffer from abnormal embryonic development, intrauterine growth restriction, obesity, autism, and other adverse consequences. Resveratrol (RSV) is a natural polyphenol compound, which is found in more than 70 plant species and their products, such as Polygonum cuspidatum, seeds of grapes, peanuts, blueberries, bilberries, and cranberries. Previous studies have shown that RSV has a potential beneficial effect on complex pregnancy, including improving the indicators of diabetes and pregnancy diabetes syndrome. This article has reviewed the molecular targets and signaling pathways of RSV, including AMP-activated protein kinase, mitogen-activated protein kinases, silent information regulator sirtuin 1, miR-23a-3p, reactive oxygen species, potassium channels and CX3C chemokine ligand 1, and the effect of RSV on gestational diabetes mellitus (GDM) and its complications. RSV improves the indicators of GDM by improving glucose metabolism and insulin tolerance, regulating blood lipids and plasma adipokines, and modulating embryonic oxidative stress and apoptosis. Furthermore, RSV can ameliorate the GDM complications by reducing oxidative stress, reducing the effects on placentation, reducing the adverse effects on embryonic development, reducing offspring's healthy risk, and so on. Thus, this review is of great significance for providing more options and possibilities for further research on medication of gestational diabetes.

Improved lycopene production by Blakeslea trispora with isopentenyl compounds and metabolic precursors.

The highest lycopene production in mated cultures of Blakeslea trispora was 578 mg/l by adding 42 mg geraniol/l to the medium after 48 h of growth. The control gave 317 mg/l. Adding isopentenyl alcohol at 40 mg/l, mevalonic acid at 17.5 mg/l or dimethyl allyl alcohol at 150 mg, each after 36 h growth, gave lycopene yields 62, 45 and 47%, respectively, higher than the control.

Microbial transformation of Norkurarinone by Cunninghamella blakesleana AS 3.970.

In this paper, microbial transformation of norkurarinone (1) by Cunninghamella blakesleana AS 3.970 was investigated and seven transformed products were isolated and characterized as kurarinone (2), 4″,5″-dihydroxykurarinone (3), 6″-hydroxyl-2'-methoxyl-norkurarinone 7-O-ß-d-glucoside (4), 6″-hydroxyl-norkurarinone 4'-O-ß-d-glucoside (5), 4″,5″-dihydroxynorkurarinone (6), 7-methoxyl-norkurarinone (7), and 7-methoxyl-4″,5″-dihydroxynorkurarinone (8), respectively. Among them, 3-5 are new compounds, and the glycosylation reaction in microbial transformation process was reported rarely. In addition, the cytotoxicities of transformed products (1-8) were also investigated.

Microbial biotransformation of kurarinone by Cunninghamella echinulata AS 3.3400.

In this paper, microbial transformation of kurarinone (1) by Cunninghamella echinulata AS 3.3400 was investigated and four transformed products were isolated and identified as 6″-hydroxykurarinone (2), 4″,5″,8″-trihydroxynorkurarinone (3), norkurarinone (4), and kurarinone-7-O-ß-glucoside (5), respectively. Among them, 3 and 5 are new compounds, and the rare glycosylation in microbial transformation was observed. In addition, the cytotoxicities of transformed products (2-5) were also investigated.

New chemical constituents from the fruits of Tetradium ruticarpum.

Two new γ-lactone derivatives, evodinoids A (1) and B (2), along with a new essential oil (3) were isolated from the nearly ripe fruits of Tetradium ruticarpum. The structures of these isolations were determined by 1D and 2D NMR, HR-ESI-MS and ECD data analysis. In addition, the cytotoxic effect of compounds 1-3 was evaluated against human cancer cells A498, A549, HepG-2, MCF-7 and SHSY-5Y, which displayed no significant cytotoxicity (IC50 > 100 µM).