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Evaluation and prediction of drug permeation.

A major challenge confronting the pharmaceutical scientist is to optimize the selective and efficient delivery of new active entities and drug candidates. Successful drug development requires not only optimization of specific and potent pharmacodynamic activity, but also efficient delivery to the target site. Following advances in rational drug design, combinatorial chemistry and high-throughput screening techniques, the number of newly discovered and promising active compounds has increased dramatically in recent years, often making delivery problems the rate-limiting step in drug research. To overcome these problems, a good knowledge of the pharmacokinetic barriers encountered by bioactive compounds is required. This review gives an overview of the properties of relevant physiological barriers and presents some important biological models for evaluation of drug permeation and transport. Physicochemical determinants in drug permeation and the relevance of quantitative and qualitative approaches to the prediction and evaluation of passive drug absorption are also discussed.

Animals↗

Identification and quantification of polyphenolic compounds in Longan (Euphoria longana Lam.) fruit.

Regular consumption of fruit and vegetables is associated with a lower risk of some chronic diseases including various forms of cancer and cardiovascular diseases. The health-promoting potential of these foods may be due, in part, to the phytochemical bioactive compounds present in the plants. Fruit of Euphoria longana Lam. (longan) are consumed throughout Asia and are a major crop in Thailand. In the present study phytochemicals were extracted with 70% methanol from peel, pulp, and seed tissues of longan fruit, and the major components were identified as gallic acid, corilagin (an ellagitannin), and ellagic acid. A high-through-put reversed phase HPLC method was developed to determine the content of these three compounds in different parts of the longan fruit and among different cultivars. The analyses showed that there was a large variation in the contents of gallic acid, corilagin, and ellagic acid in different plant tissues and cultivars. Seed contained the highest levels of the three phenolics, and pulp contained the lowest. Among commercial cultivars, Biewkiew and Edor contained the highest levels of gallic and ellagic acid while Srichompoo contained the highest content of corilagin. These three cultivars may be used in directed breeding and cultivation programs and to develop concentrated longan seed extracts to promote good health. Utilization of this byproduct material will support the use of thousands of tons of waste longan seeds after the production of canned longan pulp.

Chromatography, High Pressure Liquid↗

Advances and challenges in the identification of volatiles that mediate interactions among plants and arthropods.

The relatively new research field of Chemical Ecology has, over the last two decades, revealed an important role of plant-produced volatile organic compounds (VOCs) in mediating interactions between plants and other organisms. Of particular interest are the volatile blends that plants actively emit in response to herbivore damage. Various efforts are underway to pinpoint the bioactive compounds in these complex blends, but this has proven to be exceedingly difficult. Here we give a short overview on the role of herbivore-induced plant volatiles in interactions between plants and other organisms and we review methods that are currently employed to collect and identify key volatile compounds mediating these interactions. Our perspective on future directions of this fascinating research field places special emphasis on the need for an interdisciplinary approach. Joint efforts by chemists and biologists should not only facilitate the elucidation of crucial compounds, but can also be expected to lead to an exploitation of this knowledge, whereby ecological interactions may be chemically manipulated in order to protect crops and the environment.

Animals↗

Unsaturated fatty acids are inhibitors of bacterial conjugation.

This report describes a high-throughput assay to identify substances that reduce the frequency of conjugation in Gram-negative bacteria. Bacterial conjugation is largely responsible for the spread of multiple antibiotic resistances in human pathogens. Conjugation inhibitors may provide a means to control the spread of antibiotic resistance. An automated conjugation assay was developed that used plasmid R388 and a laboratory strain of Escherichia coli as a model system, and bioluminescence as a reporter for conjugation activity. Frequencies of conjugation could be measured continuously in real time by the amount of light produced, and thus the effects of inhibitory compounds could be determined quantitatively. A control assay, run in parallel, allowed elimination of compounds affecting cell growth, plasmid stability or gene expression. The automated conjugation assay was used to screen a database of more than 12,000 microbial extracts known to contain a wide variety of bioactive compounds (the NatChem library). The initial hit rate was 1.4 %. From these, 48 extracts containing active compounds and representing a variety of organisms and extraction conditions were subjected to fractionation (24 fractions per extract). The 52 most active fractions were subjected to a secondary analysis to determine the range of plasmid inhibition. Plasmids R388, R1 and RP4 were used as representatives of a variety of plasmid transfer systems. Only one fraction (of complex composition) affected transfer of all three plasmids, while four other fractions were active against two of them. Two separate compounds were identified from these fractions: linoleic acid and dehydrocrepenynic acid. Downstream analysis showed that the chemical class of unsaturated fatty acids act as true inhibitors of conjugation.

Conjugation, Genetic↗

Unravelling the role of the ToxR-like transcriptional regulator WmpR in the marine antifouling bacterium Pseudoalteromonas tunicata.

The dark-green-pigmented marine bacterium Pseudoalteromonas tunicata produces several target-specific compounds that act against a range of common fouling organisms, including bacteria, fungi, protozoa, invertebrate larvae and algal spores. The ToxR-like regulator WmpR has previously been shown to regulate expression of bioactive compounds, type IV pili and biofilm formation phenotypes which all appear at the onset of stationary phase. In this study a comparison of survival under starvation or stress between the wild-type P. tunicata strain and a wmpR mutant (D2W2) does not suggest a role for WmpR in regulating starvation- and stress-resistant phenotypes such as those that may be required in stationary phase. Both proteomic [2-dimensional PAGE (2D-PAGE)] and transcriptomic (RNA arbitrarily primed PCR) studies were used to discover members of the WmpR regulon. 2D-PAGE identified 11 proteins that were differentially expressed by WmpR. Peptide sequence data were obtained for six of these proteins and identified using the draft P. tunicata genome as being involved in protein synthesis, amino acid transamination and ubiquinone biosynthesis, as well as hypothetical proteins. The transcriptomic analysis identified three genes significantly up-regulated by WmpR, including a TonB-dependent outer-membrane protein, a non-ribosomal peptide synthetase and a hypothetical protein. Under iron-limitation the wild-type showed greater survival than D2W2, indicating the importance of WmpR under these conditions. Results from these studies show that WmpR controls the expression of genes encoding proteins involved in iron acquisition and uptake, amino acid metabolism and ubiquinone biosynthesis in addition to a number of proteins with as yet unknown functions.

Amino Acids↗

Uncovering ShuangZi Powder's Anti-Ovarian Cancer Mechanism: A Systems Biology and Experimental Approach.

INTRODUCTION: This study investigated the anti-ovarian cancer (OC) effects of Shuangzi Powder (SZP) and its regulatory impact on the tumor microenvironment. METHOD: This study employed systems biology approaches, integrating molecular docking and experimental validation, to explore the pharmacological mechanisms of SZP in OC treatment. To identify potential bioactive compounds and target genes of SZP, network pharmacology, protein- protein interaction network analysis,.Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were conducted. RESULTS: Among the 11 bioactive ingredients identified in SZP, 1,767 potential therapeutic targets were predicted, while 2,637 differentially expressed genes were found to be associated with OC. KEGG pathway analysis revealed significant enrichment in pathways related to cancer, apoptosis, the PI3K-Akt signaling pathway, and the PD-L1/PD-1 checkpoint pathway. Treatment of A2780 cells with β,β-Dimethylacrylshikonin (DMAS) inhibited cell viability, migration, and invasion. Moreover, DMAS downregulated the expression of cell cycle- and apoptosis-related genes (CCNB1, CHEK1, CCNE1, and PARP1) and upregulated the immune checkpoint gene PD-L1. DISCUSSION: These findings indicate that multiple components, targets, and pathways are involved in OC treatment by SZP. CONCLUSION: DMAS, one of the bioactive ingredients of SZP, was predicted and preliminarily validated to exert inhibitory effects on OC cells, mainly through the regulation of the cell cycle, apoptosis, and immune response, as demonstrated by molecular docking and experimental analyses.

Ovarian Neoplasms↗

Bioactive polyacetylenes in food plants of the Apiaceae family: occurrence, bioactivity and analysis.

Many bioactive compounds with known effects on human physiology and disease have been identified through studies of plants used in traditional medicine. Some of these substances occur also in common food plants, and hence could play a significant role in relation to human health. Food plants of the Apiaceae plant family such as carrots, celery and parsley, contain a group of bioactive aliphatic C17-polyacetylenes. These polyacetylenes have shown to be highly toxic towards fungi, bacteria, and mammalian cells, and to display neurotoxic, anti-inflammatory and anti-platelet-aggregatory effects and to be responsible for allergic skin reactions. The effect of these polyacetylenes towards human cancer cells, their human bioavailability and their ability to reduce tumour formation in a mammalian in vivo model indicates that they may also provide benefits for health. The present state of knowledge on the occurrence of polyacetylenes in Apiaceae food plants, their biochemistry and bioactivity is presented in this review as well as relatively new methods for the isolation and quantification of these compounds from plants, plant products and biological fluids.

Acetylene↗

Cyclopeptide alkaloids from Scutia buxifolia Reiss and their antimicrobial activity.

The present study reports a cyclopeptide alkaloid, scutianine M, isolated from the methanolic root bark extract of Scutia buxifolia Reiss (Rhamnaceae) along with six known compounds, scutianines-B, -C, -D, -E, -F, and scutianene D. Its structure was established on the basis of spectroscopic analyses, including application of 2D NMR spectroscopic techniques. As part of a study of the bioactive compounds of medicinal plants from southern Brazil, we also compared the antimicrobial activity of the isolated compounds towards Gram (+), Gram (-) bacteria, and yeasts.

Alkaloids↗

Antimicrobial compounds from Coleonema album (Rutaceae).

Coleonema album, a member of the South African fynbos biome, was evaluated for its antimicrobial activity associated with its secondary metabolites. Ethanol- and acetone-based extracts obtained from plants from two different geographical areas were analyzed. A bioassay-guided fractionation methodology was followed for rapid and effective screening for the presence of bioactive compounds. The TLC-bioautographic method, used to screen the plant extracts for antimicrobial activity and localization of the active compounds, indicated the presence of a number of inhibitory compounds with activity against the microorganisms (E. coli, B. subtilis, E. faecalis, P. aeruginosa, S. aureus, M. smegmatis, M. tuberculosis, C. albicans, C. cucumerinum) tested. Evaluation of the inhibitory strength of each extract by the serial microdilution assay indicated that the C. album extracts inhibited effectively all the microorganisms, with the minimum inhibitory concentrations in the low mg ml(-1) range. Identification and structural information of the bioactive components were obtained by a combination of preparative TLC and LC-MS. It revealed the presence of coumarin aglycones which were responsible for the observed antimicrobial activities. The results of this study indicate that C. album possesses strong antimicrobial activity against a wide range of microorganisms that warrants further investigation into the use of the extracts or their active constituents as a potential source for novel drugs.

Anti-Bacterial Agents↗

Actinophages as indicators of actinomycete taxa in marine environments.

It is necessary to continue to screen for new metabolites and evaluate the potential of less known and new bacterial taxa so that new and improved compounds for future use against drug-resistant bacteria or for chemical modification may be developed. There has been considerable interest in the detection and identification of marine microorganisms since they have been reported to produce bioactive compounds ranging from antitumour to antibacterial and antiviral agents. In this study, an improved technique that involves the exploitation of marine actinophages as indicators of the marine actinomycete taxa and uses marine bacteriophages as tools to reduce the numbers of common marine bacteria, which impedes the growth of rare actinomycetes on isolation plates, has been applied. This technique reduced the numbers of colony forming units of unwanted bacteria on isolation plates and hence increased the chances of detecting novel marine actinomycete genera for isolation and subsequent screening for antiviral activity.

Actinobacteria↗

A novel shape-feature based approach to virtual library screening.

The shape of and the chemical features of a ligand are both critical for biological activity. This paper presents a strategy that uses these descriptors to build a computational model for virtual screening of bioactive compounds. Molecules are represented in a binary shape-feature descriptor space as bit-strings, and their relative activities are used to identify the subset of the bit-string that is most relevant to bioactivity. This subset is used to score virtual libraries. We describe the computational details of the method and present an example validation experiment on thrombin inhibitors.

Computer Simulation↗

Enrichment of refined olive oil with phenolic compounds: evaluation of their antioxidant activity and their effect on the bitter index.

The study of the antioxidant effects of biophenolic compounds is supported by the current interest in natural products and the ongoing replacement of synthetic antioxidants by natural antioxidants from plant sources. Olives and olive oil, especially extra virgin olive oil, contain a variety of bioactive compounds (phytochemicals) widely considered to be potentially beneficial for health. This research was focused on evaluating the antioxidant activity of the enriched refined olive oil to discover a possible functional food application. Different concentrations of individual and combined phenolic compounds were added to the refined olive oil as lipid matrix, and the antioxidant activity expressed as oxidative stability in hours was determined by using the Rancimat method. Additionally, the bitter index was evaluated to assess the effect of the enrichment in relation to the organoleptic quality. The results showed that the antioxidant activity depends on the concentration of the phenol used for the assay and the chemical structure. In general, the most positive effects were observed in 3,4-dihydroxy and 3,4,5-trihydroxy structures linked to an aromatic ring that conferred to the moiety a higher proton dislocation, thus facilitating the scavenging activity.

Antioxidants↗

Strategies for efficient lead structure discovery from natural products.

This investigation aims to evaluate strategies for an efficient selection of bioactive compounds from the multitude and biodiversity of the plant kingdom. Statistics prove natural products (NPs) as a source leading most consistently to successful development of new drugs. However, there are several reasons why the interest in finding bioactive NPs has generally declined at several major pharmaceutical companies. Their substantial argument is that the research in this field is time-consuming, highly complex and ineffective. A more rational and economic search for new lead structures from nature must therefore be a priority in order to overcome these problems. In this paper, different strategies are described to exploit the molecular diversity of bioactive secondary metabolites, namely classical pharmacognostic approaches and computational methods. The latter include various data mining tools, like virtual screening filtering experiments using pharmacophore models, docking studies, and neural networks, which help to establish a relationship between chemical structure and biological activity. The strengths and weaknesses of these methods will be shown in this review. Focusing on selected targets within the arachidonic acid cascade (phospholipase A(2), 5-lipoxygenase, cyclooxygenase-1 and -2), several studies of successful discoveries in the field of anti-inflammatory NPs were scrutinized for the applied strategies. Both the compilation of relevant published data and recent studies supported by our own research clearly demonstrate the benefits of the synergistic effect of a hybridization of these strategies for an effective drug discovery from natural ingredients.

Anti-Inflammatory Agents↗

Experimental model of ischemic bowel necrosis. The role of platelet-activating factor and endotoxin.

This report deals with the experimental production of ischemic bowel necrosis in rats by the administration of combined bacterial lipopolysaccharide (LPS) and platelet-activating factor (PAF). Neither LPS alone, nor PAF at a low dose, caused ischemic intestinal necrosis when administered intraaortically. With these two compounds in combination, necrotizing lesions of the gastrointestinal tract developed consistently. The lesions showed marked morphologic similarity to human necrotizing enterocolitis (NEC). There were no thrombi in mesenteric arteries or necrotic lesions in other organs to which these bioactive compounds were delivered. These findings suggest a possible synergistic involvement of PAF and LPS in the pathogenesis of NEC and other forms of ischemic bowel necrosis. The authors further suggest that the pathogenesis of experimental NEC in rats is independent of platelet aggregation.

Animals↗

Resolvins, docosatrienes, and neuroprotectins, novel omega-3-derived mediators, and their aspirin-triggered endogenous epimers: an overview of their protective roles in catabasis.

The molecular basis for the beneficial impact of essential omega-3 fatty acids is of considerable interest. Recently, novel mediators generated from eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) that displayed potent bioactions were first identified in resolving inflammatory exudates [J. Exp. Med. 192 (2000) 1197; J. Exp. Med. 196 (2002) 1025] and in tissues enriched with DHA [J. Exp. Med. 196 (2002) 1025; J. Biol. Chem. 278 (2003) 14677]. The trivial names Resolvin (resolution phase interaction products) and docosatrienes were introduced for the bioactive compounds belonging to these novel series because they demonstrate potent anti-inflammatory and immunoregulatory actions. The compounds derived from eicosapentaenoic acid carrying potent biological actions (i.e., 1-10 nM range) are designated E series, given their EPA precursor, and denoted as Resolvins of the E series (Resolvin E1 or RvE1), and those biosynthesized from the precursor docosahexaenoic acid are Resolvins of the D series (Resolvin D1 or RvD1). Bioactive members from DHA with conjugated triene structures are docosatrienes (DT) that are immunoregulatory [J. Exp. Med. 196 (2002) 1025; J. Biol. Chem. 278 (2003) 14677], and neuroprotective [J. Biol. Chem., 278 (2003) 43807; Proc. Natl. Acad. Sci. U.S.A. [submitted for publication]] and are termed neuroprotectins. The specific receptors for these novel bioactive products from omega-3 EPA and DHA are abbreviated Resolvin D receptors (i.e., ResoDR1), Resolvin E receptor (ResoER1; RER1), and neuroprotectin D receptors (NPDR), respectively, in recognition of their respective cognate ligands. Aspirin treatment impacts biosynthesis of these compounds and a related series by triggering endogenous formation of the 17R-D series Resolvins and docosatrienes. These novel epimers are denoted as aspirin-triggered (AT)-RvDs and -DTs, and possess potent anti-inflammatory actions in vivo essentially equivalent to their 17S series pathway products. Here, we provide a syntomy overview of the formation and actions of these newly uncovered pathways and products as well as highlight their role(s) as endogenous protective mediators generated in anti-inflammation and catabasis.

Animals↗

Relationships between Molecular Complexity, Biological Activity, and Structural Diversity.

Following the theoretical model by Hann et al. moderately complex structures are preferable lead compounds since they lead to specific binding events involving the complete ligand molecule. To make this concept usable in practice for library design, we studied several complexity measures on the biological activity of ligand molecules. We applied the historical IC50/EC50 summary data of 160 assays run at Novartis covering a diverse range of targets, among them kinases, proteases, GPCRs, and protein-protein interactions, and compared this to the background of "inactive" compounds which have been screened for 2 years but have never shown any activity in any primary screen. As complexity measures we used the number of structural features present in various molecular fingerprints and descriptors. We found generally that with increasing activity of the ligands, their average complexity also increased, and we could therefore establish a minimum number of structural features in each descriptor needed for biological activity. Especially well suited in this context were the Similog keys and circular substructure fingerprints. These are those descriptors, which also perform especially well in the identification of bioactive compounds by similarity search, suggesting that structural features encoded in these descriptors have a high relevance for bioactivity. Since the number of features correlates with the number of atoms present in the molecule, also the number of atoms serves as a reasonable complexity measure and larger molecules have, in general, higher activities. Due to the relationship between feature counts and densities on one hand and biological activity on the other, the size bias present in almost all similarity coefficients becomes especially important. Diversity selections using these coefficients can influence the overall complexity of the resulting set of molecules, which has an impact on the biological activity that they exhibit. Using sphere-exclusion based diversity selection methods, such as OptiSim together with the Tanimoto dissimilarity, the average feature count distribution of the resulting selections is shifted toward lower complexity than that of the original set, particularly when applying tight diversity constraints. This size bias reduces the fraction of molecules in the subsets having the complexity required for a high, submicromolar activity. None of the diversity selection methods studied, namely OptiSim, divisive K-means clustering, and self-organizing maps, yielded subsets covering the activity space of the IC50 summary data set better than subsets selected randomly.

Drug Design↗

Prevention and management of prostate cancer using PC-SPES: a scientific perspective.

Complementary and alternative therapies are increasingly used in the United States by individuals diagnosed with cancer. PC-SPES is a multiherb dietary supplement used by many patients with prostate cancer (CaP). The wide acceptance of PC-SPES for hormone-naive and end-stage CaP relates to clinical trials demonstrating significant efficacy and low toxicity. Although the clinical efficacy of PC-SPES is highly encouraging, its scientific basis has progressed more slowly. This article describes our understanding of the in vitro mechanisms of action of PC-SPES in androgen-dependent LNCaP cells. We first demonstrated significant suppression of cancer cell growth by restriction of cell cycle progression at G(1)/S and drastic reductions in the expression of androgen receptor and prostate-specific antigen (PSA) by PC-SPES, providing a mechanistic rationale for its observed clinical effects. Further investigation of the anti-CaP properties of PC-SPES revealed that two of its multicomponent herbs, Glycyrrhiza uralensis and Scutellaria baicalensis, inhibited cell growth and down-regulated PSA in a manner comparable with PC-SPES. Exhaustive characterization of S. baicalensis resulted in the isolation of baicalein. Here we report that baicalein effectively suppressed growth and PSA expression and induced G(1)/S arrest in LNCaP cells. Although baicalein cannot account for the entire activity of PC-SPES, it does display similar anti-CaP activities. These data suggest that a single herb or bioactive compound could suffice for CaP chemoprevention by effecting multiple changes in target cells to intervene in CaP progression. These studies provide the impetus for further evaluation of the composition herbs within PC-SPES and the precise characterization of their bioactive ingredients.

Antineoplastic Agents, Phytogenic↗

Seeding of intravascular stents by the xenotransplantation of genetically modified endothelial cells.

A novel approach of cell seeding of stents using xenotransplanted endothelium is proposed. The advantages of this approach are that these doubly transgenic animals will provide a limitless supply of endothelial cells producing controllable levels of active compound. These foreign cells will act as Trojan horses, graciously accepted at face value by the host organism, but capable of modifying the pathophysiological response to vessel damage, typified by the process of restenosis. Once implanted, the production of the bioactive compound is under exogenous control by means of 'designer' genes coding for modified cell surface receptors, which are introduced with the transgene to provide controllable levels of compound. Interaction of an orally administered compound with the modified cell receptor will switch on the transgene, while in its absence the transgene remains dormant. We have been able to show the feasibility this type of approach has for other animal species, and it shows great potential for application to humans.

Animals↗