Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application

Aldehyde oxidase (AOX) is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other xenobiotics. AOX-mediated metabolism can result in unexpected outcomes, such as the production of toxic metabolites and high metabolic clearance, which can lead to the clinical failure of novel therapeutic agents. Computational models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of compounds during the early phases of drug discovery and provide valuable clues for manipulating AOX-mediated metabolism liability. In this study, we developed a novel graph neural network called AOMP for predicting AOX-mediated metabolism. AOMP integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction, while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both tasks. AOMP significantly outperformed the benchmark methods in both cross-validation and external testing. Using AOMP, we systematically assessed the AOX-mediated metabolism of common fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability, which were validated through in vitro experiments. Furthermore, for the convenience of the community, we established the first online service for AOX metabolism prediction based on AOMP, which is freely available at https://aomp.alphama.com.cn.

Remarkable Research Achievements in Traditional Chinese Medicine During New Era （2012—2022） / 中国实验方剂学杂志

Since the 18th National Congress of the Communist Party of China （CPC）， a continuous stream of scientific and technological innovations has unfolded in the realm of traditional Chinese medicine （TCM）. With the aim of implementing the spirit of the 20th National Congress of the CPC， and the Opinions on Promoting the Inheritance， Innovation and Development of TCM， and to underscore the exemplary role of significant scientific and technological achievements， the China Association of Chinese Medicine， in alignment with relevant requirements and under the guidance of authoritative experts， has organized a comprehensive review of the important scientific and technological achievements in the field of TCM since the 18th National Congress of the CPC. Through rigorous procedures， including collecting and reviewing achievements， writing achievement reports， organizing expert reviews， and seeking public opinions， remarkable research achievements in TCM during 2012—2022 were compiled.

Drug target inference by mining transcriptional data using a novel graph convolutional network framework

A fundamental challenge that arises in biomedicine is the need to characterize compounds in a relevant cellular context in order to reveal potential on-target or off-target effects. Recently, the fast accumulation of gene transcriptional profiling data provides us an unprecedented opportunity to explore the protein targets of chemical compounds from the perspective of cell transcriptomics and RNA biology. Here, we propose a novel Siamese spectral-based graph convolutional network (SSGCN) model for inferring the protein targets of chemical compounds from gene transcriptional profiles. Although the gene signature of a compound perturbation only provides indirect clues of the interacting targets, and the biological networks under different experiment conditions further complicate the situation, the SSGCN model was successfully trained to learn from known compound-target pairs by uncovering the hidden correlations between compound perturbation profiles and gene knockdown profiles. On a benchmark set and a large time-split validation dataset, the model achieved higher target inference accuracy as compared to previous methods such as Connectivity Map. Further experimental validations of prediction results highlight the practical usefulness of SSGCN in either inferring the interacting targets of compound, or reversely, in finding novel inhibitors of a given target of interest.

Mechanism of Zhizi Prescription in Protection of CCl4-induced Acute and Subacute Liver Injury in Mice / 中国实验方剂学杂志

ObjectiveTo investigate the protective effect of Zhizi prescription （ZZP） on carbon tetrachloride （CCl4）-induced acute and subacute liver injury and its mechanism. MethodAcute and subacute liver injury animal models were induced. C57 mice were randomly divided into a normal group， model group， obeccholic acid group， ZZP high-dose （0.5 g·kg-1） group， and ZZP low-dose （0.25 g·kg-1） group. According to the experiment design， the serum and liver tissue of mice were collected after the last administration. Hematoxylin-eosin （HE） and Sirius staining was used to observe the liver pathological changes. Serum alanine aminotransferase （ALT）， aspartate aminotransferase （AST）， total bilirubin （TBIL）， liver homogenate hydroxyproline （Hyp）， malondialdehyde （MDA）， and superoxide dismutase （SOD） levels were determined by kit. The levels of tumor necrosis factor-α （TNF-α） and interleukin-6 （IL-6） in the liver tissue were determined by enzyme-linked immunosorbent assay （ELISA）. Real-time fluorescence quantitative polymerase chain reaction （Real-time PCR） was used to detect the mRNA expressions of collagen 1A1 （Col1a1）， collagen 3A1 （Col3a1）， fibronectin （FN）， transforming growth factor β receptor Ⅱ （Tgfbr2） and α-smooth muscle actin （α-SMA） in the liver tissue. ResultIn terms of the acute liver injury， as compared with the normal group， the levels of ALT， AST， TBIL and MDA in the model group were significantly increased （P<0.01）， while the activity of liver SOD was significantly decreased （P<0.01）. Compared with model group， the ZZP high-dose and low-dose groups both significantly reduced the degree of liver cell injury， and protected the acute liver injury induced by CCl4. The ZZP high-dose group had a better effect than the ZZP low-dose group. In terms of the subacute liver injury， the levels of ALT， AST， MDA，TNF-α and IL-6 in the model group were significantly increased （P<0.01）， while the activity of liver SOD was significantly decreased （P<0.01）. As compared with the model group， liver Hyp content in the ZZP high-dose and low-dose groups was significantly decreased （P<0.01）， and the collagen deposition in liver of both groups was significantly reduced. The ZZP high-dose group also significantly down-regulated the mRNA expressions of α-SMA， Col1a1， Col3a1， FN， and Tgfbr2 in the liver of mice （P<0.05， P<0.01）. ConclusionZZP effectively protects the acute and subacute liver injury induced by CCl4， and the protective effect is proportional to its concentration. The mechanism may be related to the increase of the activity of antioxidant enzymes in the liver tissue， the decrease of the level of lipid peroxidation， and the inhibition of inflammatory response， thus reducing collagen deposition and improving early liver fibrosis.

Mechanism of Zhizi Prescription in Protection of CCl4-induced Acute and Subacute Liver Injury in Mice / 中国实验方剂学杂志

ObjectiveTo investigate the protective effect of Zhizi prescription （ZZP） on carbon tetrachloride （CCl4）-induced acute and subacute liver injury and its mechanism. MethodAcute and subacute liver injury animal models were induced. C57 mice were randomly divided into a normal group， model group， obeccholic acid group， ZZP high-dose （0.5 g·kg-1） group， and ZZP low-dose （0.25 g·kg-1） group. According to the experiment design， the serum and liver tissue of mice were collected after the last administration. Hematoxylin-eosin （HE） and Sirius staining was used to observe the liver pathological changes. Serum alanine aminotransferase （ALT）， aspartate aminotransferase （AST）， total bilirubin （TBIL）， liver homogenate hydroxyproline （Hyp）， malondialdehyde （MDA）， and superoxide dismutase （SOD） levels were determined by kit. The levels of tumor necrosis factor-α （TNF-α） and interleukin-6 （IL-6） in the liver tissue were determined by enzyme-linked immunosorbent assay （ELISA）. Real-time fluorescence quantitative polymerase chain reaction （Real-time PCR） was used to detect the mRNA expressions of collagen 1A1 （Col1a1）， collagen 3A1 （Col3a1）， fibronectin （FN）， transforming growth factor β receptor Ⅱ （Tgfbr2） and α-smooth muscle actin （α-SMA） in the liver tissue. ResultIn terms of the acute liver injury， as compared with the normal group， the levels of ALT， AST， TBIL and MDA in the model group were significantly increased （P<0.01）， while the activity of liver SOD was significantly decreased （P<0.01）. Compared with model group， the ZZP high-dose and low-dose groups both significantly reduced the degree of liver cell injury， and protected the acute liver injury induced by CCl4. The ZZP high-dose group had a better effect than the ZZP low-dose group. In terms of the subacute liver injury， the levels of ALT， AST， MDA，TNF-α and IL-6 in the model group were significantly increased （P<0.01）， while the activity of liver SOD was significantly decreased （P<0.01）. As compared with the model group， liver Hyp content in the ZZP high-dose and low-dose groups was significantly decreased （P<0.01）， and the collagen deposition in liver of both groups was significantly reduced. The ZZP high-dose group also significantly down-regulated the mRNA expressions of α-SMA， Col1a1， Col3a1， FN， and Tgfbr2 in the liver of mice （P<0.05， P<0.01）. ConclusionZZP effectively protects the acute and subacute liver injury induced by CCl4， and the protective effect is proportional to its concentration. The mechanism may be related to the increase of the activity of antioxidant enzymes in the liver tissue， the decrease of the level of lipid peroxidation， and the inhibition of inflammatory response， thus reducing collagen deposition and improving early liver fibrosis.

Discovery of a subtype-selective, covalent inhibitor against palmitoylation pocket of TEAD3

The TEA domain (TEAD) family proteins (TEAD1‒4) are essential transcription factors that control cell differentiation and organ size in the Hippo pathway. Although the sequences and structures of TEAD family proteins are highly conserved, each TEAD isoform has unique physiological and pathological functions. Therefore, the development and discovery of subtype selective inhibitors for TEAD protein will provide important chemical probes for the TEAD-related function studies in development and diseases. Here, we identified a novel TEAD1/3 covalent inhibitor (DC-TEADin1072) with biochemical IC

Astragaloside IV suppresses post-ischemic natural killer cell infiltration and activation in the brain: involvement of histone deacetylase inhibition / 医学前沿

Natural killer (NK) cells, a type of cytotoxic lymphocytes, can infiltrate into ischemic brain and exacerbate neuronal cell death. Astragaloside IV (ASIV) is the major bioactive ingredient of Astragalus membranaceus, a Chinese herbal medicine, and possesses potent immunomodulatory and neuroprotective properties. This study investigated the effects of ASIV on post-ischemic brain infiltration and activation of NK cells. ASIV reduced brain infarction and alleviated functional deficits in MCAO rats, and these beneficial effects persisted for at least 7 days. Abundant NK cells infiltrated into the ischemic hemisphere on day 1 after brain ischemia, and this infiltration was suppressed by ASIV. Strikingly, ASIV reversed NK cell deficiency in the spleen and blood after brain ischemia. ASIV inhibited astrocyte-derived CCL2 upregulation and reduced CCR2

Precision Medicine and Innovative Development of Traditional Chinese Medicine (TCM) / 世界科学技术-中医药现代化

Precision medicine was recognized as a research focus nowadays as it shows the promise of overcoming the challenge of health and medicine that we are currently facing.Combining novel techniques in genetics,molecular imaging and bioinformatics with clinical and personal information,precision medicine can make sound health risk prediction and accurate classification,diagnosis and therapy to establish personalized disease prevention and treatment programs and to achieve accurate assessment of individual therapy and prognosis.This paper briefly summarized the background information,scientific content,current development and potential effect of precision medicine on modern medical science.The essence of traditional Chinese medicine (TCM),which is body-oriented entirety diagnosis and treatment based on syndrome differentiation,highly matched the core notion of precision medicine,emphasizing different treatments for different people with the same disease at different stages.Therefore,further investigation of TCM with the idea of precision medicine will definitely promote its innovative development.Thus,it is important that we profoundly mine and enlarge the recognized vantages of TCM,explore new strategies,technologies and methodologies to inherit and promote precision medicine and personalized therapy in TCM;and enrich the ways of the approaches of TCM precision therapy.Taking precision diagnosis and precision therapy as our focuses,we will afford to promote TCM by emphasizing its philosophy of personalized,dynamic and entirety diagnoses and treatment.

Two new sulfated sesquiterpenoids from Petasites tricholobus / 药学学报

Two new sulfated sesquiterpenoids, megastigman-7-ene-3, 5, 6, 9-tetrol-3-O-β-D-6'-sulfonated-glucopyranoside (1) and 3-O-β-D-6'-sulfonated-glucopyranosyl-6-(3-oxo-2-butenylidenyl)-1, 1, 5-trimethylcyclohexan-5-ol (2), along with one known sesquitepenoid compound icariside B1 (3) were isolated from the whole herb of Petasites tricholobus Franch. Their structures were identified by their chemical and spectroscopic characters. All obtained compounds were tested for their cytotoxicity against four cancer cell lines.

Phenolic constituents from Lysimachia patungensis / 药学学报

To study the chemical constituents of Lysimachia patungensis Hand.-Mazz., silica gel column chromatography, reverse phase ODS column chromatography, MCI and Sephadex LH-20, were used to separate the 95% EtOH extract of the whole plant of Lysimachia patungensis Hand.-Mazz.. The structures of the isolated compounds have been established on the basis of chemical and NMR spectroscopic evidence as well as ESI-MS in some cases. Twelve phenolic compounds were obtained and identified as quercetin-3, 3'-di- O-alpha-L-rhamnoside (1), myricetrin (2), quercitrin (3), rutin (4), 2-hydroxynaringenin-4'-O-glucopyranoside (5), naringenin 7-O-glucopyranoside (6), liquiritin apioside (7), licochalcone B (8), tetrahydroxymethoxy chalcone (9), methyl-p-coumarate (10), 2, 4, 6-trihydroxy acetophenone-2-O-glucopyranoside (11) and vaccihein A (12). Among them, compound 1 is a new compound, and compounds 5, 11 and 12 are isolated from the genus Lysimachia L. for the first time, and the others are isolated from the plant for the first time.

Phenolic components from Petasites tricholobus / 中国中药杂志

<p><b>OBJECTIVE</b>To study the anti-inflammatory and antioxidant effects of Petasites tricholobus and its phenolic components.</p><p><b>METHOD</b>Phenolic compounds were separated purified by column chromatographic methods such as macroporous resin D-101, silica gel, ODS, MCI GEL CHP 20P, Sephadex LH-20. Their structures were identified on the basis of physicochemical property and multiple spectral data.</p><p><b>RESULT</b>Nineteen phenolic compounds were separated from 95% ethanol extracts from P. tricholobus Franch. and identified as sulfonated benzyl glucoside (1), 3-(4beta-D-glucopyranosyloxy-3, 5-dimethoxy) -phenyl-2E-propenol (2), dihydrosyringin (3), tangshenosides II (4), 4-hydroxy-2,6-dimethoxyphenol-1-O-beta-D-glucopyranoside (5), 4-hydroxymethyl-2, 6-dimethoxyphenyl-1-O-beta-D-glucopyranoside (6), arbutin (7), rutin (8), kaempferol-3-O-alpha-L-rhamnopyranosyl-(1 --> 6)-beta-D-glucopyranoside (9), quercetin-3-O-beta-D-glucopyranoside (10), kaempferol-3-O-beta-D-glucopyranoside (11), afzelin (12), petasiphenol (13), caffeic acid (14), chlorogenic acid (15), 2-hydroxy-5-acetylbenzoic acid (16), p-hydroxy-benzoic acid (17), protocatechuic aldehyde (18) , and p-hydroxy-phenylpropionic acid (19).</p><p><b>CONCLUSION</b>Above result shows that phenolic compounds contained in P. tricholobus mainly include simple phenols, phenolic glycosides, coffee acid and flavonoid glycosides. Among them, compound 1 was separated from the composite family for the first time; compounds 2-7, 9, 11, 12, 16, 19 were separated from the genus Petasites for the first time, and the others were separated from the plant for the first time. These compounds have been proved to have pharmacological effects such as anti-inflammation, antibiosis, antioxidantion.</p>

The preparation of paeonol transdermal delivery systems based on the microemulsion-based gels and its pharmacokinetics characters / 药学学报

Investigation of the pharmacokinetics of paeonol microemulsion, microemulsion-based gels and marketed paeonol ointments by the skin-blood synchronous microdialysis coupled with LC/MS is reported in this study. The microdialysis systems were established by linear probes and concentric circles probes. In vivo recovery of paeonol in skin is (69.7 +/- 4.8) % and in blood is (51.6 +/- 7.2)%. The paeonol microemulsion, microemulsion-based gels and marketed paeonol ointments were administered to rats. PBS (pH 7.4) served as perfused solution. The perfusion rate was 5 microL x mL(-1) and the microdialysis samples were collected every 20 min intervals. The paeonol concentration in perfused solution was determined by LC/MS. The results showed that paeonol microemulsion and microemulsion-based gels significantly raised the drug concentrations in skin more than that of paeonol ointments. The paeonol microemulsion-based gels has similar bioavailability as the paeonol ointments in blood, but its blood drug concentrations were steadier. The paeonol microemulsion-based gels may be developed into a new preparation for dermis eczema. The skin-blood synchronous microdialysis technique proved to be a new method for the pharmacokinetics study of transdermal delivery systems.