HTINet2: herb-target prediction via knowledge graph embedding and residual-like graph neural network.

Target identification is one of the crucial tasks in drug research and development, as it aids in uncovering the action mechanism of herbs/drugs and discovering new therapeutic targets. Although multiple algorithms of herb target prediction have been proposed, due to the incompleteness of clinical knowledge and the limitation of unsupervised models, accurate identification for herb targets still faces huge challenges of data and models. To address this, we proposed a deep learning-based target prediction framework termed HTINet2, which designed three key modules, namely, traditional Chinese medicine (TCM) and clinical knowledge graph embedding, residual graph representation learning, and supervised target prediction. In the first module, we constructed a large-scale knowledge graph that covers the TCM properties and clinical treatment knowledge of herbs, and designed a component of deep knowledge embedding to learn the deep knowledge embedding of herbs and targets. In the remaining two modules, we designed a residual-like graph convolution network to capture the deep interactions among herbs and targets, and a Bayesian personalized ranking loss to conduct supervised training and target prediction. Finally, we designed comprehensive experiments, of which comparison with baselines indicated the excellent performance of HTINet2 (HR@10 increased by 122.7% and NDCG@10 by 35.7%), ablation experiments illustrated the positive effect of our designed modules of HTINet2, and case study demonstrated the reliability of the predicted targets of Artemisia annua and Coptis chinensis based on the knowledge base, literature, and molecular docking.

Authentication of Platycladus Orientalis Leaves and Its Five Adulterants by Combination of Morphology and Microscopic Characteristics, TLC, and HPLC Analysis.

BACKGROUND: Platycladus orientalis leaves (POL), as the source of the traditional Chinese medicine (TCM) Platycladi Cacumen, has frequently been found to be misused with five adulterants including Chamaecyparis obtusa leaves (COL), Cupressus funebris leaves (CFL), Juniperus virginiana leaves (JVL), Sabina chinensis leaves (SCL), and Juniperus formosana leaves (JFL). OBJECTIVE: The purpose of this study was to distinguish POL (fresh leaves) from its five adulterants (fresh leaves). METHODS: The micromorphological features in terms of transection and microscopic characteristics of POL and adulterants were captured and compared using the an microscope. Both HPLC and TLC methods for the simultaneous determination of six bioactive flavonoids (myricitrin, isoquercitrin, quercitrin, amentoflavone, afzelin, and hinokiflavone) have been developed. RESULTS: There were significant differences in microscopic features of transverse section and powders. The TLC results suggested that the spots of myricitrin in POL were more obvious than those in the five adulterants. The contents of myricitrin and quercitrin, or the total content of flavonoids in POL, determined by HPLC, were significantly higher than those in the adulterants. CONCLUSION: POL was successfully distinguished from its five adulterants by the comparison of morphology, microscopic characteristics, and chemical profiles. HIGHLIGHTS: This research provides a comprehensive morphology, microscopic identification, TLC, and HPLC analysis for authenticating POL and its five adulterants.

Construction of coaxial liquid centrifugal platform for the extraction of active ingredients from natural products.

In the classical natural product extraction and separation process, it is tedious and requires large amounts of reagents and time. In this study, an efficient coaxial liquid centrifugal oil-water-oil triple-liquid-phase system with a simple structure and convenient operation was successfully constructed and used to extract flavonoids from Platycladi Cacumen. The results showed that the coaxial liquid centrifugal platform constructed in this study had good stability and 6 ml was the minimum volume of the middle phase for 1000 rpm to stabilize the system. Besides, it was easy to repeat the operation: the relative standard deviations of the extraction yields of flavonoids and sugar in six parallel operations were all less than 10%. Moreover, it was only one-tenth of the time required for this method as traditional liquid-liquid extraction while reducing the use of volatile organic reagents. Finally, the new method was more selective than the traditional method for the extraction of flavonoids. Therefore, this study provides a possibility for the coaxial liquid centrifugal platform to be used in multi-liquid phase systems to achieve the simultaneous extraction of different parts of natural products by different liquid phases. It is expected to provide a reliable reference for further expansion of small-scale experimental operations to industrial production.

Screening of hypoglycemic components in Platycladi Cacumen by phytochemical investigation, spectrum-effect relationship, and chemometric methods.

In this work, the hypoglycemic components in Platycladi Cacumen, an essential traditional Chinese medicine, were evaluated by combining phytochemical investigation, spectrum-effect relationship analysis, and chemometric methods. The phytochemical studies on Platycladi Cacumen extract lead to the isolation of 21 potential bioactive compounds. The chromatographic fingerprints of Platycladi Cacumen samples were established by high-performance liquid chromatography. The hypoglycemic effects of Platycladi Cacumen samples were further evaluated by inhibition of α-glucosidase and detected by the high-performance liquid chromatography method. The spectrum-effect relationship study by bivariate correlations analysis and orthogonal partial least squares regression revealed that myricitrin (P9), quercitrin (P13), afzelin (P18), and amentoflavone (P24) were more relevant to the α-glucosidase inhibitory activity. The results of α-glucosidase inhibitory activity of 21 isolated compounds and molecular docking studies also indicated these flavonoids had potent α-glucosidase inhibitory activity. Collectively, the present study established the spectrum-effect relationship mode of Platycladi Cacumen and discovered the major hypoglycemic components, which provides a feasible method for screening bioactive components.

A piecewise lookup table for calculating nonbonded pairwise atomic interactions.

A critical challenge for molecular dynamics simulations of chemical or biological systems is to improve the calculation efficiency while retaining sufficient accuracy. The main bottleneck in improving the efficiency is the evaluation of nonbonded pairwise interactions. We propose a new piecewise lookup table method for rapid and accurate calculation of interatomic nonbonded pairwise interactions. The piecewise lookup table allows nonuniform assignment of table nodes according to the slope of the potential function and the pair interaction distribution. The proposed method assigns the nodes more reasonably than in general lookup tables, and thus improves the accuracy while requiring fewer nodes. To obtain the same level of accuracy, our piecewise lookup table accelerates the calculation via the efficient usage of cache memory. This new method is straightforward to implement and should be broadly applicable. Graphical Abstract Illustration of piecewise lookup table method.