Discovery Of Bioactive Molecules Research Articles

The cubane paradigm in bioactive molecule discovery: further scope, limitations and the cyclooctatetraene complement.

The cubane phenyl ring bioisostere paradigm was further explored in an extensive study covering a wide range of pharmaceutical and agrochemical templates, which included antibiotics (cefaclor, penicillin G) and antihistamine (diphenhydramine), a smooth muscle relaxant (alverine), an anaesthetic (ketamine), an agrochemical instecticide (triflumuron), an antiparasitic (benznidazole) and an anticancer agent (tamibarotene). This investigation highlights the scope and limitations of incorporating cubane into bioactive molecule discovery, both in terms of synthetic compatibility and physical property matching. Cubane maintained bioisosterism in the case of the Chagas disease antiparasitic benznidazole, although it was less active in the case of the anticancer agent (tamibarotenne). Application of the cyclooctatetraene (COT) (bio)motif complement was found to optimize benznidazole relative to the benzene parent, and augmented anticancer activity relative to the cubane analogue in the case of tamibarotene. Like all bioisosteres, scaffolds and biomotifs, however, there are limitations (e.g. synthetic implementation), and these have been specifically highlighted herein using failed examples. A summary of all templates prepared to date by our group that were biologically evaluated strongly supports the concept that cubane is a valuable tool in bioactive molecule discovery and COT is a viable complement.

Expanding the terpenoid kingdom.

Terpenoids are assembled from five-carbon (C5) units, which limits the available scaffold chemical space for the discovery of bioactive molecules. A combination of enzyme and metabolic engineering now enables biosynthesis of a plethora of non-natural C11 terpenoids.

Development of Endocyclic Control Elements for Peptide Macrocycles.

Synthetic methods that provide control over macrocycle conformation represent valuable tools for the discovery of bioactive molecules. Incorporation of heterocycles into cyclic peptides may offer a way to stabilize their solution conformations. Herein, we used N-(isocyanimino)triphenylphosphorane (Pinc) to install an oxadiazole ring and an endocyclic amine into peptide macrocycles. To elucidate the conformational effect of this constellation of functionalities, we performed synthesis, variable temperature NMR analysis, and NOE-based molecular dynamics simulation of a range of macrocycles in DMSO. As part of this study, we conducted experiments to compare macrocycle conformation in aqueous and DMSO solutions. The obtained solution structures suggest that the reduced amide bond/heterocycle (RAH) motif can stabilize macrocycle conformations in both water and DMSO, which addresses an enduring challenge in molecular design. The conformational effect of the RAH was used in an effort to mimic the biologically relevant secondary structure of MAdCAM-1. This resulted in the discovery of a novel α4β7 integrin antagonist.

N,N-Dialkyl-N′-Chlorosulfonyl Chloroformamidines in Heterocyclic Synthesis. Part XV. Some Unexpected Reactions with Anilines

N,N-Dimethyl-N′-chlorosulfonyl chloroformamidine 1a underwent reactions with various anilines. In addition to the benzo[e][1,2,4]thiadiazine dioxides 8, from 1,3-NCC bis-nucleophilic substitution and bis-anilino adducts 9, some unexpected products were formed, particularly when sterically hindered or electron-poor anilines were used. In these cases, products such as the [1,3,2,4,6]dithiatriazine 1,1,3,3-tetraoxides 17 and, on occasion, N,N,5-trimethyl-4-(arylimino)-4,5-dihydro-[1,3,5]triazin-2-amines 14 were produced in significant yields. Reaction of dichloride 1a with 3-bromoaniline afforded the unusual eight-membered-ring product 2,6-bis(3-bromophenyl)-3,7-bis(dimethylamino)-2H,6H-[1,5,2,4,6,8]dithiatetrazocine 1,1,5,5-tetraoxide 28, in addition to the dithiatriazine tetraoxide 17k. These uncommon heterocyclic structures are of interest for bioactive molecule discovery screening programs.

The impact of Andean Patagonian mycoflora in the search for new lead molecules.

Secondary metabolites from fungi have become a major source of chemical innovation in programs searching for lead molecules with bioactivities, especially over the last 50 years. In this review, we discuss the fundamental considerations in the discovery of molecules for agricultural and medicinal uses. This group of organisms possesses a strong potential for scientific and industrial communities. Recently, the incorporation of new technologies for the artificial cultivation of fungi and the use of better equipment to isolate and identify active metabolites has allowed the discovery of leading molecules for the design of new and safer drugs and pesticides. The geographical region including the Patagonian Andes mountains harbors a wide diversity of fungi, many of them still unknown and so far associated with Chilean-Argentinian Andean endemic forests. There have been very few chemical studies of the fungi located in this region. However, those few studies have allowed the discovery of new molecules. We argue that the richness of fungal biodiversity in this region offers an interesting source for the discovery of bioactive molecules for the basic and applied sciences.

Greek flora as a source of new anti-oxidant, anti-elastase, anti-collagenase and anti-hyaluronidase natural agents

In order to investigate new cosmetic ingredients of natural origin, 50 plant extracts obtained from Greek flora were screened for their capacity to scavenge free radicals and inhibit enzymes related to skin ageing. Degradation of extracellular matrix (ECM) has directly been linked to skin ageing and is correlated to increase in activity of enzymes such as elastase, collagenase and hyaluronidase. Elastin, collagen and hyaluronic acid decrease, leading to a loss of strength and flexibility in skin and formation of deep wrinkles. Also free radicals induce the activity of these enzymes [1,2]. Discovery of bioactive molecules which show both anti-oxidant and anti-ageing properties is the target of the present study. Anti-elastase, anti-collagenase and anti-hyaluronidase activities of 50 methanolic and ethyl acetate extracts were determined using spectrophotometric methods. Radical scavenging activity was determined by the ability of the extracts to scavenge DPPH and ABTS radicals. The majority of the samples especially the methanolic extracts showed high anti-oxidant capacity, e.g. Rosa damascena extract exhibited IC50 value at 47.6 µg/ml. In anti-elastase assay 8 extracts showed more than 50% inhibition at 100 µg/ml, in anti-collagenase assay 15 extracts showed more than 60% inhibiton at 100 µg/ml and in anti-hyaluronidase assay 8 extracts showed more than 80% inhibition at 300 µg/ml. The methanolic extracts of Sedum sediforme and Umbilicus horizontalis aerial parts inhibited elastase and hyaluronidase by more than 85%. Rosa damascena inhibited 80% of collagenase activity at 100 µg/ml. Antioxidant and enzyme inhibitory activities of the plant extracts suggest that they can restore skin elasticity and delay wrinkling process. Bioguided isolation process was performed in order to reveal the active secondary metabolites. In the case of Rosa damascena quercetin-3-O-rhamnoside, kaempferol-3-glucopyranoside, phenylethanol were proved to exhibit high anti-collagenase activity.

An in-depth snake venom proteopeptidome characterization: Benchmarking Bothrops jararaca

A large-scale proteomic approach was devised to advance the understanding of venom composition. Bothrops jararaca venom was fractionated by OFFGEL followed by chromatography, generating peptidic and proteic fractions. The latter was submitted to trypsin digestion. Both fractions were separately analyzed by reversed-phase nanochromatography coupled to high resolution mass spectrometry. This strategy allowed deeper and joint characterizations of the peptidome and proteome (proteopeptidome) of this venom. Our results lead to the identification of 46 protein classes (with several uniquely assigned proteins per class) comprising eight high-abundance bona fide venom components, and 38 additional classes in smaller quantities. This last category included previously described B. jararaca venom proteins, common Elapidae venom constituents (cobra venom factor and three-finger toxin), and proteins typically encountered in lysosomes, cellular membranes and blood plasma. Furthermore, this report is the most complete snake venom peptidome described so far, both in number of peptides and in variety of unique proteins that could have originated them. It is hypothesized that such diversity could enclose cryptides, whose bioactivities would contribute to envenomation in yet undetermined ways. Finally, we propose that the broad range screening of B. jararaca peptidome will facilitate the discovery of bioactive molecules, eventually leading to valuable therapeutical agents. Biological SignificanceOur proteopeptidomic strategy yielded unprecedented insights into the remarkable diversity of B. jararaca venom composition, both at the peptide and protein levels. These results bring a substantial contribution to the actual pursuit of large-scale protein-level assignment in snake venomics. The detection of typical elapidic venom components, in a Viperidae venom, reinforces our view that the use of this approach (hand-in-hand with transcriptomic and genomic data) for venom proteomic analysis, at the specimen-level, can greatly contribute for venom toxin evolution studies. Furthermore, data were generated in support of a previous hypothesis that venom gland secretory vesicles are specialized forms of lysosomes. Two testable hypotheses also emerge from the results of this work. The first is that a nucleobindin-2-derived protein could lead to prey disorientation during envenomation, aiding in its capture by the snake. The other being that the venom's peptidome might contain a population of cryptides, whose biological activities could lead to the development of new therapeutical agents.

Is elite sport a driver for medical advance?

In an era where the discovery and development of new medicine have hit its peak, areas of study that generate new thinking and related opportunity for medicine development are of great value. Society requires new medicine as an expanding ageing population in the developed world and the emergence of Western world diseases in the developing world place pressure on our global healthcare capability. Here we explore the possible meaning of elite sport to global, cutting edge medical advance. Why the elite sports industry might drive such advance? We believe that there are two broad areas to do this: 1. Discovery of bioactive molecules with medicine development potential based upon the exploration of the molecular basis of responses to exercise and physical activity and area of research endeavor known as mechanotransduction. This area of study has revealed the incredible potential for a range of naturally occurring molecules to maintain musculoskeletal health and has identified some of the key cell types responsible for orchestrating the beneficial responses. In particular, the bone resident osteocyte has been transformed from a little studies quiescent cell type into the foreman in charge of bone shape, size, and strength and also distant kidney function. 2. The clinical need generated by sport injuries in the elite competing population. Injury in this professional group has greater meaning then in the amateur sports person in terms of both earnings and career progression. The generation of novel medicine and therapies is of great value and includes the emerging clinical specialty of regenerative medicine. This specialty includes the use of cell-based therapies and is emerging fast. At its best, a cellbased therapy will not just treat a clinical condition; rather, it will cure it. Instead of requiring multiple doses over extended periods to control a clinical condition, one dose will cure the condition through the establishment of live cells in the tissues of need. The future holds medical promise and a little acknowledged role that elite sport plays important role in the realization of that promise might well represent a legitimate area for clinical therapy discovery.

Catalytic asymmetric hetero-Diels-Alder reactions of enones with isatins to access functionalized spirooxindole tetrahydropyrans: scope, derivatization, and discovery of bioactives.

The development of concise methods for the synthesis of functionalized small molecules is important in the search for new bioactive molecules. To contribute to this, we have developed oxa-hetero-Diels-Alder reactions of enones with isatins catalyzed by amine-based catalyst systems. Various spirooxindole tetrahydropyranones were synthesized either in enantiomerically enriched forms or as racemic forms depending on the catalyst system. The reaction products were further transformed at the ketone carbonyl group and the indole nitrogen. Using these reactions, functionalized spirooxindole tetrahydropyran derivatives with functional groups in four directions in a three-dimensional space were concisely obtained. From these synthesized compounds, an inhibitor of human ion channel Nav1.7 with μM-level activity was identified, indicating that the developed reaction methods are useful for providing molecules for the discovery of new biofunctional molecules.

Therapeutic Potential of Temperate Forage Legumes: A Review

The discovery of bioactive molecules from botanical sources is an expanding field, preferentially oriented to plants having a tradition of use in medicine and providing high yields and availability. Temperate forage legumes are Fabaceae species that include worldwide-important crops. These plants possess therapeutic virtues that have not only been used in veterinary and folk medicine, but have also attracted the interest of official medicine. We have examined here Medicago sativa (alfalfa), Trifolium pratense and T. repens (clovers), Melilotus albus and M. officinalis (sweet clovers), Lotus corniculatus (birdsfoot trefoil), Onobrychis viciifolia (sainfoin), Lespedeza capitata (roundhead lespedeza), and Galega officinalis (goat's rue). The phytochemical complexes of these species contain secondary metabolites whose pharmacological potentials deserve investigation. Major classes of compounds include alkaloids and amines, cyanogenic glycosides, flavonoids, coumarins, condensed tannins, and saponins. Some of these phytochemicals have been related to antihypercholesterolemia, antidiabetic, antimenopause, anti-inflammatory, antiedema, anthelmintic, and kidney protective effects. Two widely prescribed drugs have been developed starting from temperate forage legumes, namely, the antithrombotic warfarin, inspired from sweet clover's coumarin, and the antidiabetic metformin, a derivative of sainfoin's guanidine. Available evidence suggests that temperate forage legumes are a potentially important resource for the extraction of active principles to be used as nutraceuticals and pharmaceuticals.

Verminoside mediates life span extension and alleviates stress in Caenorhabditis elegans

The discovery of bioactive molecules modulating aging in living organism promotes development of natural therapeutics for curing age-related afflictions. The progression in age-related disorders can be attributed to increment in intracellular reactive oxygen species (ROS) and oxidative stress level. To this end, we isolated an iridoid verminoside (VMS) from Stereospermum suaveolens (Roxb.) DC. and evaluated its effect on Caenorhabditis elegans. The present study delineates VMS-mediated alteration of intracellular ROS, oxidative stress, and life span in C. elegans. The different tested doses of VMS (5 μM, 25 μM, and 50 μM) were able to enhance ROS scavenging and extend mean life span in C. elegans. The maximal life span extension was observed in 25 μM VMS, that is, 20.79% (P < 0.0001) followed by 9.84% (P < 0.0001) in 5 μM VMS and 8.54% (P < 0.0001) in 50 μM VMS. VMS was able to alleviate juglone-induced oxidative stress and enhanced thermotolerance in worms. The stress-modulating and ROS-scavenging potential of VMS was validated by increment in mean survival by 29.54% (P < 0.0001) in VMS-treated oxidative stress hypersensitive mev-1 mutant strain. Furthermore, VMS modulates expression of DAF-16 (a FoxO transcription factor) promoting stress resistance and longevity. Altogether, our results suggest that VMS attenuates intracellular ROS and stress (oxidative and thermal) level promoting longevity. The longevity and stress modulation can be attributed to VMS-mediated alterations in daf-16 expression which regulates insulin signaling pathway. This study opens doors for development of phytomolecule-based therapeutics for prolonging life span and managing age-related severe disorders.

A chemical ecogenomics approach to understand the roles of secondary metabolites in fungal cereal pathogens.

Secondary metabolites (SMs) are known to play important roles in the virulence and lifestyle of fungal plant pathogens. The increasing availability of fungal pathogen genome sequences and next-generation genomic tools have allowed us to survey the SM gene cluster inventory in individual fungi. Thus, there is immense opportunity for SM discovery in these plant pathogens. Comparative genomics and transcriptomics have been employed to obtain insights on the genetic features that enable fungal pathogens to adapt in individual ecological niches and to adopt the different pathogenic lifestyles. Here, we will discuss how we can use these tools to search for ecologically important SM gene clusters in fungi, using cereal pathogens as models. This ecological genomics approach, combined with genome mining and chemical ecology tools, is likely to advance our understanding of the natural functions of SMs and accelerate bioactive molecule discovery.

Discovery of new PPARγ agonists based on arylopeptoids

In this study we present the design, synthesis and biological evaluation of a small, first-generation library of small molecule aromatic amides based on the arylopeptoid skeleton. The compounds were efficiently synthesized using a highly convenient submonomer solid-phase methodology which potentially allows for access to great product diversity. The synthesized compounds were tested for their ability to activate peroxisome proliferator-activated receptors (PPARs) and they all acted as PPARγ agonists in the μM range spanning from 2.5- to 14.7-fold activation of the receptor. This is the first discovery of bioactive molecules based on the arylopeptoid architecture.

Emerging Strategies to Access Peptide Macrocycles from Genetically Encoded Polypeptides

Macrocyclic peptides have emerged as attractive molecular scaffolds for the development of chemical probes and therapeutics. In this synopsis, we highlight contemporary strategies to access peptide macrocycles from ribosomally produced polypeptides. Challenges that have been tackled in this area involve orchestrating the desired macrocyclization process in the presence of unprotected polypeptide precursors and expanding the functional space encompassed by these molecules beyond that of canonical amino acid structures. Applications of these methodologies for the discovery of bioactive molecules are also discussed.

Ursolic acid in cancer prevention and treatment: Molecular targets, pharmacokinetics and clinical studies

Discovery of bioactive molecules and elucidation of their molecular mechanisms open up an enormous opportunity for the development of improved therapy for different inflammatory diseases, including cancer. Triterpenoids isolated several decades ago from various medicinal plants now seem to have a prominent role in the prevention and therapy of a variety of ailments and some have already entered Phase I clinical trials. One such important and highly investigated pentacyclic triterpenoid, ursolic acid has attracted great attention of late for its potential as a chemopreventive and chemotherapeutic agent in various types of cancer. Ursolic acid has been shown to target multiple proinflammatory transcription factors, cell cycle proteins, growth factors, kinases, cytokines, chemokines, adhesion molecules, and inflammatory enzymes. These targets can potentially mediate the chemopreventive and therapeutic effects of ursolic acid by inhibiting the initiation, promotion and metastasis of cancer. This review not only summarizes the diverse molecular targets of ursolic acid, but also provides an insight into the various preclinical and clinical studies that have been performed in the last decade with this promising triterpenoid.

Strategies and Techniques for Multi-Component Drug Design from Medicinal Herbs and Traditional Chinese Medicine

Many common diseases like diabetes, cardiovascular disease, and cancer are caused or exacerbated by disparate physiological, pathological, environmental, and lifestyle factors. However, the chief aim of current drug discovery approaches is to search for single-entity drugs that interact with well-defined molecular targets (a single receptor or enzyme). The concept of multi-target drugs or multi-component therapy is gaining increased attention with the discovery that many diseases (like hypertension) are best treated by multi-drug or multi-target therapies. Traditional medicines, such as traditional Chinese medicine (TCM) and Indian Ayurveda, have been re-evaluated and are becoming important resources for the discovery of bioactive molecules with therapeutic effects and for designing multi-targets drugs. This article provides an overview of new strategies and techniques to design therapeutic regimes that comprise more than one active ingredient to produce synergistic effects by simultaneously interacting with multiple molecular targets. Advances in phytochemistry, high throughput screening, DNA sequencing, systems biology, and bioinformatics can reveal the chemical composition and molecular mechanisms of TCM and together provide a new template for the early stages of drug discovery. Meanwhile, clinical knowledge of TCM provides a promising framework for multi-component drug design. A renaissance of multi-component drug discovery inspired by traditional medicine is possible.

Significance of the zebrafish model in the discovery of bioactive molecules from nature

Natural products have immense therapeutic potential not only due to their structural variation and complexity but also due to their range of biological activities. Research based on natural products has led to the discovery of molecules with biomedical and pharmaceutical applications in different therapeutic areas like cancer, inflammation responses, diabetes, and infectious diseases. There are still several challenges to be overcome in natural product drug discovery research programs and the challenge of high throughput screening of natural substances is one of them. Bioactivity screening is an integral part of the drug discovery process and several in vitro and in vivo biological models are now available for this purpose. Among other well-reported biological models, the zebrafish (Danio rerio) is emerging as an important in vivo model for preclinical studies of synthetic molecules in different therapeutic areas. Zebrafish embryos have a short reproductive cycle, show ease of maintenance at high densities in the laboratory and administration of drugs is a straightforward procedure. The embryos are optically transparent, allowing for the visualization of drug effects on internal organs during the embryogenesis process. In this review, we illustrate the importance of using zebrafish as an important biological model in the discovery of bioactive drugs from natural sources.

Cefaclor

The cubane phenyl ring bioisostere paradigm was further explored in an extensive study covering a wide range of pharmaceutical and agrochemical templates, which included antibiotics (cefaclor, penicillin G) and antihistamine (diphenhydramine), a smooth muscle relaxant (alverine), an anaesthetic (ketamine), an agrochemical instecticide (triflumuron), an antiparasitic (benznidazole) and an anticancer agent (tamibarotene). This investigation highlights the scope and limitations of incorporating cubane into bioactive molecule discovery, both in terms of synthetic compatibility and physical property matching. Cubane maintained bioisosterism in the case of the Chagas disease antiparasitic benznidazole, although it was less active in the case of the anticancer agent (tamibarotenne). Application of the cyclooctatetraene (COT) (bio)motif complement was found to optimize benznidazole relative to the benzene parent, and augmented anticancer activity relative to the cubane analogue in the case of tamibarotene. Like all bioisosteres, scaffolds and biomotifs, however, there are limitations (e.g. synthetic implementation), and these have been specifically highlighted herein using failed examples. A summary of all templates prepared to date by our group that were biologically evaluated strongly supports the concept that cubane is a valuable tool in bioactive molecule discovery and COT is a viable complement.