[Prediction of quality markers and medicinal value of sea buckthorn leaves based on network pharmacology, content determination, and activity evaluation].

The leaves of sea buckthorn(Hippophae rhamnoides), considered as common food raw materials, have records of medicinal use and diverse pharmacological activities, showing a potential medicinal value. However, the active substances in the sea buckthorn leaves and their mechanisms of action remain unclear. In addition, due to the extensive source and large variety variations, the quality evaluation criteria of sea buckthorn leaves remain to be developed. To solve the problems, this study predicted the main active components, core targets, key pathways, and potential pharmacological effects of sea buckthorn leaves by network pharmacology and molecular docking. Furthermore, ultra-performance liquid chromatography with diode-array detection(UPLC-DAD) was employed to determine the content of active components and establish the chemical fingerprint, on the basis of which the quality markers of sea buckthorn leaves were predicted and then verified by the enzyme activity inhibition method. The results indicated that sea buckthorn leaves had potential therapeutic effects on a variety of digestive tract diseases, metabolic diseases, tumors, and autoimmune diseases, which were consistent with the ancient records and the results of modern pharmacological studies. The core targets of sea buckthorn leaves included PTPN11, AKT1, PIK3R1, ESR1, and SRC, which were mainly involved in the PI3K-AKT, MAPK, and HIF-1 signaling pathways. In conclusion, the active components of sea buckthorn leaves are associated with the rich flavonoids and tannins, among which quercitrin, narcissoside, and ellagic acid can be used as the quality markers of sea buckthorn leaves. The findings provide a reference for the quality control and further development and utilization of sea buckthorn leaves as medicinal materials.

Mining Therapeutic Efficacy from Treasure Chest of Biodiversity and Chemodiversity: Pharmacophylogeny of Ranunculales Medicinal Plants.

Ranunculales, comprising of 7 families that are rich in medicinal species frequently utilized by traditional medicine and ethnomedicine, represents a treasure chest of biodiversity and chemodiversity. The phylogenetically related species often have similar chemical profile, which makes them often possess similar therapeutic spectrum. This has been validated by both ethnomedicinal experiences and pharmacological investigations. This paper summarizes molecular phylogeny, chemical constituents, and therapeutic applications of Ranunculales, i.e., a pharmacophylogeny study of this representative medicinal order. The phytochemistry/metabolome, ethnomedicine and bioactivity/pharmacology data are incorporated within the phylogenetic framework of Ranunculales. The most studied compounds of this order include benzylisoquinoline alkaloid, flavonoid, terpenoid, saponin and lignan, etc. Bisbenzylisoquinoline alkaloids are especially abundant in Berberidaceae and Menispermaceae. The most frequent ethnomedicinal uses are arthritis, heat-clearing and detoxification, carbuncle-abscess and sore-toxin. The most studied bioactivities are anticancer/cytotoxic, antimicrobial, and anti-inflammatory activities, etc. The pharmacophylogeny analysis, integrated with both traditional and modern medicinal uses, agrees with the molecular phylogeny based on chloroplast and nuclear DNA sequences, in which Ranunculales is divided into Ranunculaceae, Berberidaceae, Menispermaceae, Lardizabalaceae, Circaeasteraceae, Papaveraceae, and Eupteleaceae families. Chemical constituents and therapeutic efficacy of each taxonomic group are reviewed and the underlying connection between phylogeny, chemodiversity and clinical uses is revealed, which facilitate the conservation and sustainable utilization of Ranunculales pharmaceutical resources, as well as developing novel plant-based pharmacotherapy.

[Research progress in DIR gene of lignan biosynthesis in medicinal plants].

The active components, mainly derived from secondary metabolites of medicinal plants, are the material basis for the efficacy of medicinal plants. Lignans, the secondary metabolites in plants with high bioactivity, are widely distributed in a variety of plant species, and their antiviral, antitumor, antibacterial, and antioxidant activities have been proved in clinical practice. Generally, lignans are diverse in structures with many chiral centers, and most of them are optically active. The biosynthesis of lignans depends on the oxidative coupling reaction through site selection and stereo selection, which impedes synthesized lignans to form racemates, but makes them in a three-dimensional configuration. Dirigent protein(DIR) plays an important role in guiding location selection and stereo selection of lignans in biosynthesis. In vitro studies on lignan biosynthesis have shown that racemic end products are obtained in the absence of DIR proteins, while the products in a three-dimensional configuration can be yielded in the presence of DIR proteins, indicating that DIR proteins play an asymmetric role in the biosynthesis of plant secondary metabolites. The present study reviewed the biolo-gical significance of DIR protein, the cloning of DIR gene, gene structure, catalytic mechanism, and the research progress in Isatis indigotica, Eucommia ulmoides, Forsythia suspensa, Salvia miltiorrhiza, Panax pseudoginseng var. notoginseng, and Schisandra chinensis, which provides a reference for the follow-up research of DIR gene.

[Material basis and mechanism of Huangqin Tea in prevention of colorectal cancer based on network pharmacology and molecular docking].

Colorectal cancer is a malignancy with high mortality. Huangqin Tea(HQT) can exert potential preventive and therapeutic effects on colorectal cancer. Flavonoids are the main compounds in HQT, but the pharmacodynamic material basis and mechanism are unclear. Network pharmacology and molecular docking were used to predict and analyze the targets and signaling pathways of HQT in the prevention and treatment of colorectal cancer. The active components of flavonoids in HQT were searched and screened out by literature review and FAFDrugs4. The related targets of active components were predicted by SwissTargetPrediction, STITCH, and TCMSP. Colorectal cancer-related genes were collected from OMIM, TTD, and GeneCards. The common targets were obtained as the potential targets of HQT in the prevention and treatment of colorectal cancer. Metascape was used for GO function enrichment and KEGG pathway enrichment analyses. Cytoscape was used to construct the protein-protein interaction(PPI) network and "component-target-disease-pathway" network to obtained and analyze core targets and key components. AutoDock Vina was used for molecular docking verification of key components and core targets. The results showed that apigenin, luteolin, wogonin, and baicalein were presumedly the key active components in the prevention and treatment of colorectal cancer, and core targets included TP53, AKT1, VEGFA, PIK3 CA, and SRC. The key KEGG signaling pathways mainly involved PI3 K-AKT, AGE-RAGE, p53, NF-κB, Wnt, Hippo, and calcium signaling pathways. Further molecular docking results showed that four key components showed strong hydrogen bonding ability with the five core targets. This study preliminarily reveals the pharmacodynamic material basis and potential mechanism of HQT in the prevention and treatment of colorectal cancer and provides a theoretical and scientific basis for the application of HQT.

[Withania somnifera: a kind of food-medicine plant popular in world in recent years].

Withania somnifera, also known as Indian ginseng, is an important traditional medicine in the Ayurvedic medical system of India, which has a significant effect of adaptation. Modern studies have shown that the main chemical components of W. somnifera are withanolides, which have antioxidant, anti-tumor, enhancing immunity, cardiovascular protection, neuroprotection, anti-stress, anti-stress reaction and hypoglycemic activities. Studies on human, animal, mutagenesis, genotoxicity, reproductive toxicity and drug interaction showed that W. somnifera had good safety. Clinical trials have proved that W. somnifera is effective in treating a variety of human diseases. As a famous traditional medicine and modern dietary supplement, it has a high reputation and market in the international health product market, but in China, there is little scientific research, market development, product introduction and application. In this paper, the traditional application, chemical composition, pharmacological activity, safety evaluation and clinical study of the plant were introduced, so as to increase the understanding of the dual use of the plant, and to provide reference for the future introduction of the product, the service to the health of the Chinese people and the promotion of the "double cycle" of the trade of health products between China and the international community.

Ethnopharmacology, chemodiversity, and bioactivity of Cephalotaxus medicinal plants.

Cephalotaxus is the only genus of Cephalotaxaceae family, and its natural resources are declining due to habitat fragmentation, excessive exploitation and destruction. In many areas of China, folk herbal doctors traditionally use Cephalotaxus plants to treat innominate swollen poison, many of which are cancer. Not only among Han people, but also among minority ethnic groups, Cephalotaxus is used to treat various diseases, e.g., cough, internal bleeding and cancer in Miao medicine, bruises, rheumatism and pain in Yao medicine, and ascariasis, hookworm disease, scrofula in She medicine, etc. Medicinal values of some Cephalotaxus species and compounds are acknowledged officially. However, there is a lack of comprehensive review summarizing the ethnomedicinal knowledge of Cephalotaxus, relevant medicinal phytometabolites and their bioactivities. The research progresses in ethnopharmacology, chemodiversity, and bioactivities of Cephalotaxus medicinal plants are reviewed and commented here. Knowledge gaps are pinpointed and future research directions are suggested. Classic medicinal books, folk medicine books, herbal manuals and ethnomedicinal publications were reviewed for the genus Cephalotaxus (Sanjianshan in Chinese). The relevant data about ethnobotany, phytochemistry, and pharmacology were collected as comprehensively as possible from online databases including Scopus, NCBI PubMed, Bing Scholar, and China National Knowledge Infrastructure (CNKI). "Cephalotaxus", and the respective species name were used as keywords in database search. The obtained articles of the past six decades were collated and analyzed. Four Cephalotaxus species are listed in the official medicinal book in China. They are used as ethnomedicines by many ethnic groups such as Miao, Yao, Dong, She and Han. Inspirations are obtained from traditional applications, and Cephalotaxus phytometabolites are developed into anticancer reagents. Cephalotaxine-type alkaloids, homoerythrina-type alkaloids and homoharringtonine (HHT) are abundant in Cephalotaxus, e.g., C. lanceolata, C. fortunei var. alpina, C. griffithii, and C. hainanensis, etc. New methods of alkaloid analysis and purification are continuously developed and applied. Diterpenoids, sesquiterpenoids, flavonoids, lignans, phenolics, and other components are also identified and isolated in various Cephalotaxus species. Alkaloids such as HHT, terpenoids and other compounds have anticancer activities against multiple types of human cancer. Cephalotaxus extracts and compounds showed anti-inflammatory and antioxidant activities, immunomodulatory activity, antimicrobial activity and nematotoxicity, antihyperglycemic effect, and bone effect, etc. Drug metabolism and pharmacokinetic studies of Cephalotaxus are increasing. We should continue to collect and sort out folk medicinal knowledge of Cephalotaxus and associated organisms, so as to obtain new enlightenment to translate traditional tips into great therapeutic drugs. Transcriptomics, genomics, metabolomics and proteomics studies can contribute massive information for bioactivity and phytochemistry of Cephalotaxus medicinal plants. We should continue to strengthen the application of state-of-the-art technologies in more Cephalotaxus species and for more useful compounds and pharmacological activities.

[Application and modern research progress of sea buckthorn leaves].

Sea buckthorn(Hippophae rhamnoides) is widely distributed, with abundant resources, a long history of application, and rich nutrition and high medicinal value. Therefore, it has attracted extensive attention from researchers at home and abroad. The focus of attention is mainly on sea buckthorn fruit, but with weak research and development of sea buckthorn leaves. In order to develop and utilize abundant resources of sea buckthorn leaves, this paper systematically reviewed domestic and foreign literatures and summarized the current application, harvesting and processing, chemical constituents and pharmacological activities of sea buckthorn leaves. Sea buckthorn leaves have a wide development and utilization value in food raw materials(like a substituting-for-tea plant), pharmaceutical raw materials and animal feed. Modern studies have shown that the leaves of sea buckthorn are rich in polysaccharides, flavonoids, polyphenols, triterpenes and steroids, as well as vitamins(especially vitamin C), proteins, amino acids and mineral elements. It has various pharmacological effects, such as anti-obesity, hypoglycemia, anti-oxidation, antibacterial, anti-inflammatory and anti-cardiovascular diseases. Domestic and foreign studies have showed that sea buckthorn leaves have important development and utilization prospects, and are worth further study and development.

The Utility of Electrochemical Systems in Microbial Degradation of Polycyclic Aromatic Hydrocarbons: Discourse, Diversity and Design.

Polycyclic aromatic hydrocarbons (PAHs), especially high molecular weight PAHs, are carcinogenic and mutagenic organic compounds that are difficult to degrade. Microbial remediation is a popular method for the PAH removal in diverse environments and yet it is limited by the lack of electron acceptors. An emerging solution is to use the microbial electrochemical system, in which the solid anode is used as an inexhaustible electron acceptor and the microbial activity is stimulated by biocurrent in situ to ensure the PAH removal and avoid the defects of bioremediation. Based on the extensive investigation of recent literatures, this paper summarizes and comments on the research progress of PAH removal by the microbial electrochemical system of diversified design, enhanced measures and functional microorganisms. First, the bioelectrochemical degradation of PAHs is reviewed in separate and mixed PAH degradation, and the removal performance of PAHs in different system configurations is compared with the anode modification, the enhancement of substrate and electron transfer, the addition of chemical reagents, and the combination with phytoremediation. Second, the key functional microbiota including PAH degrading microbes and exoelectrogens are overviewed as well as the reduced microbes without competitive advantage. Finally, the typical representations of electrochemical activity especially the internal resistance, power density and current density of systems and influence factors are reviewed with the correlation analysis between PAH removal and energy generation. Presently, most studies focused on the anode modification in the bioelectrochemical degradation of PAHs and actually more attentions need to be paid to enhance the mass transfer and thus larger remediation radius, and other smart designs are also proposed, especially that the combined use of phytoremediation could be an eco-friendly and sustainable approach. Additionally, exoelectrogens and PAH degraders are partially overlapping, but the exact functional mechanisms of interaction network are still elusive, which could be revealed with the aid of advanced bioinformatics technology. In order to optimize the efficacy of functional community, more advanced techniques such as omics technology, photoelectrocatalysis and nanotechnology should be considered in the future research to improve the energy generation and PAH biodegradation rate simultaneously.

[Simultaneous rapid detection of ten stilbenes in serum of mice by UPLC-MS/MS].

Stilbenes is a class of natural polyphenols with 1,2-diphenylethylene as the skeleton structure which have structural and active diversity. However, there are fewer studies on their metabolic process, which limits the in-depth research and development of such components. An UPLC-MS/MS method simultaneously determining contents of ten stilbenes was firstly established in this study and applied to study the ten stilbenes of peony seed coats in the serum of C57 mice.Piceatannol was the internal standard, and methanol was used for protein precipitation, UPLC-MS/MS with negative ion mode was used for analysis, and the method was validated.The serum samples were collected and detected after mice being oral administered with 800 mg·kg~(-1) peony seed coat extracts for 8 weeks. The results showed that suffruticosol A, suffruticosol B, suffruticosol C, trans-ε-viniferin, cis-gnetin H, trans-suffruticosol D and trans-gnetin H were detected in serum samples, and the highest is suffruticosol A. The method is simple and quick with high specificity and sensitivity, and it is suitable for quantitative determination of ten stilbenes in the serum of mice.

Anticancer Drug Targets of Salvia Phytometabolites: Chemistry, Biology and Omics.

BACKGROUND: Salvia displays diverse anticancer properties, which are attributable to their diterpene and phenolic contents. There is no comprehensive review on the anticancer diversity and molecular targets of Salvia components. OBJECTIVE: We investigate the diversity and molecular targets of Salvia phytometabolites responsible for the prevention and treatment of cancer and sarcoma. RESULTS AND CONCLUSION: Traditional therapeutic knowledge suggests that Salvia species can be used to develop anticancer drugs. Lots of concerns have been raised for tanshinone (Tan) IIA and cryptotanshinone. Some Salvia compounds disturb cell cycle and induce apoptosis of tumor cells or enhance immune activities, while others inhibit the proliferation, invasion, angiogenesis, and metastasis, or reverse the multi-drug resistance of cancer cells. Salvia phytometabolites regulate most cancer hallmarks defined by Hanahan and Weinberg. The same class of phytometabolite could exert the anticancer activity via multiple pathways. ADME/T properties and pharmacokinetic bebaviors of some phytometabolites have been revealed. Fluorescent probes are powerful tools for screening substrates, inhibitors or inducers of drug metabolizing enzymes/transporters from Salvia phytometabolites. Omics platform will greatly help mining more potentially useful phytometabolites from Salvia plants. More Salvia plants have application potential in pharmaceutical industry and clinical cancer therapy.

Anticancer Chemodiversity of Ranunculaceae Medicinal Plants: Molecular Mechanisms and Functions.

The buttercup family, Ranunculaceae, comprising more than 2,200 species in at least 62 genera, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine since the beginning of human civilization. Various medicinal phytometabolites have been found in Ranunculaceae plants, many of which, such as alkaloids, terpenoids, saponins, and polysaccharides, have shown anti-cancer activities in vitro and in vivo. Most concerns have been raised for two epiphany molecules, the monoterpene thymoquinone and the isoquinoline alkaloid berberine. At least 17 genera have been enriched with anti-cancer phytometabolites. Some Ranunculaceae phytometabolites induce the cell cycle arrest and apoptosis of cancer cells or enhance immune activities, while others inhibit the proliferation, invasion, angiogenesis, and metastasis, or reverse the multi-drug resistance of cancer cells thereby regulating all known hallmarks of cancer. These phytometabolites could exert their anti-cancer activities via multiple signaling pathways. In addition, absorption, distribution, metabolism, and excretion/toxicity properties and structure/activity relationships of some phytometabolites have been revealed assisting in the early drug discovery and development pipelines. However, a comprehensive review of the molecular mechanisms and functions of Ranunculaceae anti-cancer phytometabolites is lacking. Here, we summarize the recent progress of the anti-cancer chemo- and pharmacological diversity of Ranunculaceae medicinal plants, focusing on the emerging molecular machineries and functions of anti-cancer phytometabolites. Gene expression profiling and relevant omics platforms (e.g. genomics, transcriptomics, proteomics, and metabolomics) could reveal differential effects of phytometabolites on the phenotypically heterogeneous cancer cells.

[Determination of ten stilbenes and their antioxidant activity of peony seed coat, seed kernel and seed coat extracts].

The seed of tree peony and herbaceous peony contained a variety of stilbenes which possess many pharmacological activities, such as antitumor, anti-inflammatory, allergy and neuraminidase inhibition. In order to develop and use peony seed resources, a simple and sensitive HPLC-DAD was developed for simultaneous determination of 10 stilbenes in peony samples, i.e.,suffruticosol A,suffruticosol B,suffruticosol C,trans-resveratrol,cis-ε-viniferin,trans-ε-viniferin,cis-suffruticosol D,cis-gnetin H,trans-suffruticosol D and trans-gnetin H. At the same time, the scavenging activity of DPPH free radicals was employed to evaluate their antioxidant effect. The results showed that the 10 stilbenes are mainly present in peony seed coat (total content of more than 16.7%) compared to peony seed kernel (total content less than 0.3%), and can be enriched in the extract of peony seed coat (total content of more than 75%) The extract of peony seed coat and 10 stilbenes exhibited significant antioxidant properties. This work provides a foundation for comprehensive utilization of the tree peony and herbaceous peony seed resources.

The resveratrol oligomers, cis- and trans-gnetin H, from Paeonia suffruticosa seeds inhibit the growth of several human cancer cell lines.

ETHNOPHARMACOLOGICAL RELEVANCE: Paeonia suffruticosa Andrews (PSE) is a well-known Chinese medicine that has been widely used as an anti-tumor, anti-oxidative and anti-inflammatory agent. cis- and trans-gnetin H are two resveratrol oligomers isolated from the seeds of PSE. Although resveratrol is widely considered to be one of the most valuable natural chemopreventive agents and there are numerous studies on the antitumor activities of resveratrol, little is known about the antitumor properties of cis- and trans-gnetin H. MATERIALS AND METHODS: The inhibitory effects of cis- and trans-gnetin H in different human cancer cell lines were assessed using fluorescent viability tests. Cytotoxicity in human lung and breast cancer cells was detected via nuclear condensation, cell permeability, and changes in the mitochondrial membrane potential (∆ψm). Apoptosis in human lung and breast cancer cells was assessed by flow cytometry, a luminescence assay and high-content screening analysis. Finally, a xenograft mice model was used to examine the efficacy of cis-gnetin H on lung tumors. RESULTS: cis- and trans-gnetin H have superior activity in inhibiting the proliferation of four human cancer cell lines, A549 (lung), BT20 (breast), MCF-7 (breast) and U2OS (osteosarcoma), and promote cell apoptosis, while having a minimal effect on two normal human epithelial cell lines, HPL1A (lung) and HMEC (breast) used as controls. cis- and trans-gnetin H promote apoptosis by releasing mitochondria cytochrome c, activating caspase 3/7 and inhibiting NF-κB activation. Flow cytometry analysis shows that cis- or trans-gnetin H arrested the cell cycle of cancer cells at the G0-G1 phase. Moreover, cis-gnetin H suppressed the growth of xenograft lung tumors in mice. CONCLUSION: Collectively, our findings demonstrate the promise of the natural compounds cis- and trans-gnetin H as candidates for cancer chemotherapy agents.

Minocycline inhibits ICAD degradation and the NF-κB activation induced by 6-OHDA in PC12 cells.

6-Hydroxydopamine (6-OHDA) is a neurotoxin that is commonly employed to induce lesions of the dopaminergic pathways to generating experimental models of Parkinson's disease (PD) in rodents. Antioxidant and anti-inflammatory therapy approaches have been the focus of attention in the treatment of neurodegenerative. PD and Alzheimer's diseases, and oxidative stress have been implicated in these diseases. In this study, we investigated the neuroprotective effects of minocycline and the signalling pathway that is possibly involved in a PC12 cell model of PD. The results indicated that 6-OHDA cytotoxicity was accompanied by an increment in lactate dehydrogenase (LDH) release, an increase in caspase-3 protein activity, an increase in ROS generation, MDA content and decrease in the SOD, CAT activities and cell viability. Moreover, treatment with 6-OHDA alone for 24h resulted in ICAD degradation, increased nuclear translocation of NF-κB, and increased p53 expression. However, pretreatment with minocycline (5, 10, 20 µM) for 24h significantly reduced LDH release, reduced caspase-3 protein production, reduced ROS production, MDA content and attenuated the decrease in SOD, CAT activities and cell viability. Additionally, minocycline (20 µM) markedly decreased the levels of cleaved ICAD protein, down-regulated p53 activity and inhibited the nuclear translocation of NF-κB. The neuroprotective effects of minocycline were attributable to its potent antioxidant activities, which prevented the nuclear translocation of NF-κB and the subsequent promotion of cell death. Therefore, the present study supports the notion that minocycline may be a promising neuroprotective agent for the treatment of Parkinson's disease.

[Review of research and development and significant effect of Hippophae rhamnoides].

Hippophae rhamnoides is one of the most representative economy crops for its wide uses of biological diversity and abundance of resource. As the key healthy food development and ecology protection, H. rhamnoides has been developed widely. Meanwhile, the development of H. rhamnoides has obtained great achievements. Nowadays, H. rhamnoides is still a necessary economy crop, while it has great influence on ecology protection. This paper discussed the phytochemistry, pharmacology, clinical application and product development, and propounded some suggestions for future research and economy development to get comprehensive benefit of H. rhamnoides and to serve for well-off society.

Deleterious nonsynonymous single nucleotide polymorphisms in human solute carriers: the first comparison of three prediction methods.

Abundant nsSNPs have been found in genes coding for human solute carrier (SLC) transporters, but there is little known about the relationship between the genotype and phenotype of nsSNPs in these membrane proteins. It is unknown which prediction method is better suited for the prediction of nonneutral nsSNPs of SLC transporters. We have identified 2,958 validated nsSNPs in human SLC family members 1-47 from the Ensembl genome database and the NCBI SNP database. Using three different algorithms, 37-45 % of nsSNPs in SLC genes were predicted to have functional impacts on transporter function. Predictions largely agreed with the available experimental annotations. Overall, 76.5, 74.4, and 73.5 % of nonneutral nsSNPs were predicted correctly as damaging by SNAP, SIFT, and PolyPhen, respectively, while 67.4, 66.3, and 76.7 % of neutral nsSNPs were predicted correctly as nondamaging by the three methods, respectively. This study identified many amino acids that were likely to be functionally critical but have not yet been studied experimentally. There was a significant concordance between the predicted results of different methods. Evolutionarily nonneutral (destabilizing) amino acid substitutions are predicted to be the basis for the pathogenic alteration of SLC transporter activity that is associated with disease susceptibility and altered drug/xenobiotic response.

[Research progress and trend analysis of biology and chemistry of Taxus medicinal resources].

Taxus is the source plant of anti-cancer drug paclitaxel and its biosynthetic precursor, analogs and derivatives, which has been studying for decades. There are many endemic Taxus species in China, which have been studied in the field of multiple disciplines. Based on the recent studies of the researchers, this review comments on the study of Taxus biology and chemistry. The bibliometric method is used to quantify the global scientific production of Taxus-related research, and identify patterns and tendencies of Taxus-related articles. Gaps are present in knowledge about the genomics, epigenomics, transcriptomics, proteomics, metabolomics and bioinformatics of Taxus and their endophytic fungi. Systems biology and various omics technologies will play an increasingly important role in the coming decades.

Non-neutral nonsynonymous single nucleotide polymorphisms in human ABC transporters: the first comparison of six prediction methods.

Nonsynonymous single nucleotide polymorphisms (nsSNPs) in coding regions that can lead to amino acid changes may cause alteration of protein function and account for susceptibility to disease and altered drug/xenobiotic response. Abundant nsSNPs have been found in genes coding for human ATP-binding cassette (ABC) transporters, but there is little known about the relationship between the genotype and phenotype of nsSNPs in these membrane proteins. In addition, it is unknown which prediction method is better suited for the prediction of non-neutral nsSNPs of ABC transporters. We have identified 2,172 validated nsSNPs in 49 human ABC transporter genes from the Ensembl genome database and the NCBI SNP database. Using six different algorithms, 41 to 52% of nsSNPs in ABC transporter genes were predicted to have functional impacts on protein function. Predictions largely agreed with the available experimental annotations. Overall, 78.5% of non-neutral nsSNPs were predicted correctly as damaging by SNAP, which together with SIFT and PolyPhen, was superior to the prediction methods Pmut, PhD-SNP, and Panther. This study also identified any amino acids that were likely to be functionally critical but have not yet been studied experimentally. There was significant concordance between the predicted results of SIFT and PolyPhen. Evolutionarily non-neutral (destabilizing) amino acid substitutions are predicted to be the basis for the pathogenic alteration of ABC transporter activity that is associated with disease susceptibility and altered drug/xenobiotic response.