Secondary metabolism: regulation and role in fungal biology

Filamentous fungi produce a diverse array of secondary metabolites--small molecules that are not necessary for normal growth or development. Secondary metabolites have a tremendous impact on society; some are exploited for their antibiotic and pharmaceutical activities, others are involved in disease interactions with plants or animals. The availability of fungal genome sequences has led to an enhanced effort at identifying biosynthetic genes for these molecules. Genes that regulate production of secondary metabolites have been identified and a link between secondary metabolism, light and sexual/asexual reproduction established. However, the role of secondary metabolites in the fungi that produce them remains a mystery. Many of these fungi live saprophytically in the soil and such molecules may provide protection against other inhabitants in this ecological niche.     

Bio-informatic trends for the determination of miRNA-target interactions in mammals

MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate mRNAs through a sequence-specific mechanism. By virtue of their structure and mechanism of action, computational methods have been devised to investigate the encoding of miRNA genes and the targets of miRNA action. A variety of assumptions have predicated the implementation of these various computational solutions. Evolutionary sequence conservation, secondary structure, and folding energetics are some of the assumptions that have been used. The success of these different computational solutions has been evaluated for both elucidation of new miRNAs and deducing targets of miRNA action. While the focus is on search techniques for new miRNAs, we have compared the programs miRseeker, miRScan, PalGrade, ProMiR, and miRAlign as examples of implementation of these techniques. For these programs, a benchmark comparison between theoretical estimation and actual identification is possible. We have also compared the target prediction programs TargetScanS, PicTar, DIANA-microT, miRanda, and RNAhybrid. However, it is difficult to rigorously assess the benchmark performance of these programs due to the difficulty in confirming their theoretical predictions.     

Improving success rates for lead generation using affinity binding technologies

Affinity technologies have been applied at several stages of the drug discovery process, ranging from target identification and purification to the identification of preclinical candidates. The detection of ligand-macromolecule interactions in lead discovery is the best studied and most powerful of these techniques. Although affinity methods have been in widespread use for about a decade, only recently have many reports emerged on their utility. Primary affinity screens of large libraries of small molecules or fragments have begun to produce results for challenging targets. Furthermore, in secondary assays affinity methods are opening new avenues to tackle important medicinal chemistry tasks.     

Autoantigens as substrates for apoptotic proteases: implications for the pathogenesis of systemic autoimmune disease

Systemic autoimmune diseases are a genetically complex, heterogeneous group of diseases in which the immune system targets a diverse, but highly specific group of intracellular autoantigens. The clustering and marked concentration of these molecules in the surface blebs of apoptotic cells, and their modification by apoptosis-specific proteolytic cleavage and/or phosphorylation at these sites, has focused attention on a unique apoptotic setting as the potential initiating stimulus for systemic autoimmunity. This apoptotic event is likely to (i) occur in a microenvironment containing high concentrations of the targeted antigens, (ii) be pro-immune in nature (e.g. viral infection), and (iii) allow suprathreshold concentrations of antigen with non-tolerized structure (either novel fragments, post-translational modifications, or complexes) to enter the class II processing pathway and initiate a primary immune response. Defective clearance or reduced anti-inflammatory consequences of apoptotic material may be important susceptibility factors in this group of diseases. Once the primary immune response to apoptotic antigens has been initiated, other apoptotic events (occurring in the course of homeostasis or damage) may stimulate the secondary immune response with less stringency, resulting in flares.     

Additional acetyl cholinesterase inhibitory property of diaryl pyrazoline derivatives

MAO-B and AChE are the two validated targets for Alzheimer’s disease. In pursuit of a single molecule hitting both the targets, we explored a set of previously reported extremely potent MAO-B selective inhibitors, for their additional AChE inhibitory activity. We performed molecular docking studies that formed the basis for in vitro enzyme assay, and provided necessary insights into their binding mode. Most of the compounds were found active at nano molar range, and are consistent with the docking results. The identified dual acting lead molecules may provide the basis for further exploring these chemical moieties.     

Designed molecules that fold to mimic protein secondary structures

Molecules that fold to mimic protein secondary structures have emerged as important targets of bioorganic chemistry. Recently, a variety of compounds that mimic helices, turns, and sheets have been developed, with notable advances in the design of beta-peptides that mimic each of these structures. These compounds hold promise as a step toward synthetic molecules with protein-like properties and as drugs that block protein-protein interactions.     

Microbial technologies for the discovery of novel bioactive metabolites

Soil microbes represent an important source of biologically active compounds. These molecules present original and unexpected structure and are selective inhibitors of their molecular targets. At Biosearch Italia, discovery of new bioactive molecules is mostly carried out through the exploitation of a proprietary strain collection of over 50000 strains, mostly unusual genera of actinomycetes and uncommon filamentous fungi. A critical element in a drug discovery based on microbial extracts is the isolation of unexploited groups of microorganisms that are at the same time good producers of secondary metabolites. Molecular genetics can assist in these efforts. We will review the development and application of molecular methods for the detection of uncommon genera of actinomycetes in soil DNA and for the rapid dereplication of actinomycete isolates. The results indicate a substantial presence in many soils of the uncommon genera and a large diversity of isolated actinomycetes. However, while uncommon actinomycete strains may provide an increased chance of yielding novel structures, their genetics and physiology are poorly understood. To speed up their manipulation, we have developed vectors capable of stably maintaining large segments of actinomycete DNA in Escherichia coli and of integrating site specifically in the Streptomyces genome. These vectors are suitable for the reconstruction of gene clusters from smaller segment of cloned DNA, the preparation of large-insert libraries from unusual actinomycete strains and the construction of environmental libraries.     

Natural products against hematological malignancies and identification of their targets

Naturally occurring molecules derived from higher plants, animals, microorganisms and minerals play an important role in the discovery and development of novel therapeutic agents. The identification of molecular targets is of interest to elucidate the mode of action of these compounds, and it may be employed to set up target-based assays and allow structure-activity relationship studies to guide medicinal chemistry efforts toward lead optimization. In recent years, plant-derived natural compounds possessing potential anti-tumor activities have been garnering much interest and efforts are underway to identify their molecular targets. Here, we attempt to summarize the discoveries of several natural compounds with activities against hematological malignancies, such as adenanthin, oridonin, gambogic acid and wogonoside, the identification of their targets, and their modes of actions.     

Isolation of anti-MISIIR scFv molecules from a phage display library by cell sorter biopanning

While cell surface antigens represent the most common targets for antibody-based cancer therapy, isolation of new antibodies specific for these targets from single-chain Fv phage display libraries has been hindered by limitations associated with traditional selection techniques. Solid phase panning is often associated with conformational changes to the target protein due to its immobilization on plastic tubes that can limit the ability of the isolated scFv to bind to conformational epitopes and solution panning methods require the use of secondary tags that often mask desired sequences and create unintended epitopes. Commonly utilized cell-based panning methods typically yield a panel of single-chain Fv (scFv) molecules that are specific for numerous cell surface antigens, often obscuring the desired clones. Here, we describe a novel cell sorter-based system to isolate single-chain Fv molecules specific for defined antigen targets expressed on stably-transformed mammalian cells. We employed these methods to isolate promising scFv clones that bind specifically to the Müllerian inhibiting substance type II receptor, a cell surface ovarian cancer antigen that has proven to be a difficult target for selection strategies.     

Bile acids: From digestion to cancers

Bile acids (BAs) are cholesterol metabolites that have been extensively studied these last decades. BAs have been classified in two groups. Primary BAs are synthesized in liver, when secondary BAs are produced by intestinal bacteria. Recently, next to their ancestral roles in digestion and fat solubilization, BAs have been described as signaling molecules involved in many physiological functions, such as glucose and energy metabolisms. These signaling pathways involve the activation of the nuclear receptor FXRα or of the G-protein-coupled receptor TGR5. These two receptors have selective affinity to different types of BAs and show different expression patterns, leading to different described roles of BAs. It has been suggested for long that BAs could be molecules linked to tumor processes. Indeed, as many other molecules, regarding analyzed tissues, BAs could have either protective or pro-carcinogen activities. However, the molecular mechanisms responsible for these effects have not been characterized yet. It involves either chemical properties or their capacities to activate their specific receptors FXRα or TGR5. This review highlights and discusses the potential links between BAs and cancer diseases and the perspectives of using BAs as potential therapeutic targets in several pathologies.     

Analytical approaches to investigate protein–pesticide adducts

Organophosphorus pesticides primarily elicit toxicity via their common covalent adduction of acetylcholinesterase (AChE), but pesticide binding to additional sensitive secondary targets may also compromise health. We have utilised tritiated-diisopropylfluorophosphate (³H-DFP) binding to quantify the levels of active immune and brain tissue serine hydrolases, and visualise them using autoradiography after protein separation by one-dimensional and two-dimensional techniques. Preincubation of protein extracts with pesticide in vitro or dosing of rats with pesticide in vivo was followed by ³H-DFP radiolabelling. Pesticide targets were identified by a reduction in ³H-DFP radiolabelling relative to controls, and characterised by their tissue presence, molecular weight, and isoelectric point. Conventional column chromatography was employed to enrich pesticide targets to enable their further characterisation, and/or identification by mass spectrometry. The major in vivo pesticide targets characterised were 66 kDa, serum albumin, and 60 kDa, likely carboxylesterase 1, both of which displayed differential pesticide binding character under conditions producing approximately 30% tissue AChE inhibition. The characterisation and identification of sensitive pesticide secondary targets will enable an evaluation of their potential contribution to the ill health that may arise from chronic low-dose pesticide exposures. Additionally, secondary targets may provide useful biomonitors and/or bioscavengers of pesticide exposures.     

The Yin and Yang of bone morphogenetic proteins in cancer

Bone morphogenetic proteins (BMPs) were first studied as growth factors or morphogens of the transforming growth factor-beta superfamily. These growth molecules, originally associated with bone and cartilage development, are now known to play an important role in morphogenesis and homeostasis in many other tissues. More recently, significant contributions from BMPs, their receptors, and interacting molecules have been linked to carcinogenesis and tumor progression. On the other hand, BMPs can sometimes function as a tumor suppressor. Our report highlights these new roles in the pathogenesis of cancer that may suggest novel targets for therapeutic intervention.     

Indel-based targeting of essential proteins in human pathogens that have close host orthologue(s): discovery of selective inhibitors for Leishmania donovani elongation factor-1alpha

We propose a novel strategy for selective targeting of essential pathogen proteins that contain sizable indels (insertions/deletions) in their sequences compared with their host orthologues. This approach has been tested on elongation factor-1alpha (EF-1alpha) from the protozoan pathogen Leishmania donovani. Leishmania EF-1alpha is 82% identical to the corresponding human orthologue, but possesses a 12 aminoacid sequence deletion compared with human EF-1alpha. We used this indel-differentiated region to design small molecules that selectively bind to leishmania EF-1alpha and not to the human protein. Three unrelated molecules were identified with the capacity to inhibit protein synthesis in leishmania by up to 75% while exhibiting no effect on human protein translation. These candidates may serve as prototypes for future development of antiprotozoan therapeutics. More generally, these findings provide a basis for a novel drug design platform. This platform targets essential pathogen proteins that are highly conserved across species, and consequently would not typically be considered to be conventional drug targets. We anticipate that such indel-directed targeting of essential proteins in microbial pathogens may help address the growing problem of antibiotic resistance.     

Tetrodecamycin: An unusual and interesting tetronate antibiotic

The tetrodecamycins are a group of secondary metabolites that are characterized by the presence of a tetronate ring in their structure. Originally discovered for their antibiotic activity against Photobacterium damselae ssp. piscicida, the causative agent of pseudotuberculosis in fish, this family of molecules has also been shown to have potent antibiotic activity against methicillin-resistant Staphylococcus aureus. Due to their small size and highly cyclized nature, they represent an unusual member of the much larger group of bioactive molecules called the tetronates. Herein, we review what is known about the mechanism of action of these molecules and also present a hypothesis for their biosynthesis. A deeper understanding of the tetrodecamycins will provide a more holistic view of the tetronate-family, provide new chemical probes of bacterial biology, and may provide therapeutic lead molecules.     

Eukaryotic interference with homoserine lactone-mediated prokaryotic signalling.

Acylated homoserine lactones (AHLs) play a widespread role in intercellular communication among bacteria. The Australian macroalga Delisea pulchra produces secondary metabolites which have structural similarities to AHL molecules. We report here that these metabolites inhibited AHL-controlled processes in prokaryotes. Our results suggest that the interaction between higher organisms and their surface-associated bacteria may be mediated by interference with bacterial regulatory systems.     

Comparisons of large subunit rRNAs reveal some eukaryote-specific elements of secondary structure

All large rRNAs possess a common core of secondary structure. However, large variations in the size of the molecule have arisen during evolution, which are accommodated over a dozen rapidly evolving domains. Most of the enlargement of the eukaryotic molecules (as compared to prokaryotes) is in fact restricted over only two of these divergent domains, which are dramatically expanded in vertebrates. We have derived secondary structure models for these two domains through a systematic comparison of all the pro- and eukaryotic sequences published so far. Within each of these domains, a subset of secondary structure elements which are specific to eukaryotes is detected. Archaebacterial-specific secondary structures can also be identified which appear to be maintained through a strong selective constraint. The relative preservation of such group-specific structures raises the issue of their potential involvement in some diversification of ribosomal functions among the three fundamental phylogenetic groups, eubacteria, archaebacteria and eukaryotes. We also show that eukaryotic ribosomal RNAs are subjected, over their entire length, to a unique type of compositional constraint which may largely differ among the major eukaryotic taxa.