Evaluation of selected 3D virtual screening tools for the prospective identification of peroxisome proliferator-activated receptor (PPAR) γ partial agonists.

The peroxisome proliferator-activated receptor (PPAR) γ regulates the expression of genes involved in adipogenesis, lipid homeostasis, and glucose metabolism, making it a valuable drug target. However, full activation of the nuclear receptor is associated with unwanted side effects. Research therefore focuses on the discovery of novel partial agonists, which show a distinct protein-ligand interaction pattern compared to full agonists. Within this study, we employed pharmacophore- and shape-based virtual screening and docking independently and in parallel for the identification of novel PPARγ ligands. The ten top-ranked hits retrieved with every method were further investigated with external in silico bioactivity profiling tools. Subsequent biological testing not only confirmed the binding of nine out of the 29 selected test compounds, but enabled the direct comparison of the method performances in a prospective manner. Although all three methods successfully identified novel ligands, they varied in the numbers of active compounds ranked among the top-ten in the virtual hit list. In addition, these compounds were in most cases exclusively predicted as active by the method which initially identified them. This suggests, that the applied programs and methods are highly complementary and cover a distinct chemical space of PPARγ ligands. Further analyses revealed that eight out of the nine active molecules represent novel chemical scaffolds for PPARγ, which can serve as promising starting points for further chemical optimization. In addition, two novel compounds, identified with docking, proved to be partial agonists in the experimental testing.

Identification of plumericin as a potent new inhibitor of the NF-κB pathway with anti-inflammatory activity in vitro and in vivo.

BACKGROUND AND PURPOSE: The transcription factor NF-κB orchestrates many pro-inflammatory signals and its inhibition is considered a promising strategy to combat inflammation. Here we report the characterization of the natural product plumericin as a highly potent inhibitor of the NF-κB pathway with a novel chemical scaffold, which was isolated via a bioactivity-guided approach, from extracts of Himatanthus sucuuba, an Amazonian plant traditionally used to treat inflammation-related disorders. EXPERIMENTAL APPROACH: A NF-κB luciferase reporter gene assay was used to identify NF-κB pathway inhibitors from H. sucuuba extracts. Monitoring of TNF-α-induced expression of the adhesion molecules VCAM-1, ICAM-1 and E-selectin by flow cytometry was used to confirm NF-κB inhibition in endothelial cells, and thioglycollate-induced peritonitis in mice to confirm effects in vivo. Western blotting and transfection experiments were used to investigate the mechanism of action of plumericin. KEY RESULTS: Plumericin inhibited NF-κB-mediated transactivation of a luciferase reporter gene (IC50 1 µM), abolished TNF-α-induced expression of the adhesion molecules VCAM-1, ICAM-1 and E-selectin in endothelial cells and suppressed thioglycollate-induced peritonitis in mice. Plumericin exerted its NF-κB pathway inhibitory effect by blocking IκB phosphorylation and degradation. Plumericin also inhibited NF-κB activation induced by transfection with the constitutively active catalytic subunit of the IκB kinase (IKK-ß), suggesting IKK involvement in the inhibitory action of this natural product. CONCLUSION AND IMPLICATIONS: Plumericin is a potent inhibitor of NF-κB pathways with a new chemical scaffold. It could be further explored as a novel anti-inflammatory lead compound.

Catechol alkenyls from Semecarpus anacardium: acetylcholinesterase inhibition and binding mode predictions.

ETHNOPHARMACOLOGICAL RELEVANCE: The fruits of Semecarpus anacardium L. f. (Anacardiaceae) are used in Ayurvedic medicine and also in Iranian Traditional Medicine for various indications, among those for retarding and treatment of dementia. AIM OF THE STUDY: The severity of Alzheimer's disease obviously correlates with a cholinergic deficit. In a screening for acetylcholinesterase (AChE) inhibitory activity, an extract from the fruit resin of Semecarpus anacardium was among the most active ones. Thus, the aim of this study was to isolate the active compounds and to investigate them in detail. Their binding mode to the active site of AChE was investigated by in silico docking experiments. MATERIALS AND METHODS: From a dichloromethane extract in an activity-guided fractionation the active compounds were isolated under use of different chromatographic techniques. Their structures were unambiguously identified by one and two-dimensional (1)H and (13)C NMR spectroscopy and mass spectrometry and their cholinesterase inhibitory activities were determined by a microplate assay. In order to compare the 3D active sites of AChE from Torpedo californica (TcAChE) and from Electrophorus electricus (EeAChE), three files from the Protein Data Bank (PDB) were used and for docking experiments, GOLD 3.1 software was employed. The concentrations of active compounds in the extract and the fruits were determined by HPLC analysis. RESULTS: The active compounds were determined as 1',2'-dihydroxy-3'-pentadec-8-enylbenzene (A) and 1',2'-dihydroxy-3'-pentadeca-8,11-dienylbenzene (B). Their IC(50) values in an in vitro assay on AChE inhibition were determined as 12 and 34 µg/mL, respectively, while they were not active in the inhibition of butyrylcholinesterase (BChE). In silico docking experiments showed a similar bioactivity for compounds A and B. The concentration of compounds A and B in the fruits was 1.85% and 1.88%, respectively. CONCLUSION: In the search for the active principle of the fruit resin of Semecarpus anacardium, compounds A and B were identified as two selective inhibitors for AChE versus BChE.

Laboratory evaluation of products to reduce settling of sweetpotato whitefly adults.

The impact of trademarked and commercial products on settling of adults of the sweetpotato whitefly, Bemisia tabaci (Gennadius), was studied in the laboratory. A no-choice bioassay using leaf disks of tomato, Solanum esculentum L., was developed to evaluate the impact of concentration series of products on settling of B. tabaci adults. The concentration of each product that would reduce settling by 50% (SC50) was estimated for each product using standard probit analyses, and the values were compared with that of Ultra-Fine Oil, a paraffinic oil product that is known to reduce settling of whitefly adults. Twenty-two trademarked products and 42 other products were evaluated in the laboratory bioassay. Based upon comparisons of fiducial limits of the respective SC50 values, Dawn detergent and E-RASE jojoba oil were the only trademarked products that were as effective as Ultra-Fine Oil in reducing settling of B. tabaci adults. Of the nontrademarked products, 25 were similar to Ultra-Fine Oil, although cedar, geranium, ginger, Hamlin (citrus), patchouli, olive and wintergreen oils, as well as citronellal and limonene, had ratios of respective SC50 values with that of Ultra-Fine Oil of approximately 1.5 or less. Combinations of limonene and citronellal with either olive oil or Ultra-Fine Oil were 15 and 30 times, respectively, more effective than Ultra-Fine Oil alone. Candidate products and combinations of products were further evaluated on tomato seedlings in no-choice screenhouse trials for effects on oviposition and on transmission of Tomato yellow leaf curl virus (family Geminiviridae, genus Begomovirus, TYLCV) by B. tabaci. Ultra-Fine Oil and olive oil reduced oviposition and transmission of TYLCV in the screenhouse trials. Ginger oil and limonene reduced oviposition in at least one screenhouse trial but did reduce transmission of TYLCV. The laboratory bioassay provided a rapid and relatively easy method to compare products for reducing settling of B. tabaci adults. Even though the reduced settling indicated in the laboratory bioassays was not always reflected in reduced oviposition or TYLCV transmission in the screenhouse trials, the bioassay was useful in rapidly identifying products that reduce settling and that could be investigated further.

Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates.

Computational chemistry software for lead discovery has become well established in pharmaceutical industry and has found its way to the desktop computers of medicinal chemists for different purposes, providing insight on the mode of action and binding properties, and creating new ideas for lead structure refinement. In this review we investigate the performance and reliability of recent state-of-the-art data modeling techniques, as well as ligand-based and structure-based modeling approaches for 3D virtual screening. We discuss and summarize recently published success stories and lately developed techniques. Parallel screening is one of these emerging approaches allowing for efficient activity in silico profiling of several compounds against different targets or anti-targets simultaneously. This is of special interest to medicinal chemists, as the approach allows revealing unknown binding modes ('target-fishing') as well as integrated ADME profiling or--more generally--the prediction of off-target effects.

Improvement of immune functions in HIV infection by sulfur supplementation: two randomized trials.

To determine the therapeutic effect of sulfur amino acid supplementation in HIV infection we randomized 40 patients with antiretroviral therapy (ART; study 1) and 29 patients without ART (study 2) to treatment for 7 months with N-acetyl-cysteine or placebo at an individually adjusted dose according to a defined scheme. The main outcome measures were the change in immunological parameters including natural killer (NK) cell and T cell functions and the viral load. Both studies showed consistently that N-acetyl-cysteine causes a marked increase in immunological functions and plasma albumin concentrations. The effect of N-acetyl-cysteine on the viral load, in contrast, was not consistent and may warrant further studies. Our findings suggest that the impairment of immunological functions in HIV+ patients results at least partly from cysteine deficiency. Because immune reconstitution is a widely accepted aim of HIV treatment, N-acetyl-cysteine treatment may be recommended for patients with and without ART. Our previous report on the massive loss of sulfur in HIV-infected subjects and the present demonstration of the immunoreconstituting effect of cysteine supplementation indicate that the HIV-induced cysteine depletion is a novel mechanism by which a virus destroys the immune defense of the host and escapes immune elimination.

Effects of cabbage leaf extract on breast engorgement.

The effectiveness of cabbage leaf extract was compared with that of a placebo in treating breast engorgement in lactating women. In a double-blind experiment with a pretest/posttest design, 21 participants received a cream containing cabbage leaf extract, while 18 received placebo cream. The placebo group received equal relief to the treated group, with the two groups showing no difference on all outcome measures. However, mothers perceived both creams to be effective in relieving discomfort. Feeding had a greater effect than the application of cream on relieving discomfort and decreasing tissue hardness. It is therefore recommended that lactation consultants encourage mothers to breastfeed if possible to relieve the discomfort of breast engorgement.

The integrative hospital explored via acupuncture.

To integrate complementary and allopathic medicine within a single hospital requires close attention to models of health care delivery, economics, and medical philosophy. The practice of acupuncture can be used as a heuristic device to examine these issues and how solutions may apply to other complementary modalities in the creation of such a hospital facility.

Hospital 2000: the interface of radiology within a combined "complementary-allopathic" medicine framework.

The field of radiology can play a crucial role in the movement beyond allopathic and complementary medicine to a true combination approach. Radiologists are proponents of minimal invasiveness and are familiar with the overreliance on diagnostic imaging tests. Their experience can be used to design appropriate applications for technology and to plan research methods to explore the questions raised by a combination medicine paradigm.

Regional lung water measurements with PET: accuracy, reproducibility, and linearity.

We evaluated the accuracy, reproducibility, and linearity of lung water concentration (LWC) measurements using positron emission tomography (PET) in anesthetized supine dogs. First, we evaluated whether errors in attenuation correction, which might occur during the development of pulmonary edema, significantly affect LWC and pulmonary blood flow (PBF) measurements obtained with PET. In 10 animals, PET scans of LWC and PBF were obtained before and after oleic acid induced lung injury. Changes in LWC and PBF after injury were underestimated by 12%-25% if the postinjury LWC scan was reconstructed using attenuation data obtained prior to injury, before lung density had changed, instead of attenuation data obtained after lung injury. Next, in four other dogs, we did not administer oleic acid, but instead instilled progressive amounts of autologous plasma into the left caudal lobe and obtained LWC measurements after each. Changes in LWC were linearly related to the amount of plasma instilled (r = 0.99). The average coefficient of variation for LWC in the control right lobe was 4 +/- 2% and the average percent change between measurements was 1.5% +/- 5.8%. The correlation of regional LWC determined gravimetrically after the last scan, when corrected for differences in regional lung density, with LWC determined by PET, was excellent (r = 0.92). We conclude that when the correct attenuation scan is used for emission scan reconstruction. PET measurements of LWC are accurate, linear, and reproducible.

Sequential high dose methotrexate, 5-fluorouracil and folinic acid does not improve response rates in advanced colorectal cancer.

27 patients with advanced colorectal cancer were treated in a phase-II trial with high dose sequential methotrexate (MTX), 5-fluorouracil (5-FU), and folinic acid (FA). Following a 4 h infusion of 800 mg/m2 MTX and a 4 h interval, 1,500 mg/m2 5-FU and 200 mg/m2 FA were given as a 24 h infusion. Out of 23 evaluable patients we observed one partial remission and 9 disease stabilizations. Median survival time of all patients was 10.4 months. Overall toxicity was low. In comparison to a previous trial we did not observe better treatment results by adding high dose FA to a sequential MTX/5-FU schedule.