Natural Product Drug Discovery Research Articles

Chemoprevention in gastrointestinal physiology and disease. Targeting the progression of cancer with natural products: a focus on gastrointestinal cancer.

The last decade has witnessed remarkable progress in the utilization of natural products for the prevention and treatment of human cancer. Many agents now in the pipeline for clinical trial testing have evolved from our understanding of how human nutritional patterns account for widespread differences in cancer risk. In this review, we have focused on many of these promising agents arguing that they may provide a new strategy for cancer control: natural products once thought to be only preventive in their mode of action now are being explored for efficacy in tandem with cancer therapeutics. Natural products may reduce off-target toxicity of therapeutics while making cancers more amenable to therapy. On the horizon is the use of certain natural products, in their own right, as mitigants of late-stage cancer, a new frontier for small-molecule natural product drug discovery.

Cell-based bioreporter assay coupled to HPLC micro-fractionation in the evaluation of antimicrobial properties of the basidiomycete fungus Pycnoporus cinnabarinus

Context Identification of bioactive components from complex natural product extracts can be a tedious process that aggravates the use of natural products in drug discovery campaigns. Objective This study presents a new approach for screening antimicrobial potential of natural product extracts by employing a bioreporter assay amenable to HPLC-based activity profiling. Materials and methods A library of 116 crude extracts was prepared from fungal culture filtrates by liquid–liquid extraction with ethyl acetate, lyophilised, and screened against Escherichia coli using TLC bioautography. Active extracts were studied further with a broth microdilution assay, which was, however, too insensitive for identifying the active microfractions after HPLC separation. Therefore, an assay based on bioluminescent E. coli K-12 (pTetLux1) strain was coupled with HPLC micro-fractionation. Results Preliminary screening yielded six fungal extracts with potential antimicrobial activity. A crude extract from a culture filtrate of the wood-rotting fungus, Pycnoporus cinnabarinus (Jacq.) P. Karst. (Polyporaceae), was selected for evaluating the functionality of the bioreporter assay in HPLC-based activity profiling. In the bioreporter assay, the IC50 value for the crude extract was 0.10 mg/mL. By integrating the bioreporter assay with HPLC micro-fractionation, the antimicrobial activity was linked to LC-UV peak of a compound in the chromatogram of the extract. This compound was isolated and identified as a fungal pigment phlebiarubrone. Discussion and conclusion HPLC-based activity profiling using the bioreporter-based approach is a valuable tool for identifying antimicrobial compound(s) from complex crude extracts, and offers improved sensitivity and speed compared with traditional antimicrobial assays, such as the turbidimetric measurement.

Preparative isolation of a cytotoxic principle of a forest mushroom Suillus luteus by sodium dodecyl sulfate based "salting-in" countercurrent chromatography.

In the course of screening new anticancer natural products, an edible forest mushroom Suillus luteus (L. Ex Franch). Gray was found to have potent cytotoxicity against several human cancer cells. However, the lipophilic sample made some countercurrent chromatography solvent systems emulsify, which caused difficulties in the separation of its cytotoxic components. Here, we found that the addition of an organic salt sodium dodecyl sulfate could efficiently shorten the settling time of the mushroom sample solutions by eliminating the emulsification of two-phase solvent systems. Moreover, we found that sodium dodecyl sulfate could play a new "salting-in" role and made the partition coefficients of the solutes decrease with the increased concentrations. Thus, a sodium dodecyl sulfate based salting-in countercurrent chromatography method has been successfully established for the first time for preparative isolation of a cytotoxic principle of the mushroom. The active component was identified as isosuillin. Whole results indicated that sodium dodecyl sulfate could be used as an efficient salting-in reagent for two-phase solvent system selection and targeted countercurrent chromatography isolation. It is very useful for current natural products isolation and drug discovery.

Palladium catalysed meta-C-H functionalization reactions.

The directing group assisted site selective C-H functionalization approach is having a continuous impact in the field of natural product synthesis, drug discovery and material sciences. While ortho-selective C-H functionalization has been studied extensively, meta-selective C-H functionalization has been less explored. Recent studies have highlighted the efficacy of palladium as a catalyst in activating the meta-C-H bond of arenes. Notably, the introduction of a novel palladium catalysed directing template based approach to activate the remote meta-position has created a revolutionary impact towards seeking a solution to this long standing challenge. In this review we summarize recent advances in palladium catalysed meta-C-H functionalization that have helped in creating a new outlook towards modern organic synthesis.

A New Golden Age of Natural Products Drug Discovery

The 2015 Nobel Prize in Physiology or Medicine has been awarded to William C. Campbell, Satoshi Omura, and Youyou Tu for the discovery of avermectins and artemisinin, respectively, therapies that revolutionized the treatment of devastating parasite diseases. With the recent technological advances, a New Golden Age of natural products drug discovery is dawning.

Targeting the Hedgehog Signaling Pathway with Small Molecules from Natural Sources

Natural products drug discovery has allowed the identification of many biologically active compounds from plants, microbial species, and marine organisms. A significant number of these compounds are currently used as drugs in therapeutic protocols, while other naturally occurring chemical entities gave suggestions for designing nonnatural-product derived drugs or have been modified in their structure to have semi-synthetic analogues. In the last decade, experimental evidence that correlated the aberrant activation of the Hedgehog (Hh) signaling pathway with many types of cancer, prompted the researchers to check natural compounds for their ability to modulate this signaling cascade. As a result, many compounds from natural sources showed inhibitory activity toward one or more of the Hh signaling pathway components, such as Smoothened (Smo) and the downstream effectors Gli. On the other hand, only a few natural compounds were able to stimulate the same pathway. This review reports a survey of the compounds extracted from natural sources (especially plants) that showed activity in inhibiting the Hh signaling machinery by interfering with its components.

Biosynthetic engineering and fermentation media development leads to gram-scale production of spliceostatin natural products in Burkholderia sp.

A key challenge in natural products drug discovery is compound supply. Hundreds of grams of purified material are needed to advance a natural product lead through preclinical development. Spliceostatins are polyketide-nonribosomal peptide natural products that bind to the spliceosome, an emerging target in cancer therapy. The wild-type bacterium Burkholderia sp. FERM BP-3421 produces a suite of spliceostatin congeners with varying biological activities and physiological stabilities. Hemiketal compounds such as FR901464 were the first to be described. Due to its improved properties, we were particularly interested in a carboxylic acid precursor analog that was first reported from Burkholderia sp. MSMB 43 and termed thailanstatin A. Inactivation of the iron/α-ketoglutarate-dependent dioxygenase gene fr9P had been shown to block hemiketal biosynthesis. However, a 4-deoxy congener of thailanstatin A was the main product seen in the dioxygenase mutant. We show here that expression of the cytochrome P450 gene fr9R is a metabolic bottle neck, as use of an l-arabinose inducible system led to nearly complete conversion of the 4-deoxy analog to the target molecule. By integrating fermentation media development approaches with biosynthetic engineering, we were able to improve production titers of the target compound >40-fold, going from the starting ~60mg/L to 2.5g/L, and to achieve what is predominantly a single component production profile. These improvements were instrumental in enabling preclinical development of spliceostatin analogs as chemotherapy.

The ascidian natural product eusynstyelamide B is a novel topoisomerase II poison that induces DNA damage and growth arrest in prostate and breast cancer cells.

As part of an anti-cancer natural product drug discovery program, we recently identified eusynstyelamide B (EB), which displayed cytotoxicity against MDA-MB-231 breast cancer cells (IC50 = 5 μM) and induced apoptosis. Here, we investigated the mechanism of action of EB in cancer cell lines of the prostate (LNCaP) and breast (MDA-MB-231). EB inhibited cell growth (IC50 = 5 μM) and induced a G2 cell cycle arrest, as shown by a significant increase in the G2/M cell population in the absence of elevated levels of the mitotic marker phospho-histone H3. In contrast to MDA-MB-231 cells, EB did not induce cell death in LNCaP cells when treated for up to 10 days. Transcript profiling and Ingenuity Pathway Analysis suggested that EB activated DNA damage pathways in LNCaP cells. Consistent with this, CHK2 phosphorylation was increased, p21CIP1/WAF1 was up-regulated and CDC2 expression strongly reduced by EB. Importantly, EB caused DNA double-strand breaks, yet did not directly interact with DNA. Analysis of topoisomerase II-mediated decatenation discovered that EB is a novel topoisomerase II poison.

Marine polysaccharide-based nanomaterials as a novel source of nanobiotechnological applications

Research on marine polysaccharide-based nanomaterials is emerging in nanobiotechnological fields such as drug delivery, gene delivery, tissue engineering, cancer therapy, wound dressing, biosensors, and water treatment. Important properties of the marine polysaccharides include biocompatibility, biodegradability, nontoxicity, low cost, and abundance. Most of the marine polysaccharides are derived from natural sources such as fucoidan, alginates, carrageenan, agarose, porphyran, ulvan, mauran, chitin, chitosan, and chitooligosaccharide. Marine polysaccharides are very important biological macromolecules that widely exist in marine organisms. Marine polysaccharides exhibit a vast variety of structures and are still under-exploited and thus should be considered as a novel source of natural products for drug discovery. An enormous variety of polysaccharides can be extracted from marine organisms such as algae, crustaceans, and microorganisms. Marine polysaccharides have been shown to have a variety of biological and biomedical properties. Recently, research and development of marine polysaccharide-based nanomaterials have received considerable attention as one of the major resources for nanotechnological applications. This review highlights the recent research on marine polysaccharide-based nanomaterials for biotechnological and biomedical applications.

LC-MS- and (1)H NMR Spectroscopy-Guided Identification of Antifungal Diterpenoids from Sagittaria latifolia.

Antifungal screening of small-molecule natural product libraries showed that a column fraction (CF) derived from the plant extract of Sagittaria latifolia was active against the fungal pathogen Cryptococcus neoformans. Dereplication analysis by liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy ((1)H NMR) indicated the presence of new compounds in this CF. Subsequent fractionation of the plant extract resulted in the identification of two new isopimaradiene-type diterpenoids, 1 and 2. The structures of 1 and 2 were determined by chemical methods and spectroscopic analysis as isopimara-7,15-dien-19-ol 19-O-α-l-arabinofuranoside and isopimara-7,15-dien-19-ol 19-O-α-l-(5'-acetoxy)arabinofuranoside, respectively. Compound 1 exhibited IC50 values of 3.7 and 1.8 μg/mL, respectively, against C. neoformans and C. gattii. Its aglycone, isopimara-7,15-dien-19-ol (3), resulting from acid hydrolysis of 1, was also active against the two fungal pathogens, with IC50 values of 9.2 and 6.8 μg/mL, respectively. This study demonstrates that utilization of the combined LC-MS and (1)H NMR analytical tools is an improved chemical screening approach for hit prioritization in natural product drug discovery.

ChemInform Abstract: The Chemistry and Bioactivity of Southern African Flora II: Flavonoids, Quinones and Minor Compound Classes

AbstractReview: 134 refs + subrefs.

Considerations of the chemical biology of microbial natural products provide an effective drug discovery strategy.

Conventional approaches to natural product drug discovery rely mainly on random searches for bioactive compounds using bioassays. These traditional approaches do not incorporate a chemical biology perspective. Searching for bioactive molecules using a chemical and biological rationale constitutes a powerful search paradigm. Here, the authors review recent examples of the discovery of bioactive natural products based on chemical and biological interactions between hosts and symbionts, and propose this method provides a more effective means of exploring natural chemical diversity and eventually of discovering new drugs.

Countercurrent Separation of Natural Products: An Update.

This work assesses the current instrumentation, method development, and applications in countercurrent chromatography (CCC) and centrifugal partition chromatography (CPC), collectively referred to as countercurrent separation (CCS). The article provides a critical review of the CCS literature from 2007 since our last review (J. Nat. Prod.2008, 71, 1489–1508), with a special emphasis on the applications of CCS in natural products research. The current state of CCS is reviewed in regard to three continuing topics (instrumentation, solvent system development, theory) and three new topics (optimization of parameters, workflow, bioactivity applications). The goals of this review are to deliver the necessary background with references for an up-to-date perspective of CCS, to point out its potential for the natural product scientist, and thereby to induce new applications in natural product chemistry, metabolome, and drug discovery research involving organisms from terrestrial and marine sources.

Discovery of novel bioactive natural product-like compounds based on diversity-enhanced reactions

Diversity-enhanced reaction (DER), a non-selectivity and non-specificity reaction, is proposed to increase the diversified chemical structures of natural products for drug discovery (Fig. 1). We have applied this method to quickly synthesize a number of BB1608-like derivatives (Scheme 1). 2 underwent DER to afford a mixture. Separation and derivatization provided 3 – 12, Compounds 3 – 12 were evaluated for their anticancer and antiviral activities. The development of more complex DER is in progress. [The work described in this paper was supported by HKBU Interdisciplinary Research Matching Scheme (RC-IRMS/12 – 13/03) and Natural Science Foundation of China (No. 21402166)].

Microbial genomics: New opportunities for natural product biosynthesis, engineering, and drug discovery

Microbial genomics: New opportunities for natural product biosynthesis, engineering, and drug discovery

LCMS-based hierarchal clustering as a method to assess biosynthetic relationships among bacteria

With the recent outpouring in whole genome sequencing technologies, natural product chemists now have greater access than ever before to the genomic information surrounding biosynthetic potential. The continued decrease in cost for whole genome sequencing holds great promise as a tool for prioritizing bacterial strains for drug discovery. Nonetheless, rapid methods to prioritize strains for discovery programs are still needed. We sought to investigate hierarchal clustering analysis (HCA) based on LCMS profiles as a method to evaluate metabolomic relationships among strains and examine how these relationships were reflected in genomes using whole genome analysis. To test this method, we analyzed a group of marine Streptomyces spp. using LCMS, and developed open-source workflows in R with XCMS to generate hierarchal clusters. We ensured clusters produced using R were comparable to clusters made using proprietary software. Trees from LCMS data were directly compared to 16S rDNA phylogenetic trees, and relationships between these clusters were investigated further using principal component analysis (PCA). A second group of Streptomyces spp. with whole genomes assembled were also analyzed by LCMS-HCA. The relationships identified based on metabolites were assessed in tandem with whole genome analysis. Overall, our LCMS-based HCA methods aim to assist the strain selection process for natural product drug discovery platforms, and in addition can offer an alternative “pre-selection” tool to guide future genomic analyses.

Marine natural products drug discovery from actinomycetes at fundacion MEDINA

Marine natural products drug discovery from actinomycetes at fundacion MEDINA

The value of central-African traditional medicine for lead finding: Some case studies

Ethnoparmaological relevance: One of the possible methodologies for the discovery of novel drugs is the screening of selected plant extracts for a broad array of pharmacological activities.Materials and Methods: The selection based on enthnomedicinal uses, combined with a follow-up of existing literature on the plants’ chemotaxonomic properties, would seem to be the most cost-effective strategy for finding active plant extracts. A bioassay-guided fractionation of the active extracts should subsequently lead to the isolation and identification of the active lead constituent(s).Results and Discussion: Taking into account the enormous number and the amazing structural diversity of the currently known plant constituents, one might hope that promising model compounds with new structures and/or novel mechanisms of action might be found. In order, however, to optimize such a natural product drug discovery methodology, dereplication and selectivity of activity should be included in the screening system. Dereplication by which known compounds can rapidly be identified from a partially purified mixture prevents a research group from wasting resources by rediscovering known compounds. The use of single-target specific bioassays such as tests on isolated enzymes or on receptor-binding, or multiple target functional bioassays on isolated organs or intact cells must allow at an early stage to isolate compounds with specific pharmacological properties.Conclusions: In this publication, several examples of bioassay-guided isolation and identification of pharmacologically active lead compounds from plants used in Central-African traditional medicine by our research group will be presented and discussed.

Analysis of Physicochemical Properties for Drugs of Natural Origin.

The impact of time, therapy area, and route of administration on 13 physicochemical properties calculated for 664 drugs developed from a natural prototype was investigated. The mean values for the majority of properties sampled over five periods from pre-1900 to 2013 were found to change in a statistically significant manner. In contrast, lipophilicity and aromatic ring count remained relatively constant, suggesting that these parameters are the most important for successful prosecution of a natural product drug discovery program if the route of administration is not focused exclusively on oral availability. An examination by therapy area revealed that anti-infective agents had the most differences in physicochemical property profiles compared with other areas, particularly with respect to lipophilicity. However, when this group was removed, the variation between the mean values for lipophilicity and aromatic ring count across the remaining therapy areas was again found not to change in a meaningful manner, further highlighting the importance of these two parameters. The vast majority of drugs with a natural progenitor were formulated for either oral and/or injectable administration. Injectables were, on average, larger and more polar than drugs developed for oral, topical, and inhalation routes.

Synthesis and evaluation of 8,4'-dideshydroxy-leinamycin revealing new insights into the structure-activity relationship of the anticancer natural product leinamycin.

Leinamycin (LNM, 1) is a novel antitumor antibiotic produced by Streptomyces atroolivaceus S-140 and features an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. The 1,3-dioxo-1,2-dithiolane moiety of LNM is essential for its antitumor activity via an episulfonium ion-mediated DNA alkylation upon reductive activation in the presence of cellular thiols. We recently isolated leinamycin E1 (LNM E1, 2) from an engineered strain S. atroolivaceus SB3033, which lacks the 1,3-dioxo-1,2-dithiolane moiety. Here we report the chemical synthesis of 8,4'-dideshydroxy-LNM (5) from 2 and determination of the cytotoxicity of 5 against selected cancer cell lines in comparison with 1; 5 exhibits comparable activity as 1 with the EC50 values between 8.21 and 275 nM. This work reveals new insight into the structure-activity relationship of LNM and highlights the synergy between metabolic pathway engineering and medicinal chemistry for natural product drug discovery.