Activity of selected aromatic amino acids in biological systems

Besides the structural function in proteins, aromatic amino acids are precursors of many important biological compounds essential for normal functioning of the human organism. Many of these compounds may be used as markers for identification of specific pathological states. Comprehensive knowledge about the metabolism of aromatic amino acids and mechanisms of action of their metabolites made it possible to develop effective treatments for many disorders. However, it should not be forgotten that in some pathological conditions, these compounds could not only be involved in the pathogenesis of many disease entities but could also be used as an important tool in prediction of many diseases. This paper contains a review of published literature on aromatic amino acids in the context of physiological processes of the human body and chosen social disorders, such as cancers; psychiatric disorders: depression, anxiety states, schizophrenia, bipolar affective disorders; neurodegenerative, and cardiovascular diseases; chronic kidney insufficiency or diabetes.     

Biologically active secondary metabolites from myxobacteria

New chemical structures with proven biological activity still are badly needed for a host of applications and are intensively screened for. Suitable compounds may be used as such, or in the form of their derivatives or, equally important, may serve as lead compounds for designing synthetic analogs. One way to new compounds is the exploitation of new producer organisms. During the past 15 years the myxobacteria have been shown in our laboratories to be a rich source of novel secondary metabolites, many of the compounds showing interesting and sometimes unique mechanisms of action. About 50 basic structures and nearly 300 structural variants have been elucidated, and almost all of them turned out to be new compounds. Several myxobacterial substances may have a good chance of an application.     

Rediscovery of known natural compounds: nuisance or goldmine?

Do all natural compounds have a distinct biological activity, or are most of them merely biosynthetic debris? Many natural compounds have important biological functions, and certainly many more of the ample 200,000 currently known will ultimately prove to be more than just 'secondary metabolites'. The question is how to select the most promising candidates for potential new drugs. 'Rediscovery' of known natural compounds is regarded as a nuisance or disappointment by scientists involved with the identification of novel compounds. The other side of the coin, however, is that the discovery that a particular compound occurs in unrelated species can be a valuable clue toward the identification of a novel receptor or enzyme. Here, we put forward the hypothesis that when a natural compound occurs in unrelated species, it must have an important biological function by interacting with a specific molecular target. This is because it is extremely improbable that in nature one particular compound is synthesized in totally unrelated species for no reason at all. For many compounds occurring in unrelated species, it is already known that they act on specific molecular targets. For others, it is just known that they occur in different species. In some cases, biological activities are known but not the underlying mechanisms of action. It is from this category of compounds that important discoveries are likely to be made. Some (around 70) of them were identified. They represent important clues from nature offering an alternative approach to the classical screening of large numbers of compounds.     

A comparison between the homocyclic aromatic metabolic pathways from plant-derived compounds by bacteria and fungi

Aromatic compounds derived from lignin are of great interest for renewable biotechnical applications. They can serve in many industries e.g. as biochemical building blocks for bioplastics or biofuels, or as antioxidants, flavor agents or food preservatives. In nature, lignin is degraded by microorganisms, which results in the release of homocyclic aromatic compounds. Homocyclic aromatic compounds can also be linked to polysaccharides, tannins and even found freely in plant biomass. As these compounds are often toxic to microbes already at low concentrations, they need to be degraded or converted to less toxic forms. Prior to ring cleavage, the plant- and lignin-derived aromatic compounds are converted to seven central ring-fission intermediates, i.e. catechol, protocatechuic acid, hydroxyquinol, hydroquinone, gentisic acid, gallic acid and pyrogallol through complex aromatic metabolic pathways and used as energy source in the tricarboxylic acid cycle. Over the decades, bacterial aromatic metabolism has been described in great detail. However, the studies on fungal aromatic pathways are scattered over different pathways and species, complicating a comprehensive view of fungal aromatic metabolism. In this review, we depicted the similarities and differences of the reported aromatic metabolic pathways in fungi and bacteria. Although both microorganisms share the main conversion routes, many alternative pathways are observed in fungi. Understanding the microbial aromatic metabolic pathways could lead to metabolic engineering for strain improvement and promote valorization of lignin and related aromatic compounds.     

Phytodegradation of organic compounds

The phytodegradation of organic compounds can take place inside the plant or within the rhizosphere of the plant. Many different compounds and classes of compounds can be removed from the environment by this method, including solvents in groundwater, petroleum and aromatic compounds in soils, and volatile compounds in the air. Although still a relatively new area of research, there are many laboratories studying the underlying science necessary for a wide range of applications for plant-based remediation of organic contaminants.     

Catabolism of citronellol and related acyclic terpenoids in pseudomonads

Terpenes are a huge group of natural compounds characterised by their predominantly pleasant smell. They are built up by isoprene units in cyclic or acyclic form and can be functionalised by carbonyl, hydroxyl or carboxyl groups and by presence of additional carbon–carbon double bonds (terpenoids). Currently, much more than 10,000 terpenoid compounds are known, and many thereof are present in different iso- and stereoforms. Terpenoids are secondary metabolites and can have important biological functions in living organisms. In many cases, the biological functions of terpenoids are not known at all. Nevertheless, terpenoids are used in large quantities as perfumes and aroma compounds for food additives. Terpenoids can be also precursors and building blocks for synthesis of complex chiral compounds in chemical and pharmaceutical industry. Unfortunately, only few terpenoids are available in large quantities at reasonable costs. Therefore, characterisation of suited biocatalysts specific for terpenoid compounds and development of biotransformation processes of abundant terpenoids to commercially interesting derivates becomes more and more important. This minireview summarises knowledge on catabolic pathways and biotransformations of acyclic monoterpenes that have received only little attention. Terpenoids with 20 or more carbon atoms are not a subject of this study.     

Phosphorus in sediments — speciation and analysis

Characterization of sediment phosphorus is commonly based on sequential chemical extractions, in which phosphorus is supposed to be selectively removed from different compounds in the sediments. The first extraction schemes were designed to quantify discrete chemical or mineralogical compounds. As extraction schemes have been tested on different sediments, several systematic errors have been detected and the schemes have been modified and simplified accordingly. Other chemical extractions or treatments have attempted to determine phosphorus bound to particles with a certain strength or binding energy, the purpose being to determine the labile, loosely bound, exchangeable, mobile or algal-available fraction of sediment phosphorus. All extraction procedures yield operationally defined fractions and cannot be used for identification of discrete phosphorus compounds. The many methodological modifications make it necessary to be cautious when comparing results from the literature in this field.     

Functional selectivity, ligand-directed trafficking, conformation-specific agonism: what's in a name?

Research on the design of compounds to selectively affect specific subsets of signals downstream of receptors has burgeoned lately, and several reports discussed at Experimental Biology 2005 indicate progress is being made in the understanding of what makes a drug functionally selective. Different conformations adopted by receptors after associating with specific ligands can determine which intracellular signaling pathways get activated and which do not. The appeal of such specific compounds is enormous when one considers that many disease states might require the subtle manipulation of some (or even one) but not all downstream events stemming from specific receptor activation. Additionally, a better understanding of functional selectivity would likely improve the drug delivery process: if compounds are screened through several functional assays appropriately designed to look for compounds exhibiting a high degree of selectivity, then many potential lead compounds might not be as frequently overlooked.     

Biotechnological applications of microbial bioconversions

Modern research has focused on the microbial transformation of a huge variety of organic compounds to obtain compounds of therapeutic and/or industrial interest. Microbial transformation is a useful tool for producing new compounds, as a consequence of the variety of reactions for natural products. This article describes the production of many important compounds by biotransformation. Emphasis is placed on reporting the metabolites that may be of special interest to the pharmaceutical and biotechnological industries, as well as the practical aspects of this work in the field of microbial transformations.     

Microalgae as sources of pharmaceuticals and other biologically active compounds

In the last decade the screening of microalgae, especially the cyanobacteria (blue-green algae), for antibiotics and pharmacologically active compounds has received ever increasing interest. A large number of antibiotic compounds, many with novel structures, have been isolated and characterised. Similarly many cyanobacteria have been shown to produce antiviral and antineoplastic compounds. A range of pharmacological activities have also been observed with extracts of microalgae, however the active principles are as yet unknown in most cases. Several of the bioactive compounds may find application in human or veterinary medicine or in agriculture. Others should find application as research tools or as structural models for the development of new drugs. The microalgae are particularly attractive as natural sources of bioactive molecules since these algae have the potential to produce these compounds in culture which enables the production of structurally complex molecules which are difficult or impossible to produce by chemical synthesis.     

Categorization of metabolome in bacterial systems

Analyses of biological databases such as those of genome, proteome, metabolome etc., have given insights in organization of biological systems. However, current efforts do not utilize the complete potential of available metabolome data. In this study, metabolome of bacterial systems with reliable annotations are analyzed and a simple method is developed to categorize pathways hierarchically, using rational approach. Ninety-four bacterial systems having for each ≥ 250 annotated metabolic pathways were used to identify a set of common pathways. 42 pathways were present in all bacteria which are termed as Core/Stage I pathways. This set of pathways was used along with interacting compounds to categorize pathways in the metabolome hierarchically. In each metabolome non-interacting pathways were identified including at each stage. The case study of Escherichia coli O157, having 433 annotated pathways, shows that 378 pathways interact directly or indirectly with 41 core pathways while 14 pathways are noninteracting. These 378 pathways are distributed in Stage II (289), Stage III (75), Stage IV (13) and Stage V (1) category. The approach discussed here allows understanding of the complexity of metabolic networks. It has pointed out that core pathways could be most ancient pathways and compounds that interact with maximum pathways may be compounds with high biosynthetic potential, which can be easily identified. Further, it was shown that interactions of pathways at various stages could be one to one, one to many, many to one or many to many mappings through interacting compounds. The granularity of the method discussed being high; the impact of perturbation in a pathway on the metabolome and particularly sub networks can be studied precisely. The categorizations of metabolic pathways help in identifying choke point enzymes that are useful to identify probable drug targets. The Metabolic categorizations for 94 bacteria are available at http://115.111.37.202/mpe/.     

Evaluation of the Biological Activity of Several Analogs of the Dopaminergic Neurotoxin 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine

Several analogs of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) were synthesized and screened for their capacity to be oxidized by monoamine oxidase (MAO-A or MAO-B) and their capacity to produce nigrostriatal dopaminergic neurotoxicity in mice. All of the compounds were relatively weak substrates for MAO-A but many of the compounds were found to be good substrates for MAO-B. Only three of the compounds, in addition to MPTP itself, were found to be neurotoxic. These were 1-methyl-4-cyclohexyl-1,2,3,6-tetrahydropyridine, 1-methyl-4-(2'-methylphenyl)-1,2,3,6-tetrahydropyridine and 1-methyl-4-(3'-methoxyphenyl)-1,2,3,6-tetrahydropyridine. All three of these neurotoxic compounds were found to be substrates for MAO-B; in contrast no compound was found to be neurotoxic that was not oxidized by MAO-B. The capacity of the compounds studied to be oxidized by MAO-B appears to be an important aspect of the neurotoxic process.     

河狸亲缘信息素的遗传力:遗传关系的信息是怎样编码的?

本研究利用几种亲缘关系对河狸 (Castorcanadensis)肛腺分泌物中的单个化合物和其整体组合的狭义遗传力进行了估算。使用气相色谱和质谱对河狸肛腺化合物进行定性和定量分析 ,发现了单个化合物的遗传力很低 ,但化合物的整体组合却显示有适度的遗传力。因此 ,我们认为亲缘关系的编码可能涉及多种化合物 ,并以数量和数字编码并用的方式进行     

人羧酯酶的研究进展

羧酯酶是一类可与有机磷化合物结合且活性受抑制的B－酯酶,分布很广,能水解许多羧酯类、酰胺类、硫酯类物质,其天然底物尚未清楚,故其生理功能仍在研究中,可能与脂质代谢,药物或毒物的生物转化有关．对羧酯酶的一级结构及基因序列的研究表明,羧酯酶是由许多生化特性不同的同工酶组成．     

In vitro bone marrow granulocyte-macrophage progenitor cultures in the assessment of hematotoxic potential of the new drugs

In pharmaceutical research, in vitro toxicity tests, for assessing the potential toxicity of new chemical entities are necessary in the early stages of the developmental process, when no information is available about the metabolism or even the target organ toxicity of the compounds to be tested. In vitro specific organ toxicity tests, such as the granulocyte-macrophage colony-forming unit (CFU-GM) clonogenic assay, are useful tools for predicting the adverse effects of new compounds on the blood-forming system, provided that some reference points are available, e.g., toxicological information about compounds belonging to the same chemical class and structure-activity relationship data. Furthermore, when no information is available about metabolism, the in vitro system should cover as many possibilities as possible, to avoid false positive or false negative results. In fact, while many compounds are metabolized to a variety of inactive chemical species, some undergo bioactivation to form more active metabolites. The addition of a metabolic activation system to the CFU-GM assay enables assessment of direct and metabolism-mediated toxicity. The regulatory agencies and industry value the concept of assays performed with and without metabolic activation, since they often have to take decisions about compounds with unknown mechanisms of action. CFU-GM assay, designed in this way, is an example of such a mechanism-naive assay. It has been suggested that, for new compounds, metabolites should be generated and tested both in the presence and in the absence of the parent compound itself, to identify the possible contribution of metabolites to the hematotoxicity observed, and to determine whether there is any synergistic or antagonistic effect between metabolites and the parent compound that might affect hematotoxicity in vivo. Various approaches can be used to obtain such information.     

The ecological significance of toxic nectar

Although plant-herbivore and plant-pollinator interactions have traditionally been studied separately, many traits are simultaneously under selection by both herbivores and pollinators. For example, secondary compounds commonly associated with herbivore defense have been found in the nectar of many plant species, and many plants produce nectar that is toxic or repellent to some floral visitors. Although secondary compounds in nectar and toxic nectar are geographically and phylogenetically widespread, their ecological significance is poorly understood. Several hypotheses have been proposed for the possible functions of toxic nectar, including encouraging specialist pollinators, deterring nectar robbers, preventing microbial degradation of nectar, and altering pollinator behavior. All of these hypotheses rest on the assumption that the benefits of toxic nectar must outweigh possible costs; however, to date no study has demonstrated that toxic nectar provides fitness benefits for any plant. Therefore, in addition to these adaptive hypotheses, we should also consider the hypothesis that toxic nectar provides no benefits or is tolerably detrimental to plants, and occurs due to previous selection pressures or pleiotropic constraints. For example, secondary compounds may be transported into nectar as a consequence of their presence in phloem, rather than due to direct selection for toxic nectar. Experimental approaches are necessary to understand the role of toxic nectar in plant-animal interactions.     

High-throughput ligand screening via preclustering and evolved neural networks

The pathway for novel lead drug discovery has many major deficiencies, the most significant of which is the immense size of small molecule diversity space. Methods that increase the search efficiency and/or reduce the size of the search space, increase the rate at which useful lead compounds are identified. Artificial neural networks optimized via evolutionary computation provide a cost and time-effective solution to this problem. Here, we present results that suggest preclustering of small molecules prior to neural network optimization is useful for generating models of quantitative structure-activity relationships for a set of HIV inhibitors. Using these methods, it is possible to prescreen compounds to separate active from inactive compounds or even actives and mildly active compounds from inactive compounds with high predictive accuracy while simultaneously reducing the feature space. It is also possible to identify "human interpretable" features from the best models that can be used for proposal and synthesis of new compounds in order to optimize potency and specificity.     

Liposomal systems as carriers for bioactive compounds

Since the revolutionary discovery that phospholipids can form closed bilayered structures in aqueous systems, the study of liposomes has become a very interesting area of research. The versatility and amazing biocompatibility of liposomes has resulted in their wide-spread use in many scientific fields, and many of their applications, especially in medicine, have yielded breakthroughs in recent decades. Specifically, their easy preparation and various structural aspects have given rise to broadly usable methodologies to internalize different compounds, with either lipophilic or hydrophilic properties. The study of compounds with potential biotechnological application(s) is generally related to evaluation and risk assessment of the possible cytotoxic or therapeutic effects of the compound under study. In most cases, undesirable side-effects are associated with an interaction of the liposome with the cell membrane and/or its absorption and subsequent interaction with a cellular biomolecule. Liposomal carrier systems have an unprecedented potential for delivering bioactive substances to specific molecular targets due to their biocompatibility, biodegradability and low toxicity. Liposomes are therefore considered to be an invaluable asset in applied biotechnology studies due to their potential for interaction with both hydrophilic and lipophilic compounds.     

Synthetic antimicrobial peptides as agricultural pesticides for plant-disease control

There is a need of antimicrobial compounds in agriculture for plant-disease control, with low toxicity and reduced negative environmental impact. Antimicrobial peptides are produced by living organisms and offer strong possibilities in agriculture because new compounds can be developed based on natural structures with improved properties of activity, specificity, biodegradability, and toxicity. Design of new molecules has been achieved using combinatorial-chemistry procedures coupled to high-throughput screening systems and data processing with design-of-experiments (DOE) methodology to obtain QSAR equation models and optimized compounds. Upon selection of best candidates with low cytotoxicity and moderate stability to protease digestion, anti-infective activity has been evaluated in plant-pathogen model systems. Suitable compounds have been submitted to acute toxicity testing in higher organisms and exhibited a low toxicity profile in a mouse model. Large-scale production can be achieved by solution organic or chemoenzymatic procedures in the case of very small peptides, but, in many cases, production can be performed by biotechnological methods using genetically modified microorganisms (fermentation) or transgenic crops (plant biofactories).     

Report of the IWGT working group on strategy/interpretation for regulatory in vivo tests II. Identification of in vivo-only positive compounds in the bone marrow micronucleus test

A survey conducted as part of an International Workshop on Genotoxicity Testing (IWGT) has identified a number of compounds that appear to be more readily detected in vivo than in vitro. The reasons for this property varies from compound to compound and includes metabolic differences; the influence of gut flora; higher exposures in vivo compared to in vitro; effects on pharmacology, in particular folate depletion or receptor kinase inhibition. It is possible that at least some of these compounds are detectable in vitro if a specific in vitro test is chosen as part of the test battery, but the 'correct' choice of test may not always be obvious when testing a compound of unknown genotoxicity. It is noted that many of the compounds identified in this study interfere with cell cycle kinetics and this can result in either aneugenicity or chromosome breakage. A decision tree is outlined as a guide for the evaluation of compounds that appear to be genotoxic agents in vivo but not in vitro. The regulatory implications of these findings are discussed.