New Directions for Neurodegenerative Disease Therapy: Using Chemical Compounds to Boost the Formation of Mutant Protein Inclusions

Neurodegenerative disease such as Huntington’s, Parkinson’s, and Alzheimer’sdiseases are marked by neuronal accumulation of toxic misfolded protein. Developingtherapies for these misfolding diseases requires finding chemical compounds that caneither clear toxic misfolded protein, or can protect neurons from their impact. Suchcompounds could not only provide the starting points for potential drugs, but could alsoprovide valuable research tools for untangling the complexities of the disease process.Until now, chemical screens for these diseases have focused on finding compoundsthat prevent aggregation of mutant protein. We recently published a compound, B2,which promotes the formation of large inclusions by mutant Huntingtin and α-synuclein,while rescuing some of the toxic effects of these proteins. As inclusions were longbelieved to be toxic to cells, this contradicts previous therapeutic approaches. At thesame time, the results support growing evidence for the protective effects of inclusions.In this review, we discuss these results, and place them in the context of ongoingtherapeutic discovery efforts for HD and other neurodegenerative diseases.     

Triggers and cues that activate antibiotic production by actinomycetes

Actinomycetes are a rich source of natural products, and these mycelial bacteria produce the majority of the known antibiotics. The increasing difficulty to find new drugs via high-throughput screening has led to a decline in antibiotic research, while infectious diseases associated with multidrug resistance are spreading rapidly. Here we review new approaches and ideas that are currently being developed to increase our chances of finding novel antimicrobials, with focus on genetic, chemical, and ecological methods to elicit the expression of biosynthetic gene clusters. The genome sequencing revolution identified numerous gene clusters for natural products in actinomycetes, associated with a potentially huge reservoir of unknown molecules, and prioritizing them is a major challenge for in silico screening-based approaches. Some antibiotics are likely only expressed under very specific conditions, such as interaction with other microbes, which explains the renewed interest in soil and marine ecology. The identification of new gene clusters, as well as chemical elicitors and culturing conditions that activate their expression, should allow scientists to reinforce their efforts to find the necessary novel antimicrobial drugs.     

Surface Chemicals Inform about Sex and Breeding Status in the Biparental Burying Beetle Nicrophorus vespilloides

The multicomponent nature of chemical cues and signals are not very well understood. One reason for the often found complexity of chemical blends might be that they provide multiple messages. Burying beetles which use vertebrate carcasses as food for their larvae and defend these carcasses against inter- and intraspecific competitors are able to recognise the sex and breeding status of conspecifics. Studies have shown that the chemical composition of cuticular lipids is correlated with sex and breeding status, but there is no definitive evidence that these chemicals function in recognition. In the present study, we performed behavioural bioassays to directly asses the role of chemical cues in the recognition system of the burying beetle Nicrophorus vespilloides . After finding a carcass, females were more tolerant of dead males than of females. The behaviour was reversed when a solvent extract from the opposite sex was applied. An earlier experiment had shown that females breeding on a carcass treat non-breeding males more aggressively than breeding ones. In the present study, we could trigger the same dichotomous behaviours by presenting a single elytron from a breeding and a non-breeding beetle. In an additional experiment, females tolerated the elytra of non-breeding beetles if we had first applied an extract from a breeding beetle to these elytra. Our study is the first behavioural proof that female burying beetles obtain multiple information from chemical cues.     

Statistical prediction of protein chemical interactions based on chemical structure and mass spectrometry data

MOTIVATION: Prediction of interactions between proteins and chemical compounds is of great benefit in drug discovery processes. In this field, 3D structure-based methods such as docking analysis have been developed. However, the genomewide application of these methods is not really feasible as 3D structural information is limited in availability. RESULTS: We describe a novel method for predicting protein-chemical interaction using SVM. We utilize very general protein data, i.e. amino acid sequences, and combine these with chemical structures and mass spectrometry (MS) data. MS data can be of great use in finding new chemical compounds in the future. We assessed the validity of our method in the dataset of the binding of existing drugs and found that more than 80% accuracy could be obtained. Furthermore, we conducted comprehensive target protein predictions for MDMA, and validated the biological significance of our method by successfully finding proteins relevant to its known functions. AVAILABILITY: Available on request from the authors.     

Experimental evidence for a hierarchy of mate- and host-induced cues in a fish ectoparasite, Argulus coregoni (Crustacea: Branchiura)

Argulus coregoni is an ectoparasite primarily infesting freshwater salmonids. Sexually reproducing parasites such as A. coregoni are confronted with a dilemma between finding a mate and the costs involved in doing so; if mating partners are unavailable on a host, by leaving to search for a mate on a new host, the parasite is exposed to risks such as predation and energy loss. The utilization of chemical cues could enhance the probability of finding a host and/or a suitable mating partner and thus decrease the level of costs associated with detachment from the host. In this study we constructed a Y-maze arena to determine if adult A. coregoni respond to mate- and host-related chemical cues. We also tested the directional response towards light, since it has been suggested that photic cues are the most important cues for juvenile A. coregoni locating a host. Our results showed that both sexes were attracted to light and fish odour. Free-swimming A. coregoni males responded to chemical cues produced by adult females but not vice versa. The hierarchy of these stimuli was analyzed by pitting the cues against one another in the Y-maze, showing that light was the most salient stimulus for both male and female parasites. Moreover, male parasites were more strongly attracted towards light and fish odour than female odour. In another experiment in a semi-natural environment, we examined whether the ability of A. coregoni males to detect female odour influences their host choice. Free-swimming males did not preferentially infest fish infected with female parasites over parasite-free fish. We suggest that a hierarchy of stimulus responses exists, whereby free-swimming parasites first respond to host-related signals and most dominantly to visual cues. However, cues connected to mate finding may become a priority for late adult stages and/or once the parasite has attached to the host.     

Structural Characterization and Chemical Classification of Some Bryophytes Found in Latvia

Bryophytes are the second largest taxonomic group in the plant kingdom; yet, studies conducted to better understand their chemical composition are rare. The aim of this study was to characterize the chemical composition of bryophytes common in Northern Europe by using elemental, spectral, and non‐destructive analytical methods, such as Fourier transform IR spectrometry (FT‐IR), solid‐phase ¹³C‐NMR spectrometry, and pyrolysis‐gas chromatography/mass spectrometry (Py‐GC/MS), for the purpose of investigating their chemotaxonomic relationships on the basis of chemical‐composition data. The results of all these analyses showed that bryophytes consist mainly of carbohydrates. Judging by FT‐IR spectra, the OH groups in combination of C? O groups were the most abundant groups. The ¹³C‐NMR spectra provided information on the presence of such compounds as phenolics and lipids. It was found that the amount of phenolic compounds in bryophytes is relatively small. This finding definitely confirmed the absence of lignin in the studied bryophytes. Cluster analysis was used to better understand differences in the chemical composition of bryophyte samples and to evaluate possible usage of these methods in the chemotaxonomy of bryophytes.     

Polyglutamine-mediated neurodegeneration: Use of chaperones as prevention strategy

Polyglutamine diseases are a class of inherited neurodegenerative disorders caused by the expansion of a polyglutamine tract within the respective proteins. Clinical studies have revealed that the forming of neuronal intranuclear inclusions by the disease protein is a common pathological feature of polyglutamine diseases. Although there has been considerable progress in understanding polyglutamine diseases, many questions regarding their mechanism are still unanswered. The finding that molecular chaperones are associated with ubiquitinated intranuclear inclusions clearly indicates a crucial role of molecular chaperones in the generation of these fatal diseases. Molecular and chemical chaperones have been found to be a good agent for suppressing many polyglutamine diseases in several animal models. In this review, I discuss the roles of the ubiquitin-proteasome pathway and molecular chaperones in the development of polyglutamine diseases and probable approach for the prevention of many of these fatal disorders using molecular chaperones as a therapeutic agent. Newly found chemical chaperones have been demonstrated to be potentially useful and could be used as a therapeutic strategy in preventing many versions of polyglutamine diseases.     

Effect of the mating plug on female chemical attractiveness and mating acceptance in a scorpion

After mating, females may experience a decline in sexual receptivity and attractiveness that may be associated with changes in the production and emission of sex pheromones. In some cases, these changes are produced by chemical substances or structures (e.g., mating plugs) produced by males as a strategy to avoid or reduce sperm competition. In scorpions, sex pheromones may be involved in finding potential mates and starting courtship. Here, we tested the hypothesis that the males of Urophonius brachycentrus, a species that produces a mating plug, use chemical communication (sex pheromones) to detect, localize, and discriminate females according to their mating status (virgin or inseminated), aided by chemical signaling. We also explored the effect of extracting of the mating plug on chemical communication and mating acceptance. We used Y‐maze olfactometers with different stimuli to analyze male choice and exploration time. To evaluate mating acceptance, we measured the attractiveness and receptivity of females of different mating status. We found that chemical communication occurs through volatile pheromones, but not contact pheromones. Males equally preferred sites with virgin or inseminated females with removed mating plug. In turn, females with these mating statuses were more attractive and receptive for males than inseminated females. This study suggests that the mating plug significantly affects female chemical attractiveness with an effect on volatile pheromones and decreasing sexual mating acceptance of females. The decline in the female's sexual receptivity is a complex process that may respond to several non‐exclusive mechanisms imposed by males and strategically modulated by females.     

New aspects and strategies for methane mitigation from ruminants

The growing demand for sustainable animal production is compelling researchers to explore the potential approaches to reduce emissions of greenhouse gases from livestock that are mainly produced by enteric fermentation. Some potential solutions, for instance, the use of chemical inhibitors to reduce methanogenesis, are not feasible in routine use due to their toxicity to ruminants, inhibition of efficient rumen function or other transitory effects. Strategies, such as use of plant secondary metabolites and dietary manipulations have emerged to reduce the methane emission, but these still require extensive research before these can be recommended and deployed in the livestock industry sector. Furthermore, immunization vaccines for methanogens and phages are also under investigation for mitigation of enteric methanogenesis. The increasing knowledge of methanogenic diversity in rumen, DNA sequencing technologies and bioinformatics have paved the way for chemogenomic strategies by targeting methane producers. Chemogenomics will help in finding target enzymes and proteins, which will further assist in the screening of natural as well chemical inhibitors. The construction of a methanogenic gene catalogue through these approaches is an attainable objective. This will lead to understand the microbiome function, its relation with the host and feeds, and therefore, will form the basis of practically viable and eco-friendly methane mitigation approaches, while improving the ruminant productivity.     

The strigolactone germination stimulants of the plant-parasitic Striga and Orobanche spp. are derived from the carotenoid pathway

The seeds of parasitic plants of the genera Striga and Orobanche will only germinate after induction by a chemical signal exuded from the roots of their host. Up to now, several of these germination stimulants have been isolated and identified in the root exudates of a series of host plants of both Orobanche and Striga spp. In most cases, the compounds were shown to be isoprenoid and belong to one chemical class, collectively called the strigolactones, and suggested by many authors to be sesquiterpene lactones. However, this classification was never proven; hence, the biosynthetic pathways of the germination stimulants are unknown. We have used carotenoid mutants of maize (Zea mays) and inhibitors of isoprenoid pathways on maize, cowpea (Vigna unguiculata), and sorghum (Sorghum bicolor) and assessed the effects on the root exudate-induced germination of Striga hermonthica and Orobanche crenata. Here, we show that for these three host and two parasitic plant species, the strigolactone germination stimulants are derived from the carotenoid pathway. Furthermore, we hypothesize how the germination stimulants are formed. We also discuss this finding as an explanation for some phenomena that have been observed for the host-parasitic plant interaction, such as the effect of mycorrhiza on S. hermonthica infestation.     

Aspartate-phobia of thermophiles as a reaction to deleterious chemical transformations

Prokaryotes growing at high temperatures have a high proportion of charged residues in their proteins to stabilize their 3D structure. By mining 175 disparate bacterial and archaeal proteomes we found that, against the general trend for charged residues, the frequency of aspartic acid residues decreases strongly as natural growth temperature increases. In search of the explanation, we hypothesized that the reason for such unusual correlation is the deleterious consequences of spontaneous chemical transformations of aspartate at high temperatures. Our subsequent statistical analysis supported this hypothesis. This finding reveals that organisms have likely adapted to high temperatures by minimizing the harmful consequences of spontaneous chemical transformations.     

Recent advances in drug design methods: Where will they lead?

Drug design methods have made significant new advances over the last ten years, mainly in the areas of molecular modelling. In more recent times important developments in theory have led to a different type of modelling becoming possible, the so-called de novo or automated design algorithms. In this new method the programs perform much of the chemist's thinking, in finding appropriately sized chemical groups to fit into a target site. However this is a combinatoric problem which has no general analytical solution; it is ripe for optimization. Other advances, such as combinatorial chemical synthesis and screening, will dramatically influence the search for new lead structures for target sites, which at present are poorly understood. Already these methods are being applied to peptide libraries. Peptides do not make good drug compounds because of their poor bioavailability; further, their flexibility reduces their affinity. In some cases peptide backbones can be removed and replaced with rigid non-peptide scaffolds.     

Natural compounds with important medical potential found in Helleborus sp.

Helleborus (family Ranunculaceae) are well-known as ornamental plants, but less known for their therapeutic benefits. Over the past few years, Helleborus sp. has become a subject of interest for phytochemistry, pharmacology and other medical research areas. On the basis of their usefulness in traditional medicine, it was assumed that their biochemical profile could be a source of metabolites with the potential to overcome critical medical issues. There are studies involving natural extracts from these species which demonstrate that Helleborus plants are a valuable source of chemical compounds with great medical potential. Some phytochemicals produced by these species have been separated and identified a few decades ago: hellebrin, deglucohellebrin, 20-hydroxyecdysone and protoanemonin. Lately, many other active compounds have been reported and considered as promising remedies for severe diseases such as cancer, ulcer, diabetes and also for common medical problems such as toothache, eczema, low immunity and arthritis. This paper is an overview of the Helleborus genus focusing on some recentlydiscovered compounds and their potential for finding new drugs and useful biochemicals derived from these species.     

Reaction of phenylglyoxal and (p-hydroxyphenyl) glyoxal with arginines and cysteines in the alpha subunit of tryptophan synthase

The alpha subunit of tryptophan synthase from Escherichia coli is inactivated by phenylglyoxal and by (p-hydroxyphenyl)glyoxal. The use of these chemical modification reagents to determine the role of arginyl residues in the alpha subunit of tryptophan synthase has been complicated by our finding that these reagents react with sulfhydryl groups of the alpha subunit, as well as with arginyl residues. Analyses of the data for incorporation of phenyl[2-14C]glyoxal, for inactivation, and for sulfhydryl modification in the presence and absence of indole-3-glycerol phosphate indicate that two sulfhydryl groups and one arginine are essential for the activity. Our finding that the substrate protects the single essential arginyl residue but not the two sulfhydryl groups is consistent with the observed kinetics of partial protection by substrate or by a substrate analogue, indole-3-propanol phosphate. In contrast to phenylglyoxal, (p-hydroxyphenyl)glyoxal modifies two to three sulhydryl groups that are not protected by indole-3-glycerol phosphate and modifies none of the arginyl residues that are modified by phenylglyoxal.     

Recent advances in oligonucleotide synthesis and their applications

Short synthetic oligonucleotides are finding wide variety of applications in area of genomics and medicinal chemistry. Since the isolation of nucleic acids to the mapping of human genome, chemical synthesis of nucleic acids has undergone tremendous advancements. Further improvements in this area such as, introduction of high throughput synthesizers, better coupling reagents, improved polymer supports, newer sets of protecting groups for exocyclic amino groups of nucleic bases and introduction of universal polymer supports have completely revolutionized the entire field of nucleic acids chemistry. Most of these developments have been targeted to assemble these molecules more efficiently in a cost-effective manner and rapidly. Preparation of oligonucleotide conjugates has further helped in identifying the newer areas of their applications. A number of conjugates with biological and abiological ligands have been discussed in this article along with their possible wide spectrum of applications. Recently developed microarray technology, which refers to attachment of short oligonucleotides on a solid/polymeric surface, has proved to be useful for screening of genetic mutations, study of polymorphism, as diagnostics, etc. The major developments in these areas are presented in the review.     

Does chemical defence increase niche space? A phylogenetic comparative analysis of the Musteloidea

Avoidance of predation can impose opportunity costs on prey species that use behavioural avoidance strategies to evade detection. An animal that spends much time hiding or remaining immobile, for example, may have less time for other important activities such as foraging or finding mates. Here we examine the idea that the evolution of chemical defence may act to release prey from these constraints, freeing defended prey to exploit their habitats more effectively, and increasing their niche space. We tested this hypothesis using comparative methods on a mammal group containing both chemically defended and non-defended species: Musteloidea. We found that defended species had a more omnivorous diet and were more likely to be active during both day and night than non-defended species. We also found that chemically defended species were less likely to be strictly diurnal or to show sexual size dimorphism, and had earlier maturing females and a shorter lifespan than non-defended species. Taken together, our results support the hypothesis that chemical defence increases the niche space available to a species. More generally, this also supports recent suggestions that strategies taken to avoid natural enemies can have important effects on diverse components of life history.     

Intragroup and intragenomic conflict over chemical defense against predators

Insects are often chemically defended against predators. There is considerable evidence for a group‐beneficial element to their defenses, and an associated potential for individuals to curtail their own investment in costly defense while benefitting from the investments of others, termed “automimicry.” Although females in chemically defended taxa often lay their eggs in clusters, leading to siblings living in close proximity, current models of automimicry have neglected kin‐selection effects, which may be expected to curb the evolution of such selfishness. Here, we develop a general theory of automimicry that explicitly incorporates kin selection. We investigate how female promiscuity modulates intragroup and intragenomic conflicts overinvestment into chemical defense, finding that individuals are favored to invest less than is optimal for their group, and that maternal‐origin genes favor greater investment than do paternal‐origin genes. We translate these conflicts into readily testable predictions concerning gene expression patterns and the phenotypic consequences of genomic perturbations, and discuss how our results may inform gene discovery in relation to economically important agricultural products.     

Vibrations as a novel signal for host location by parasitic nematodes

Nematodes are known to parasitise all major invertebrate groups in soils, and it has been assumed that their host finding relies on attraction to chemical cues. We studied movement of three species of insect-parasitic nematodes, Steinernema carpocapsae, Steinernema feltiae and Heterorhabditis megidis in response to chemical and vibrational cues. All species showed strong, significant taxes towards the vibrations. We also show that in soils, the utility of chemical cues as attractants is substantially reduced by the presence of organic matter.     

Oxidation of carboxyamidomethyl cysteine may add complexity to protein identification

Protein identification by interrogation of databases requires a comprehensive compilation of modified amino acids forms. Here, we describe the chemical oxidation of carboxyamidomethyl cysteine to the sulfoxide and sulfone forms, species that may add more complexity to peptide analyses. They can be easily distinguished by tandem mass spectrometry (MS/MS) due to their characteristic pattern of side chain neutral eliminations either from the parent ion or ion series that generate dehydroalanine as detected by MS(3). This finding was supported by the MS(n) spectra recorded for a peptide isolated from a mixture of tryptic peptides and for a derivatized/oxidized synthetic peptide with a different sequence. These modifications and their diagnostic neutral losses should be included in the list of chemical modifications and in algorithms designed for the automatic sequencing of peptides and database searching.     

Tetrazine ligation for chemical proteomics

Determining small molecule—target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition. Among 20 different bioorthogonal reactions, tetrazine ligation has been spotlighted as the most advanced bioorthogonal chemistry because of their extremely faster kinetics and higher specificity than others. Therefore, tetrazine ligation has a tremendous potential to enhance the proteomic research. This review highlights the current status of tetrazine ligation reaction as a molecular tool for the chemical proteomics.