A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19.

BACKGROUND: COVID-19 highly caused contagious infections and massive deaths worldwide as well as unprecedentedly disrupting global economies and societies, and the urgent development of new antiviral medications are required. Medicinal herbs are promising resources for the discovery of prophylactic candidate against COVID-19. Considerable amounts of experimental efforts have been made on vaccines and direct-acting antiviral agents (DAAs), but neither of them was fast and fully developed. PURPOSE: This study examined the computational approaches that have played a significant role in drug discovery and development against COVID-19, and these computational methods and tools will be helpful for the discovery of lead compounds from phytochemicals and understanding the molecular mechanism of action of TCM in the prevention and control of the other diseases. METHODS: A search conducting in scientific databases (PubMed, Science Direct, ResearchGate, Google Scholar, and Web of Science) found a total of 2172 articles, which were retrieved via web interface of the following websites. After applying some inclusion and exclusion criteria and full-text screening, only 292 articles were collected as eligible articles. RESULTS: In this review, we highlight three main categories of computational approaches including structure-based, knowledge-mining (artificial intelligence) and network-based approaches. The most commonly used database, molecular docking tool, and MD simulation software include TCMSP, AutoDock Vina, and GROMACS, respectively. Network-based approaches were mainly provided to help readers understanding the complex mechanisms of multiple TCM ingredients, targets, diseases, and networks. CONCLUSION: Computational approaches have been broadly applied to the research of phytochemicals and TCM against COVID-19, and played a significant role in drug discovery and development in terms of the financial and time saving.

New monoterpenoids from the stigmas of Crocus sativus.

One new compound, crocusatin M (1), and three new glycosidic compounds, crocusatins N-P (2-4), along with nine known compounds were isolated from the dried stigmas of Crocus sativus. The structures of new compounds were elucidated on the basis of spectroscopic analysis, and the absolute configurations of 1, 2, and 3 were unambiguously assigned by the comparison of experimental and calculated ECD data. This is the first report of the isolation of 4 with the HMG moiety from the genus Crocus. Compounds 1 and 4 exhibited weak anti-inflammatory activities on inhibiting lipopolysaccharide (LPS)-induced NO production.

Novel Meroterpenoids from Hypericum patulum: Highly Potent Late Nav1.5 Sodium Current Inhibitors.

Hypulatones A and B (1 and 2), two racemic meroterpenoids possessing an unprecedented spiro[benzofuran-2,1'-cycloundecan]-4'-ene-4,6(5H)-dione core, were characterized from Hypericum patulum. Compound 2 was found to significantly inhibit the late current of Nav1.5 (late INa, IC50 = 0.2 µM). Importantly, 2 exhibited remarkable separation (>100-fold) of late INa relative to peak INa and notable selectivity over Cav3.1, Kv1.5, and hERG. 1 showed comparable inhibition on late INa compared to that of 2 with poorer selectivity.

Cytotoxic Prenylated Xanthones from the Leaves of Garcinia bracteata.

Six new prenylated xanthones (1: -6: ) and seventeen known xanthones were isolated from extracts of Garcinia bracteata leaves. Their structures were determined by extensive NMR and MS spectroscopic data analysis. The inhibitory activities of the isolates were assayed on HeLa, A549, PC-3, HT-29, and WPMY-1 cell lines. Compounds 1: and 15: -17: showed moderate inhibitory effects on tumor cell growth, with IC50s ranging from 3.7 to 14.7 µM.

Oblongifolin C and guttiferone K extracted from Garcinia yunnanensis fruit synergistically induce apoptosis in human colorectal cancer cells in vitro.

Oblongifolin C (OC) and guttiferone K (GUTK) are two anticancer compounds extracted from Garcinia yunnanensis Hu, but they act by different mechanisms. In this study we investigated whether a combination of OC and GUTK (1:1 molar ratio) could produce synergistic anticancer effects against human colorectal cancer cells in vitro. For comparison, we also examined the anticancer efficacy of ethanol extracts from G yunnanensis fruit, which contain OC and GUTK up to 5%. Compared to OC and GUTK alone, the combination of OC and GUTK as well as the ethanol extracts more potently inhibited the cancer cell growth with IC50 values of 3.4 µmol/L and 3.85 µg/mL, respectively. Furthermore, OC and GUTK displayed synergistic inhibition on HCT116 cells: co-treatment with OC and GUTK induced more prominent apoptosis than treatment with either drug alone. Moreover, the combination of OC and GUTK markedly increased cleavage of casapse-3 and PARP, and enhanced cellular ROS production and increased JNK protein phosphorylation. In addition, the combination of OC and GUTK exerted stronger effects under nutrient-deprived conditions than in complete medium, suggesting that autophagy played an essential role in regulating OC- and GUTK-mediated cell death. OC and GUTK are the main components that contribute to the anticancer activity of G yunnanensis and the compounds have apoptosis-inducing effects in HCT116 cells in vitro.

Bioassay-Guided Isolation of Prenylated Xanthone Derivatives from the Leaves of Garcinia oligantha.

Four new dihydroxanthone derivatives (1-4), four new tetrahydroxanthone derivatives (5-8), two new xanthone derivatives (9 and 10), and two known caged tetrahydroxanthones were isolated from extracts of the leaves of Garcinia oligantha by bioassay-guided fractionation. These structures of the new compounds were elucidated by NMR and MS spectroscopic data analysis, and the absolute configurations of compounds 1 and 5-7 were determined by electronic circular dichroism and/or single-crystal X-ray diffraction analysis. Compounds 6-9 were shown to be unusual xanthone derivatives with an isopropyl group, which was confirmed by the X-ray crystallographic structure of compound 8. The inhibitory activities of these isolates against four human tumor cell lines (A549, HepG2, HT-29, and PC-3) were assayed, and compounds 1, 2, 5, 11, and 12 showed inhibitory effects on tumor cell growth, with IC50 values ranging from 2.1 to 8.6 µM.

Yiguanjian decoction and its ingredients inhibit angiogenesis in carbon tetrachloride-induced cirrhosis mice.

BACKGROUND: Cirrhosis is associated with angiogenesis and disruption of hepatic vascular architecture. Yiguanjian (YGJ) decoction, a prescription from traditional Chinese medicine, is widely used for treating liver diseases. We studied whether YGJ or its ingredients (iYGJ) had an anti-angiogenic effect and explored possible mechanisms underlying this process. METHODS: Cirrhosis was induced with carbon tetrachloride (CCl4) (ip) in C57BL/6 mice for 6 weeks. From week 4 to week 6, cirrhotic mice were randomly divided into four groups: sorafenib-treated, YGJ-treated and iYGJ-treated mice and placebo. Serum biochemistries, hydroxyproline (Hyp) content and histopathological changes of hepatic tissues were measured as were α-smooth muscle actin (α-SMA), collagen I, CD31, vascular endothelial growth factor (VEGF), VEGF receptor (VEGFR) 2 and hypoxia-inducible factor (HIF)-1α. RESULTS: Both YGJ and iYGJ improved serum biochemistries. Changes of histopathology showed that YGJ and iYGJ reduced hepatic tissue necroinflammatory and collagen fiber deposition in cirrhosis mice. Compared to the CCl4 treated animals, Hyp, α-SMA, collagen I, CD31, VEGF, VEGFR, and HIF-1α expression decreased in YGJ and iYGJ groups. CONCLUSIONS: YGJ and iYGJ inhibited liver angiogenesis in cirrhotic mice treated with CCl4 by inhibiting the HIF-1α/VEGF signaling pathway, suggesting that anti-angiogenic effects of YGJ and iYGJ are associated with improving the hepatic hypoxic microenvironment.

Xanthine oxidase inhibitors from Garcinia esculenta twigs.

The EtOAc-soluble portion of the 80 % (v/v) EtOH extract from the twigs of Garcinia esculenta exhibited strong xanthine oxidase inhibition in vitro. Bioassay-guided purification led to the isolation of 1,3,6,7-tetrahydroxyxanthone (3) and griffipavixanthone (8) as the main xanthine oxidase inhibitors, along with six additional compounds (1, 2, 4-7), including two new compounds (1 and 2). This enzyme inhibition was dose dependent with an IC50 value of approximately 1.2 µM for 3 and 6.3 µM for 8. The inhibitory activity of 3 was stronger than the control allopurinol (IC50 value: 5.3 µM). To our knowledge, compound 8 is the first bixanthone that demonstrated potent XO inhibitory activity in vitro. The structures of the new compounds were established by spectroscopic analysis, and the optical properties and absolute stereochemistry of racemic (±) esculentin A (2) were further determined by the calculation of the DP4 probability and analysis of its MTPA ester derivatives.

Cytotoxic and anti-inflammatory prenylated benzoylphloroglucinols and xanthones from the twigs of Garcinia esculenta.

Five new prenylated benzoylphloroglucinol derivatives, garciesculentones A-E (1-5), a new xanthone, garciesculenxanthone A (6), and 15 known compounds were isolated from the petroleum ether extract and the EtOAc-soluble fraction of a 80% (v/v) EtOH extract of Garcinia esculenta. The structures of the new compounds were elucidated by 1D- and 2D-NMR spectroscopic analysis and mass spectrometry. Experimental and calculated ECD and a convenient modified Mosher's method were used to determine the absolute configurations. The cytotoxicity of these compounds were evaluated by MTT assay against three human cancer cell lines (HepG2, MCF-7, and MDA-MB-231) and against normal hepatic cells (HL-7702). In addition, these isolates were evaluated for their inhibitory effects on interferon-γ plus lipopolysaccharide-induced nitric oxide production in RAW264.7 cells.

[Research progress of chemistry and anti-cancer activities of natural products from Chinese Garcinia plants].

Garcinia plants are one of the rich sources of natural xanthones and benzophenones which have attracted a great deal of attention from the scientists in the fields of chemistry and pharmacology. Recently, many structurally unique constituents with various bioactivities, especially anti-tumor activity, have been isolated from Garcinia plants. This concise review focused on the anti-cancer activity natural products isolated from Chinese Garcinia plants, and the research finding by authors and collaborators over the past several years were cited.

Prenylated benzoylphloroglucinols and xanthones from the leaves of Garcinia oblongifolia with antienteroviral activity.

An acetone extract of the leaves of Garcinia oblongifolia showed antiviral activity against enterovirus 71 (EV71) using a cytopathic effect inhibition assay. Bioassay-guided fractionation yielded 12 new prenylated benzoylphloroglucinols, oblongifolins J-U (1-12), and five known compounds. The structures of 1-12 were elucidated by spectroscopic analysis including 1D- and 2D-NMR and mass spectrometry methods. The absolute configurations were determined by a combination of a Mosher ester procedure carried out in NMR tubes and ECD calculations. Compared to ribavirin (IC50 253.1 µM), compounds 1, 4, and 13 exhibited significant anti-EV71 activity in vitro, with IC50 values of 31.1, 16.1, and 12.2 µM, respectively. In addition, the selectivity indices of these compounds were 1.5, 2.4, and 3.0 in African green monkey kidney (Vero) cells, respectively.

Chemical comparison of two dosage forms of Hemp Seed Pills by UHPLC-Q-ToF-MS/MS and multivariate statistical techniques.

Hemp seed soft gel capsule (HSSGC) is a modernised dosage form that is derived from a traditional Chinese patent medicine, Hemp Seed Pills (HSP). Two dosage forms claim the same therapeutic effects; however, their chemical components and chemical equivalency are unclear. In the present study, an ultra performance liquid chromatography coupled with time-of-flight mass spectrometry (UHPLC-ToF-MS)-based chemical profiling approach was proposed to rapidly evaluate the chemical differences between HSP and HSSGC as model dosage forms. Samples of the two dosage forms were subjected to UHPLC-ToF-MS analysis. The datasets of retention time (TR) and mass-to-charge ratio (m/z) pairs, ion intensities and sample codes were processed with principal component analysis (PCA) and partial least squares discriminate analysis (PLS-DA) to holistically compare the difference between these two dosage form samples. A clear classification trend was observed in the score plot, and a loading bi-plot was generated in which the variables are correlated with the group and the samples that were observed. The important chemical components that caused differences among the samples were explored with a Variables Importance Projection (VIP) index. Using the proposed approach, global chemical differences were found between the two dosage forms and among samples of the same dosage form. The most important components that are related to the differences were identified and most of them were attributed to Fructus Aurantii Immaturus. It is suggested that this newly established approach could be used for pre-clinical trial chemical equivalence study or the quality evaluation of the traditional medicinal products with large variations in quality.

[Dynamic change of lipid peroxidation-related protein expression and the intervention effects of Yiguanjian decoction in a rat model of CCl4-induced liver fibrosis].

To investigate the dynamic change of lipid peroxidation-related protein expression and the intervention effects of Yiguanjian (YGJ) Decoction on liver fibrosis induced by CCl4 in rat. Fifty-seven male Wistar rats were randomly divided into a liver fibrosis group (n = 39) and a normal group (n = 18). The liver fibrosis was treated with peritoneal injection of 50% CCl4 for nine weeks. At the end of weeks 3 and 6 of CCl4 treatment, six rats were sacrificed to assess the status of liver fibrosis. At the end of week 7, the remaining -fibrotic rats were randomly divided into an untreated model group (M, n=15) and a YGJ-treated group (n = 12). The YGJ group was administered daily, oral YGJ Decoction for three weeks, concomitant with continued CCl4 treatment. The M group and normal group received the same treatment oral regimen and volume of distilled water. At the end of week 8, four rats in group M were sacrificed to observed the fibrosis status. At the end of week 9, the fibrotic rats were sacrificed for sampling. Liver function, histological changes, contents of hydroxyproline (Hyp) and malondialdehyde (MDA), activity of super oxidase dismutase (SOD) and L-glutathione (GSH), protein expression of heat shock protein (HSP)70, heme oxygenase (HO)-1, transferrin, peroxiredoxin (Prxd) 6 and liver fatty acid binding protein (L-FABP) were detected. Compared with normal group-, the MDA content was increased significantly in M group at week 6 (M: 4.23+/-0.45 nmol/mg vs. normal: 2.22+/-0.59 nmol/mg, F = 60.13, P less than 0.01) and week 9 (M: 6.29+/-1.23 nmol/mg vs. normal: 2.22+/-0.59 nmol/mg, F = 66.99, P less than 0.01), but the SOD activity was decreased significantly at the same time points [week 6: (M: 196.94+/-39.20 U/mg vs. normal: 264.50+/-30.44 U/mg, F = 11.12, P less than 0.01]); [week 9: (M: 152.2+/-51.65 U/mg vs. normal: 264.50+/-30.44 U/mg, F = 23.11, P less than 0.01)], as were the GSH content [week 6: (M: 48.47+/-7.27 nmol/mg vs. 60.74+/-9.04 nmol/mg, F = 6.71, P less than 0.05]]; [week 9: (M: 37.89+/-9.01 nmol/mg vs. 60.74+/-9.04 nmol/mg, F = 24.06, P less than 0.01]]. Compared with group M at week 9, the YGH-treated model group had markedly decreased MDA (YGJ: 4.25+/-0.86 nmol/mg vs. M: 6.29+/-1.23 nmol/mg, F = 19.52, P less than 0.01], but significantly increased SOD (YGJ: 198.35+/-46.48 U/mg vs. 152.21+/-51.65 U/mg, F = 4.65, P less than 0.05] and GSH (YGJ: 53.73+/-7.54 nmol/mg vs. M: 37.89+/-9.01 nmol/mg, F = 19.23, P less than 0.01). Compared to normal rats at week 9, group M had significantly higher protein levels of HSP70 (normal: 1.21+/-0.06 vs. M: 0.58+/-0.07, F = 166.87, P less than 0.01) and HO-1 (normal: 1.11+/-0.06 vs. M: 0.58+/-0.06, F = 123.96, P less than 0.01), but significantly decreased levels of Prxd6 (normal: 0.04+/-0.05 vs. M: 1.49+/-0.05, F = 1215.85, P less than 0.01), transferrin (normal: 0.67+/-0.03 vs. M: 1.67+/-0.04, F = 301.35, P less than 0.01), and L-FABP (normal: 0.24+/-0.02 vs. M: 1.44+/-0.14, F = 219.05, P less than 0.01). Compared to group M at week 9, the YGJ treatment group showed significantly reduced HSP70 (YGJ: 0.82+/-0.04 vs. M: 1.21+/-0.06, F = 92.31, P less than 0.01) and HO-1 (YGJ: 0.90+/-0.04 vs. 1.11+/-0.06, F = 26.89, P less than 0.01), but significantly increased Prxd6 (YGJ: 0.88+/-0.11 vs. 0.04+/-0.05, F = 150.17, P less than 0.01), transferrin (YGJ: 1.36+/-0.13 vs. 0.24+/-0.02, F = 237.19, P less than 0.01), and L-FABP (YGJ: 1.04+/-0.12 vs. 0.67+/-0.03, F = 27.53, P less than 0.01). YGJ treatment of fibrotic liver rats reduces lipid peroxidation damage by preventing generation of oxidizing substances.

Simultaneous determination of five nucleosides and nucleobases of Rehmannia glutinosa Libosch. by high performance liquid chromatography.

This study is to establish a method for simultaneously determination of five nucleosides and nucleobases, including hypoxanthine, uridine, adenine, guanosine and adenosine in Rehmannia glutinosa Libosch. which was collected from different regions in China. A Diamonsil C18 column (250 mm x 4.6 mm, 5 microm) was used. Acetonitrile and 0.04 mol L(-1) potassium dihydrogen phosphate solution were adopted as mobile phase with gradient elution. The flow rate was 1 mL min(-1) and column temperature was 30 degrees C. The detection wavelength was at 254 nm. The method had good linearity over the range of 1.0 - 16.0 microg mL(-1) (r2 = 0.999 8), 5.0 - 80.0 microg mL(-1) (r2 = 0.999 8), 1.0 - 16.0 microg mL(-1) (r2 = 0.999 5), 1.25 - 20.0 microg mL(-1) (r2 = 0.999 8) and 1.0 - 16.0 microg mL(-1) (r2 = 0.999 8) for hypoxanthine, uridine, adenine, guanosine and adenosine, respectively. The average recoveries were between 98.8% and 100.7%. The content of hypoxanthine, uridine, adenine, guanosine and adenosine in Rehmannia glutinosa Libosch. from different regions was significantly different. This established method was sensitive and reliable for the quantification of five chemical constituents in Rehmannia glutinosa Libosch.

[Saponins of polygalacic acid type from Platycodon grandiflorum].

AIM: To isolate triterpene saponins of polygalacic acid type from the roots of Platycodon grandiflorum (Jacq.) A. DC and to identify their structures. METHODS: The compounds were separated by means of extraction, chromatography on silica gel, MPLC and HPLC, and their structures were elucidated on the basis of spectral analyses (FAB-MS, IR, 1H NMR, 13C NMR etc.). RESULTS: Three triterpene saponins were isolated from the roots of Platycodon grandiflorum. They were identified as 3-O-beta-D-laminaribiosyl polygalacic acid (I), 3-O-beta-D-glucopyranosyl polygalacic acid (II), polygalacin D (III), separately. CONCLUSION: Compound I is a new compound, compounds II, III are known triterpene saponins. The compound I and II were isolated from the plant for the first time, which is also the monodesmoside from the plant for the first time.

Diosgenin glucuronides from Solanum lyratum and their cytotoxicity against tumor cell lines.

Bioassay-directed fractionation of the cytotoxicity active fraction of the whole plant from Solanum lyratum led to the isolation of a new steroidal saponin, diosgenin 3-O-beta-D-glucopyranosiduronic acid methyl ester (2), as well as four known compounds, diosgenin (1), diosgenin 3-O-beta-D-glucopyranosiduronic acid (3), diosgenin 3-O-alpha-L-rhamnopyranosyl-(1-->2)-beta-D-glucopyranosiduronic acid (4), diosgenin 3-O-alpha-L-rhamnopyranosyl-(1-->2)-beta-D-glucuroniduronic acid methyl ester (5). The structures of the isolated compounds were elucidated on the basis of their spectral data and chemical evidences. Compound 1 was isolated for the first time from this plant, and compound 3 was isolated as a new natural product. Cytotoxic activities of the isolated compounds were evaluated and the cytotoxicities of compounds 2-5 reported for the first time.

Five new triterpenoid saponins from the roots of Platycodon grandiflorum.

Five new triterpenoid saponins, platycoside H [3-O-beta-D-glucopyranosyl-(1-->6)-beta-D-glucopyranosyl-2beta,3beta,16alpha,23-tetrahydroxyolean-12-en-28-oic acid 28-O-beta-D-xylopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->2)-alpha-L-arabinopyranoside], platycoside I [3-O-beta-D-glucopyranosyl-(1-->6)-beta-D-glucopyranosyl-(1-->6)-beta-D-glucopyranosyl-2beta,3beta,16alpha,23-tetrahydroxyolean-12-en-28-oic acid 28-O-beta-D-xylopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->2)-alpha-L-arabinopyranoside], platycoside J [3-O-beta-D-glucopyranosyl-2beta,3beta,16alpha,23-tetrahydroxyolean-12-en-28-oic acid 28-O-beta-D-xylopyranosyl-(1-->4)-alpha-L-rhamnopyranosyl-(1-->2)-alpha-L-arabinopyranoside], platycoside K [3-O-beta-D-glucopyranosyl-(1-->3)-beta-D-glucopyranosyl-2beta,3beta,16alpha,23,24-pentahydroxyolean-12-en-28-oic acid], and platycoside L [3-O-beta-D-glucopyranosyl-(1-->6)-beta-D-glucopyranosyl-2beta,3beta,16alpha,23,24-pentahydroxyolean-12-en-28 oic acid], and three known triterpenoid saponins, platycoside F, platycoside B, and platycoside C, were isolated from the roots of Platycodon grandiflorum A. DC. Their chemical structures were elucidated on the basis of their spectral data and chemical evidence.

Cytotoxic constituents from Solanum lyratum.

Activity-guided fractionation of the ethanol extract of the whole plant from Solanum lyratum resulted in the isolation of a new pregnane derivative glycoside, 16-dehydropregnenolone 3-O-alpha-L-rhamnopyranosyl-(1 --> 2)-beta-D-glucopyranosid uronic acid (2), as well as other six known compounds: 16-dehydropregnenolone (1), allopregenolone (3), protocatechuic acid (4), vanillic acid (5), caffeic acid (6), and scopoletin (7). The structures of the isolated compounds were elucidated on the basis of their spectral data and chemical evidences. Compounds 1, 3, 4 were isolated for the first time from this plant. Cytotoxic activities of the isolated compounds were evaluated. Compound 1 exhibited significant cytotoxic activity against A375-S2, HeLa, SGC-7901, and Bel-7402 with IC50 values of 13.1 +/- 0.9, 21.5 +/- 1.0, 40.2 +/- 0.7, and 49.8 +/- 1.2 microg/mL, respectively.

Quantitative analysis of the marker compounds in Salvia miltiorrihiza root and its phytomedicinal preparations.

A HPLC method is described in order to separate and identify 4 phenolic compounds including lithospermic acid B, 3,4-dihydroxyphenyllactic acid (danshensu), rosmarinic acid, and protocatechuic aldehyde as well as 3 lipophilic ones (tanshinone I, tanshinone II(A) and cryptotanshinone) from the roots of Salvia miltiorrihiza or the herbal product containing S. miltiorrihiza available in Chinese or Japanese market. The influence of extractive conditions, such as method, solvents and time, on the 4 phenolic marker components in S. miltiorrihiza is well discussed. In order to investigate the stability of lithospermic acid B, the preparation samples of an injection and a granule were analyzed after being stored at 4 degrees C, 20 degrees C and 40 degrees C for up to six months.