Assessment of Polygonum capitatum Buch.-Ham. ex D.Don by metabolomics based on gas chromatography with mass spectrometry.

Polygonum capitatum is widely used in southwest China. It has considerable therapeutic efficacy for urinary tract infections. P. capitatum contains multiple components and quality assessment can be achieved by means of metabolic fingerprinting. In this paper, a new strategy for P. capitatum quality determination was developed. Eleven batches of P. capitatum were collected from five geographical areas in China including a standard batch regulated by Good Agriculture Practice. Gas chromatography with mass spectrometry was used to generate fingerprints from triplicate extractions to each batch (n = 33). Hierarchical clustering analysis was applied to assess similarities among the ten batches to the standard batches. Orthogonal projection to latent structures discriminate analysis, cross-validated with permutation tests, was performed to investigate discriminating metabolites. Results demonstrated that the overall evaluation hierarchical clustering analysis clustered two batches with distance > 3. Orthogonal projection to latent structures discriminate analysis (R(2) Y (cum) = 0.997, Q(2) (cum) = 0.97, CV-ANOVA = 8.48 × 10(-11) ) indicated that several sugars contributed to batch classification. This method is a rational approach that can classify against a regulated plant standard and distinguishes samples from different origins or processing time in a holistic manner and metabolites driving any differences can be easily identified.

The quest for modernisation of traditional Chinese medicine.

Traditional Chinese medicine (TCM) is an integral part of mainstream medicine in China. Due to its worldwide use, potential impact on healthcare and opportunities for new drug development, TCM is also of great international interest. Recently, a new era for modernisation of TCM was launched with the successful completion of the Good Practice in Traditional Chinese Medicine Research in the Post-genomic Era (GP-TCM) project, the European Union's Seventh Framework Programme (FP7) coordination action on TCM research. This 3.5-year project that involved inputs from over 200 scientists resulted in the production of 20 editorials and in-depth reviews on different aspects of TCM that were published in a special issue of Journal of Ethnopharmacology (2012; volume 140, issue 3). In this narrative review, we aim to summarise the findings of the FP7 GP-TCM project and highlight the relevance of TCM to modern medicine within a historical and international context. Advances in TCM research since the 1950s can be characterised into three phases: Phase I (1950s-1970s) was fundamental for developing TCM higher education, research and hospital networks in China; Phase II (1980s-2000s) was critical for developing legal, economic and scientific foundations and international networks for TCM; and Phase III (2011 onwards) is concentrating on consolidating the scientific basis and clinical practice of TCM through interdisciplinary, interregional and intersectoral collaborations. Taking into account the quality and safety requirements newly imposed by a globalised market, we especially highlight the scientific evidence behind TCM, update the most important milestones and pitfalls, and propose integrity, integration and innovation as key principles for further modernisation of TCM. These principles will serve as foundations for further research and development of TCM, and for its future integration into tomorrow's medicine.

Antifibrotic activities of Scutellariae Radix extracts and flavonoids: Comparative proteomics reveals distinct and shared mechanisms.

BACKGROUND: Scutellariae Radix (SR), the root of Scutellaria baicalensis Georgi, and SR flavonoids have antifibrotic activities. It remains obscure, however, amongst SR aqueous extract (SRA), SR methanolic extract (SRM) and five major SR flavonoids (baicalein, baicalin, wogonoside, wogonin and oroxyloside), which ones are the most promising antifibrotics and what their mechanisms are. PURPOSE: To compare the antifibrotic activities of SR extracts and flavonoids, and the proteomic signatures of selected SR extract and flavonoid, versus IN1130 phosphate, an antifibrotic positive control (abbreviated as IN1130), in TGF-ß1-induced in vitro model of fibrosis in NRK-49F renal fibroblasts. METHODS: Isobaric labelling-based mass spectrometry was used for proteomic studies. Differentially expressed proteins were further analyzed using Gene Ontology annotation enrichment, protein-protein interaction network analysis and pathway analysis. Selected proteins of interest were validated by enzyme-linked immunosorbent assay (ELISA). RESULTS: Baicalein was the SR flavonoid with the best efficacy-toxicity ratio. SRM contained 8-fold more flavonoids and was more potently antifibrotic than SRA. Proteomic analysis of cells treated by TGF-ß1, with or without baicalein (40 and 80 µM), SRM (40 and 80 µg/ml) and IN1130 (1 µM) suggested that baicalein, SRM and IN1130 all repressed TGF-ß1-induced ribosomal proteins in cell lysates, while baicalein and SRM, but not IN1130, regulated the intracellular lysosome pathway; secretomic analysis suggested that 40 and 80 µg/ml SRM and 80 µM baicalein, but not IN1130 and 40 µM baicalein increased ribosomal proteins in conditioned media, whereas only baicalein regulated the lysosome pathway. ELISA verified secretomic findings that baicalein, SRM and IN1130 repressed TGF-ß1-induced PAI-1 (Serpine1), Plod2, Ctgf (Ccn2), Ccl2 and Ccl7; baicalein and IN1130, but not SRM, reversed TGF-ß1-induced Cyr61 (Ccn1) and Tsku; only baicalein reversed TGF-ß1 repression of Mmp3; only IN1130 reversed TGF-ß1-repressed Nov (Ccn3). ELISA validated cell-lysate proteomic findings that baicalein, SRM and IN1130 all reversed TGF-ß1-induced Enpp1; only IN1130 reversed TGF-ß1-induced Impdh2 and Sqstm1 and TGF-ß1-repressed Aldh3a1. Baicalein and SRM induced Ccdc80, while only baicalein induced Tfrc. CONCLUSION: Baicalein, SRM and IN1130 repress TGF-ß1-induced fibrogenesis in renal fibroblasts by regulating overlapping protein targets and biological pathways. Our findings offer a comprehensive view of shared, drug- and dose-specific pharmacological and toxicological mechanisms and provide a valuable resource for further research and development of more efficacious and safer antifibrotics.

In silico search for multi-target anti-inflammatories in Chinese herbs and formulas.

Chinese herbs were screened for compounds which may be active against four targets involved in inflammation, using pharmacophore-assisted docking. Multiple LigandScout (LS) pharmacophores built from ligand-receptor complexes in the protein databank (PDB) were first employed to select compounds. These compounds were then docked using LS-derived templates and ranked according to docking score. The targets comprised cyclo-oxygenases 1 & 2 (COX), p38 MAP kinase (p38), c-Jun terminal-NH(2) kinase (JNK) and type 4 cAMP-specific phosphodiesterase (PDE4). The results revealed that multi-target inhibitors are likely to be relatively common in Chinese herbs. Details of their distribution are given, in addition to experimental evidence supporting these results. Examples of compounds predicted to be active against at least three targets are presented, and their features outlined. The distribution of herbs containing predicted inhibitors was also analysed in relation to 192 Chinese formulas from over 50 herbal categories. Among those found to contain a high proportion of these herbs were formulas traditionally used to treat fever, headache, rheumatoid arthritis, inflammatory bowel disorders, skin disease, cancer, and traumatic injury. Relationships between multi-target drug discovery and Chinese medicine are discussed.

Proteomic landscape of TGF-ß1-induced fibrogenesis in renal fibroblasts.

Transforming growth factor-ß1 (TGF-ß1) plays a premier role in fibrosis. To understand the molecular events underpinning TGF-ß1-induced fibrogenesis, we examined the proteomic profiling of a TGF-ß1-induced in vitro model of fibrosis in NRK-49F normal rat kidney fibroblasts. Mass spectrometric analysis indicated that 628 cell-lysate proteins enriched in 44 cellular component clusters, 24 biological processes and 27 molecular functions were regulated by TGF-ß1. Cell-lysate proteins regulated by TGF-ß1 were characterised by increased ribosomal proteins and dysregulated proteins involved in multiple metabolic pathways, including reduced Aldh3a1 and induced Enpp1 and Impdh2, which were validated by enzyme-linked immunosorbent assays (ELISA). In conditioned media, 62 proteins enriched in 20 cellular component clusters, 40 biological processes and 7 molecular functions were regulated by TGF-ß1. Secretomic analysis and ELISA uncovered dysregulated collagen degradation regulators (induced PAI-1 and reduced Mmp3), collagen crosslinker (induced Plod2), signalling molecules (induced Ccn1, Ccn2 and Tsku, and reduced Ccn3) and chemokines (induced Ccl2 and Ccl7) in the TGF-ß1 group. We conclude that TGF-ß1-induced fibrogenesis in renal fibroblasts is an intracellular metabolic disorder and is inherently coupled with inflammation mediated by chemokines. Proteomic profiling established in this project may guide development of novel anti-fibrotic therapies in a network pharmacology approach.

In vitro anti-fibrotic activities of herbal compounds and herbs.

BACKGROUND: We recently developed high-throughput assays of inflammation-independent anti-fibrotic activities based on TGF-beta1-induced total collagen accumulation and nodule formation in normal rat kidney fibroblasts. METHODS: These assays were applied to examine the anti-fibrotic activities of 21 compounds isolated from plants used in Chinese medicine and methanol extracts of 12 Chinese herbs. Lactate dehydrogenase release assay and cell detachment index were used to monitor cytotoxicity. Changes in fibrogenic molecular markers were observed by reverse transcriptase quantitative polymerase chain reaction and high-content imaging analysis of immunofluorescence. RESULTS: Three flavonoids (quercetin, baicalein and baicalin) and two non-flavonoids (salvianolic acid B and emodin) demonstrated anti-fibrotic activities in both total collagen accumulation and nodule formation assays. The remaining 16 compounds had little anti-fibrotic effect or were cytotoxic. The anti-fibrotic compounds suppressed collagen I expression at both mRNA and protein levels and also variably suppressed alpha-smooth muscle actin expression and bromodeoxyuridine incorporation. Methanol extracts of Scutellaria baicalensis Georgi, Salvia miltiorrhiza Bunge and Rheum palmatum L., which are rich sources of baicalein, baicalin, salvianolic acid B and emodin, respectively, also showed in vitro anti-fibrotic activities. CONCLUSIONS: Five herbal compounds and three herbal extracts have in vitro anti-fibrotic activities. These data warrant further studies on these anti-fibrotic entities and suggest it a promising strategy to discover new anti-fibrotic drugs by screening more plant materials.

Cytotoxic effects of compounds from Iris tectorum on human cancer cell lines.

In the course of searching for novel cytotoxic compounds which can be used in chemotherapy, several Traditional Chinese Medicines (TCM) have been screened by bioassay-guided fractionation and isolation. An extract of rhizomes of Iris tectorum Maxim., a TCM used to treat cancer, exhibited highest potency and led to the isolation of two flavonoids, 7-O-methylaromadendrin and tectorigenin, and four iridal-type triterpenes, iritectols A and B, isoiridogermanal and iridobelamal A. The cytotoxicities of the isolated compounds against four human cancer cell lines were evaluated by the SRB assay. Iritectol B, isoiridogermanal and iridobelamal A showed similar cytotoxicity with IG(50) around 11 microM and 23 microM against MCF-7 and C32 cell lines, respectively. Cell cycle-specific inhibition and apoptosis induced by the isolated compounds were determined using flow cytometry with two sets of co-labelling systems: annexin V-FITC/propidium iodide and fluorescein diacetate/propidium iodide. Iritectol B demonstrated dose-dependent apoptotic effect against COR-L23 cells with an apoptotic rate of 33% at 100 microM. Tectorigenin (an analogue of genistein) showed cell cycle specific inhibition and arrested cells at G(2)/M phase up to 400 microM, but did not demonstrate apoptotic effect against COR-L23 cells up to 1 mM. The overall activities of isolated compounds observed in the present study support the traditional use of Iris tectorum Maxim. in the treatment of cancer.

Metabolomics reveals immunomodulation as a possible mechanism for the antibiotic effect of Persicaria capitata (Buch.-Ham. ex D. Don) H.Gross.

INTRODUCTION: In spite of advances in antibiotics, urinary tract infection (UTI) is still among the most common reasons for antibiotic medication worldwide. Persicaria capitata (Buch.-Ham. ex D. Don) H.Gross (P. capitata) is a herbal medicine used by the Miao people in China to treat UTI. However studies of its mechanism are challenging, owing to the complexity of P. capitata with multiple constituents acting on multiple metabolic pathways. OBJECTIVE: The objective of this study was to explore the working mechanism of P. capitata on urinary tract infection. METHODS: Relinqing® granule, which is solely made from aqueous extracts of the whole P. capitata plant, was used in this study. Urine metabolomics based on gas chromatography-mass spectroscopy was employed to assess the metabolic changes caused by administration of Relinqing® granule in a UTI mouse model. Female specific-pathogen-free Kunming mice were divided into control group (mock infection, saline treatment), model group (E.coli infection, saline treatment), Relinqing® group (E.coli infection, Relinqing® granule treatment), ciprofloxacin group (E.coli infection, ciprofloxacin treatment), and sham-Relinqing® group (no surgery, Relinqing® granule treatment). RESULTS: The results showed that after the treatments, urine levels of itaconic acid in Relinqing® group increased by 4.9 fold and 11.3 fold compared with model and ciprofloxacin groups respectively. Itaconic acid is an endogenous antibacterial metabolite produced by macrophages, which also functions as a checkpoint for metabolic reprogramming of macrophage. CONCLUSION: Our findings suggest that this herbal medicine can cure urinary tract infection through modulation of immune system.

Antibacterial and antioxidant cassane diterpenoids from Caesalpinia benthamiana.

Bioactivity-guided fractionation of the light petroleum extract of Caesalpinia benthamiana (=Mezoneuron benthamianum) root bark has led to the isolation of two cassane diterpenoids, designated as benthaminin 1 and 2. A third compound, a deoxy form of caesaldekarin C (also referred to as methyl vouacapenate) which has previously been isolated from Caesalpinia major, C. bonducella, Vouacapoua americana and V. macropetala, was also isolated, together with beta-sitosterol and stigmastenone. The antibacterial and antioxidant activities of these cassane diterpenoids have been assessed using the microdilution assay method and DPPH spectrophotometric and TBA lipid peroxidation assays. Benthaminin 1 was the more active antibacterial compound with MIC values of 47.8 microM for both Staphylococcus aureus and Micrococcus flavus. Benthaminin 2 was the more active antioxidant compound and showed IC50 values of 42.7 microM and 74.2 microM for the DPPH and TBA assays, respectively. Deoxycaesaldekarin C possessed both antibacterial and antioxidant activities. The presence of methyl ester and methyl functional groups as well as an unsaturated furan ring appears to confer antibacterial activity. On the other hand, the relatively stronger antioxidant activity of benthaminin 2 may be associated with the presence of an exocyclic methylene function.

Isolation and structure determination of triterpenes from Iris tectorum.

Four iridal-type triterpenoids, two of which were new compounds, have been isolated from rhizomes of Iris tectorum Maxim. Their structures were determined by 1D and 2D NMR spectroscopy and ESI-MS spectrometry. The compounds were identified as the iritectols A and B, and the known iridobelamal A and isoiridogermanal. The presence of epoxide and tetrahydrofuran functions are not common in previously isolated iridal-type triterpenoids.

Comparison of rosmarinic acid content in commercial tinctures produced from fresh and dried lemon balm (Melissa officinalis).

PURPOSE: To measure the rosmarinic acid content of eight commercial tinctures derived from fresh (n= 5) and dried (n=3) Melissa officinalis herb. METHODS: Rosmarinic acid and the internal standard (esculin) were purchased from Aldrich Chemical Co. The column used was a Luna C18, 5 um (150 x 4.6 mm I.D., Phenomenex) maintained at ambient room temperature. The HPLC system consisted of a Shimadzu SCL-6B controller, Shimadzu LC-6A pumps, Shimadzu SPD-6A UV single wavelength spectrophotometric detector set to 320 nm and Shimadzu SIL-6B autosampler. Gradient elution of the samples and standard were performed using ammonium formate (0.02 M; pH 6.25 at 27 oC; eluent A) and methanol (eluent B). The gradient elution initial conditions were 2% of eluent B with linear gradient to 60% at 30 min, followed by linear gradient to 90% of eluent B at 31 min, this proportion being maintained for 4 min. The column was then returned to the initial condition at 36 min and maintained until the end of the run at 43 min. The flow rate was 1 mL/min. The assay was validated for sensitivity, accuracy and reproducibility. RESULTS: The content of rosmarinic acid in commercial tinctures was significantly higher in the tinctures made from dried plant material (2.96 - 22.18 mg/mL) compared to fresh plant tinctures (

Metabolic phenotyping in the mouse model of urinary tract infection shows that 3-hydroxybutyrate in plasma is associated with infection.

Urinary tract infection is one of the most common bacterial infections worldwide. Current diagnosis of urinary tract infection chiefly relies on its clinical presentation, urine dipstick tests and urine culture. Small molecules found in bio-fluids related with both infection and recovery would facilitate diagnosis and management of UTI. Mass spectrometry-based fingerprinting of plasma and urine at 3 time points, pre-infection (t = -24h), infection (t = 24h) and post 3-day treatment (t = 112h), were acquired in the following four groups: mice which were healthy, infected but not treated, infected and treated with ciprofloxacin, and infected and treated with Relinqing® granules (n = 6 per group). A metabolomics workflow including multivariate analysis and ROC regression was employed to select metabolic features that correlated with UTI and its treatment. Circa 4,000 molecular features were acquired for each sample. The small acid 3-hydroxybutyrate in plasma was found to be differentiated for urinary tract infection, with an area under the curve = 0.97 (95% confidence interval: 0.93-1.00, accuracy = 0.91, sensitivity = 0.92 and specificity = 0.91). The level of 3-hydroxybutyrate in plasma was depleted after infection with a fold change of -22 (q < 0.0001). Correlation between plasma 3-hydroxybutyrate and urine bacterial number in all groups and time points was r = -0.753 (p < 0.0001). The findings show that 3-hydroxybutyrate is depleted in blood and strongly associated with UTI at both infection and post-treatment stage in a UTI mouse model. Further work is envisaged to assess the clinical potential of blood tests to assist with UTI management.

A metabonomic strategy for the detection of the metabolic effects of chamomile (Matricaria recutita L.) ingestion.

A metabonomic strategy, utilizing high-resolution 1H NMR spectroscopy in conjunction with chemometric methods (discriminant analysis with orthogonal signal correction), has been applied to the study of human biological responses to chamomile tea ingestion. Daily urine samples were collected from volunteers during a 6-week period incorporating a 2-week baseline period, 2 weeks of daily chamomile tea ingestion, and a 2-week post-treatment phase. Although strong intersubject variation in metabolite profiles was observed, clear differentiation between the samples obtained before and after chamomile ingestion was achieved on the basis of increased urinary excretion of hippurate and glycine with depleted creatinine concentration. Samples obtained up to 2 weeks after daily chamomile intake formed an isolated cluster in the discriminant analysis map, from which it was inferred that the metabolic effects of chamomile ingestion were prolonged during the 2-week postdosing period. This study highlights the potential for metabonomic technology in the assessment of nutritional interventions, despite the high degree of variation from genetic and environmental sources.

Metabolomic quality control of commercial Asian ginseng, and cultivated and wild American ginseng using (1)H NMR and multi-step PCA.

Ginseng, mainly Asian ginseng and American ginseng, is the most widely consumed herbal product in the world . However, the existing quality control method is not adequate: adulteration is often seen in the market. In this study, 31 batches of ginseng from Chinese stores were analyzed using (1)H NMR metabolite profiles together with multi-step principal component analysis. The most abundant metabolites, sugars, were excluded from the NMR spectra after the first principal component analysis, in order to reveal differences contributed by less abundant metabolites. For the first time, robust, distinctive and representative differences of Asian ginseng from American ginseng were found and the key metabolites responsible were identified as sucrose, glucose, arginine, choline, and 2-oxoglutarate and malate. Differences between wild and cultivated ginseng were identified as ginsenosides. A substitute cultivated American ginseng was noticed. These results demonstrated that the combination of (1)H NMR and PCA is effective in quality control of ginseng.

Prediction of anti-plasmodial activity of Artemisia annua extracts: application of 1H NMR spectroscopy and chemometrics.

We describe the application of 1H NMR spectroscopy and chemometrics to the analysis of extracts of Artemisia annua. This approach allowed the discrimination of samples from different sources, and to classify them according to anti-plasmodial activity without prior knowledge of this activity. The use of partial least squares analysis allowed the prediction of actual values for anti-plasmodial activities for independent samples not used in producing the models. The models were constructed using approximately 70% of the samples, with 30% used as a validation set for which predictions were made. Models generally explained >90% of the variance, R(2) in the model, and had a predictive ability, Q(2) of >0.8. This approach was also able to correlate 1H NMR spectra with cytotoxicity (R2=0.9, Q2=0.8). This work demonstrates the potential of NMR spectroscopy and chemometrics for the development of predictive models of anti-plasmodial activity.

Omic techniques in systems biology approaches to traditional Chinese medicine research: present and future.

Omic techniques have become key tools in the development of systems biology. As the holistic approaches underlying the practice of traditional Chinese medicine (TCM) and new tendencies in Western medicine towards personalised medicine require in-depth knowledge of mechanisms of action and active compounds, the use of omic techniques is crucial for understanding and interpretation of TCM development, especially in view of its expansion in Western countries. In this short review, omic applications in TCM research are reviewed which has allowed some speculation regarding future perspectives for these approaches in TCM modernisation and standardisation. Guidelines for good practice for the application of omics in TCM research are also proposed.

Traditional Chinese medicine research in the post-genomic era: good practice, priorities, challenges and opportunities.

BACKGROUND AND AIMS: GP-TCM is the 1st EU-funded Coordination Action consortium dedicated to traditional Chinese medicine (TCM) research. This paper aims to summarise the objectives, structure and activities of the consortium and introduces the position of the consortium regarding good practice, priorities, challenges and opportunities in TCM research. Serving as the introductory paper for the GP-TCM Journal of Ethnopharmacology special issue, this paper describes the roadmap of this special issue and reports how the main outputs of the ten GP-TCM work packages are integrated, and have led to consortium-wide conclusions. MATERIALS AND METHODS: Literature studies, opinion polls and discussions among consortium members and stakeholders. RESULTS: By January 2012, through 3 years of team building, the GP-TCM consortium had grown into a large collaborative network involving ∼200 scientists from 24 countries and 107 institutions. Consortium members had worked closely to address good practice issues related to various aspects of Chinese herbal medicine (CHM) and acupuncture research, the focus of this Journal of Ethnopharmacology special issue, leading to state-of-the-art reports, guidelines and consensus on the application of omics technologies in TCM research. In addition, through an online survey open to GP-TCM members and non-members, we polled opinions on grand priorities, challenges and opportunities in TCM research. Based on the poll, although consortium members and non-members had diverse opinions on the major challenges in the field, both groups agreed that high-quality efficacy/effectiveness and mechanistic studies are grand priorities and that the TCM legacy in general and its management of chronic diseases in particular represent grand opportunities. Consortium members cast their votes of confidence in omics and systems biology approaches to TCM research and believed that quality and pharmacovigilance of TCM products are not only grand priorities, but also grand challenges. Non-members, however, gave priority to integrative medicine, concerned on the impact of regulation of TCM practitioners and emphasised intersectoral collaborations in funding TCM research, especially clinical trials. CONCLUSIONS: The GP-TCM consortium made great efforts to address some fundamental issues in TCM research, including developing guidelines, as well as identifying priorities, challenges and opportunities. These consortium guidelines and consensus will need dissemination, validation and further development through continued interregional, interdisciplinary and intersectoral collaborations. To promote this, a new consortium, known as the GP-TCM Research Association, is being established to succeed the 3-year fixed term FP7 GP-TCM consortium and will be officially launched at the Final GP-TCM Congress in Leiden, the Netherlands, in April 2012.

Secondary metabolite mapping identifies Scutellaria inhibitors of human lung cancer cells.

Scutellaria baicalensis root is widely used in China as an adjuvant to orthodox chemotherapy of lung cancer. However, functional biomarkers of this plant for anti-lung cancer activity have not yet been reported. We therefore determined the growth inhibition activity by MTT assay of eight solvent extracts of S. baicalensis in the human lung cancer cell line SK-MES-1. This activity was then mapped onto the secondary metabolite profile of crude extracts by principal components analysis (PCA) of proton NMR and HPLC-UV data. NMR- and HPLC-PCA maps revealed highest inhibitory activity for the non-aqueous extracts. The first two components of both maps discriminated extract activity mainly based on the differential content of three compounds, which were then tested individually. The IC(50) values for baicalin (IC(50): 64+/-5 microM), baicalein (IC(50): 80+/-6 microM) and wogonin (IC(50): 39+/-10 microM) were comparable to that of the antineoplastic cisplatin (IC(50): 79+/-16 microM). A partial least squares regression (PLS)-NMR model highly correlated with the corresponding PLS-HPLC model for prediction of inhibition. Secondary metabolite mapping of lung cancer growth inhibitors in crude extracts may be an important first step to qualify Chinese herbal prescriptions required for meaningful clinical trials of such integrated therapies.

Phytochemical databases of Chinese herbal constituents and bioactive plant compounds with known target specificities.

Two databases have been constructed to facilitate applications of cheminformatics and molecular modeling to medicinal plants. The first contains data on known chemical constituents of 240 commonly used Chinese herbs, the other contains information on target specificities of bioactive plant compounds. Structures are available for all compounds. In the case of the Chinese herbal constituents database, further details include trivial and systematic names, compound class and skeletal type, botanical and Chinese (pinyin) names of associated herb(s), CAS registry number, chirality, pharmacological and toxicological information, and chemical references. For the bioactive plant compounds database, details of molecular target(s), IC50 and related measures, and associated botanical species are given. For Chinese herbs, approximately 7000 unique compounds are listed, though some are found in more than one herb, the total number for all herbs being 8264. For bioactive plant compounds, 2597 compounds active against 78 molecular targets are covered. Statistical relationships within and between the two databases are explored.

Virtual screening of Chinese herbs with Random Forest.

Random Forest, a form of multiple decision trees, has been used to screen a database of Chinese herbal constituents for potential inhibitors against several therapeutically important molecular targets. These comprise cyclic adenosine 3'-5'-monophosphate phosphodiesterases, protein kinase A, cyclooxygenases, lipoxygenases, aldose reductase, and three HIV targets-integrase, protease, and reverse transcriptase. In addition, compounds were identified which may inhibit the expression of inducible nitric oxide synthase and/or nitric oxide production in vivo. A total of 240 Chinese herbs containing 8264 compounds were screened in silico, including many used on a regular basis in traditional Chinese medicine. Active compounds were selected from another database of 2597 phytochemicals and related natural products with known target affinities and covered a wide range of structural classes. Random Forest was found to perform well, even on highly unbalanced data characteristic of ligand-based screening where the compounds to be screened are far more numerous than the number of active compounds used in training. Despite a conservative screening protocol, a wide variety of compounds from Chinese herbs were hit. Of particular interest were the relatively large number of herbs predicted to inhibit multiple targets, as well as a number which appeared to contain inhibitors of the same target from different phytochemical classes. The latter point to the possibility that individual species may make use of alternative phytochemical strategies in target inhibition. A literature search provided evidence to support 83 herb-target predictions.