Commentary: "A systems view on the future of medicine: inspiration from Chinese medicine?".

Chinese medicine could serve as a source of inspiration for drug development. Using systems biology in combination with reverse pharmacology is a novel way for the discovery of novel biological active compounds and targets as well as for proving the occurrence of synergy and prodrugs. A key factor for coming to evidence-based Chinese medicine will be the quality control. Metabolomics is a very promising tool for this purpose.

The art and practice of systems biology in medicine: mapping patterns of relationships.

Systems biology has developed in recent years from a technology-driven enterprise to a new strategic tool in Life Sciences, particularly for innovative drug discovery and drug development. Combining the ultimate in systems phenotyping with in-depth investigations of biomolecular mechanisms will enable a revolution in our understanding of disease pathology and will advance translational medicine, combination therapies, integrative medicine, and personalized medicine. A prerequisite for deriving the benefits of such a systems approach is a reliable and well-validated bioanalytical platform across complementary measurement modalities, especially transcriptomics, proteomics, and metabolomics, that operates in concert with a megavariate integrative biostatistical/bioinformatics platform. The applicable bioanalytical methodologies must undergo an intense development trajectory to reach an optimal level of reliable performance and quantitative reproducibility in daily practice. Moreover, to generate such enabling systems information, it is essential to design experiments based on an understanding of the complexity and statistical characteristics of the large data sets created. Novel insights into biology and system science can be obtained by evaluating the molecular connectivity within a system through correlation networks, by monitoring the dynamics of a system, or by measuring the system responses to perturbations such as drug administration or challenge tests. In addition, cross-compartment communication and control/feed-back mechanisms can be studied via correlation network analyses. All these data analyses depend critically upon the generation of high-quality bioanalytical platform data sets. The emphasis of this paper is on the characteristics of a bioanalytical platform that we have developed to generate such data sets. The broad applicability of Systems Biology in pharmaceutical research and development is discussed with examples in disease biomarker research, in pharmacology using system response monitoring, and in cross-compartment system toxicology assessment.

Screening of natural products extracts for the presence of phosphodiesterase inhibitors using liquid chromatography coupled online to parallel biochemical detection and chemical characterization.

The ability to rapidly identify active compounds in a complex mixture (e.g., natural products extract) is still one of the major problems in natural products screening programs. An elegant way to overcome this problem is to separate the complex mixture by gradient liquid chromatography followed by online biochemical detection parallel with chemical characterization, referred to as high-resolution screening (HRS). To find and identify phosphodiesterase (PDE) inhibitors in natural products extracts using the HRS technology, the authors developed a continuous-flow PDE enzymatic assay. The suitability of the continuous-flow PDE enzymatic assay for natural products screening was demonstrated. After optimization of the continuous-flow PDE assay, the limit of detection for 3-isobutyl-1-methyl-xanthine (IBMX) was 1 muM, with a dynamic range from 1 to 100 muM IBMX. The applicability of the HRS technology for the detection of PDE inhibitors in natural products extracts was demonstrated by the analysis of a plant extract spiked with 2 naturally occurring PDE inhibitors. The plant extract was analyzed with 2 assay lines in parallel, enabling background fluorescence correction of the sample. The simultaneous quantification of the active compounds using evaporative light-scattering detection allowed the estimation of the IC(50) value of the active compounds directly in the crude extract.

A generic assay for phosphate-consuming or -releasing enzymes coupled on-line to liquid chromatography for lead finding in natural products.

A generic continuous-flow assay for phosphate-consuming or -releasing enzymes coupled on-line to liquid chromatography (LC) has been developed. Operating the LC-biochemical assay in combination with mass spectrometry allows the fast detection and identification of inhibitors of these enzymes in complex mixtures. The assay is based on the detection of phosphate, released by the on-line continuous-flow enzymatic reaction, using a fluorescent probe. The probe consists of fluorophore-labeled phosphate-binding protein, which shows a strong fluorescence enhancement upon binding to inorganic phosphate. To detect very small changes of the phosphate concentration in a postcolumn enzymatic reaction medium, the enzymatic removal of phosphate impurities from solvents, reagents, and samples was optimized for application in continuous flow. The potential of the phosphate probe is demonstrated by monitoring the enzymatic activity, i.e., the phosphate release, from alkaline phosphatase. The selectivity of the phosphate readout, necessary to distinguish between phosphate containing substrate or product and free inorganic phosphate released after enzymatic conversion, is shown. The applicability of LC coupled to the enzymatic assay using the phosphate readout was demonstrated by detection of tetramisole in a plant extract as inhibitor of alkaline phosphatase. Parallel mass spectrometry allowed the simultaneous confirmation of the identity of the inhibitor.

High-performance liquid chromatography with on-line coupled UV, mass spectrometric and biochemical detection for identification of acetylcholinesterase inhibitors from natural products.

A high-performance liquid chromatography (HPLC) method with on-line coupled ultraviolet (UV), mass spectrometry (MS) and biochemical detection for acetylcholinesterase (AChE) inhibitory activity has been developed. By combining the separation power of HPLC, the high selectivity of biochemical detection, and the ability to provide molecular mass and structural information of MS, AChE inhibitors can be rapidly identified. The biochemical detection was based on a colorimetric method using Ellman's reagent. The detection limit of galanthamine, an AChE inhibitor, in the HPLC-biochemical detection is 0.3 nmol. The three detector lines used, i.e., UV, MS and Vis for the biochemical detection were recorded simultaneously and the delay times of the peaks obtained were found to be consistent. This on-line post-column detection technique can be used for the identification of AChE inhibitors in plant extracts and other complex mixtures such as combinatorial libraries.