AfroDb: a select highly potent and diverse natural product library from African medicinal plants

Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We assess the bioactivity and "drug-likeness" of a relatively small but structurally diverse dataset (containing >1,000 compounds) from African medicinal plants, which have been tested and proven a wide range of biological activities. The geographical regions of collection of the medicinal plants cover the entire continent of Africa, based on data from literature sources and information from traditional healers. For each isolated compound, the three dimensional (3D) structure has been used to calculate physico-chemical properties used in the prediction of oral bioavailability on the basis of Lipinski's "Rule of Five". A comparative analysis has been carried out with the "drug-like", "lead-like", and "fragment-like" subsets, as well as with the Dictionary of Natural Products. A diversity analysis has been carried out in comparison with the ChemBridge diverse database. Furthermore, descriptors related to absorption, distribution, metabolism, excretion and toxicity (ADMET) have been used to predict the pharmacokinetic profile of the compounds within the dataset. Our results prove that drug discovery, beginning with natural products from the African flora, could be highly promising. The 3D structures are available and could be useful for virtual screening and natural product lead generation programs.

Marine-derived Aspergillus species as a source of bioactive secondary metabolites

This report reviews biologically active secondary metabolites from marine-derived members of the fungal genus Aspergillus. Pharmacological activities and biological roles of the secondary metabolites from marine-derived Aspergillus spp. were addressed in respect of pharmaceutical potential.

High-resolution MS, MS/MS, and UV database of fungal secondary metabolites as a dereplication protocol for bioactive natural products

A major problem in the discovery of new biologically active compounds from natural products is the reisolation of known compounds. Such reisolations waste time and resources, distracting chemists from more promising leads. To address this problem, dereplication strategies are needed that enable crude extracts to be screened for the presence of known compounds before isolation efforts are initiated. In a project to identify anticancer drug leads from filamentous fungi, a significant dereplication challenge arises, as the taxonomy of the source materials is rarely known, and, thus, the literature cannot be probed to identify likely known compounds. An ultraperformance liquid chromatography-photodiode array-high-resolution tandem mass spectrometric (UPLC-PDA-HRMS-MS/MS) method was developed for dereplication of fungal secondary metabolites in crude culture extracts. A database was constructed by recording HRMS and MS/MS spectra of fungal metabolites, utilizing both positive- and negative-ionization modes. Additional details, such as UV-absorption maxima and retention times, were also recorded. Small-scale cultures that showed cytotoxic activities were dereplicated before engaging in the scale-up or purification processes. Using these methods, approximately 50% of the cytotoxic extracts could be eliminated from further study after the confident identification of known compounds. The specific attributes of this dereplication methodology include a focus on bioactive secondary metabolites from fungi, the use of a 10 min chromatographic method, and the inclusion of both HRMS and MS/MS data.

Use of diffusion-ordered NMR spectroscopy and HPLC-UV-SPE-NMR to identify undeclared synthetic drugs in medicines illegally sold as phytotherapies

The informal (and/or illegal) e-commerce of pharmaceutical formulations causes problems that governmental health agencies find hard to control, one of which concerns formulas sold as natural products. The purpose of this work was to explore the advantages and limitations of DOSY and HPLC-UV-SPE-NMR. These techniques were used to identify the components of a formula illegally marketed in Brazil as an herbal medicine possessing anti-inflammatory and analgesic properties. DOSY was able to detect the major components present at higher concentrations. Complete characterization was achieved using HPLC-UV-SPE-NMR, and 1D and 2D NMR analyses enabled the identification of known synthetic drugs. These were ranitidine and a mixture of orphenadrine citrate, piroxicam, and dexamethasone, which are co-formulated in a remedy called Rheumazim that is used to relieve severe pain, but it is prohibited in Brazil because of a lack of sufficient pharmacokinetic and pharmacodynamic information.

Discovery and widespread occurrence of polyhalogenated 1,1'-dimethyl-2,2'-bipyrroles (PDBPs) in marine biota

Polyhalogenated 1,1'-dimethyl-2,2'-bipyrroles (PDBPs) are halogenated natural products (HNPs) previously shown to bioaccumulate in marine mammals and birds. Since their discovery in 1999, six hexahalogenated and a few lesser halogenated congeners have been identified in diverse marine mammal samples. Here we report the identification of 17 additional hexahalogenated PDBPs in the blubber extract of a humpback dolphin (Sousa chinensis) from Queensland, Australia. Thirteen of these new PDBPs were also detected in an Australian sea cucumber (Holothuria sp.). Additional samples were also tested positive on several new PDBPs, including an Australian venus tuskfish (Choerodon venustus) as well as a white whale (Delphinapterus leucas) and a sperm whale (Physeter macrocephalus) from the Northern Hemisphere. GC/ECNI-MS-SIM quantification of the molecular ions was carried out with the help of synthesized standards. The sum concentration of PDBPs was 1.1 mg/kg lipid in the humpback dolphin and 0.48 mg/kg lipid in the sea cucumber.

Complex marine natural products as potential epigenetic and production regulators of antibiotics from a marine Pseudomonas aeruginosa

Marine microbes are capable of producing secondary metabolites for defense and competition. Factors exerting an impact on secondary metabolite production of microbial communities included bioactive natural products and co-culturing. These external influences may have practical applications such as increased yields or the generation of new metabolites from otherwise silent genes in addition to reducing or limiting the production of undesirable metabolites. In this paper, we discuss the metabolic profiles of a marine Pseudomonas aeruginosa in the presence of a number of potential chemical epigenetic regulators, adjusting carbon sources and co-culturing with other microbes to induce a competitive response. As a result of these stressors certain groups of antibiotics or antimalarial agents were increased most notably when treating P. aeruginosa with sceptrin and co-culturing with another Pseudomonas sp. An interesting cross-talking event between these two Pseudomonas species when cultured together and exposed to sceptrin was observed.

[Detection of uncultivable bacteria forms in probiotic lyophilized preparations]

AIM

Detection of viable but uncultivable forms among lyophilized cells of commercial probiotics.

MATERIALS AND METHODS

9 series of probiotic preparations (colibacterin, bificol, bifidumbacterin, bifiform) with expired (up to 30 years of storage) or valid shelf life were objects of the study. Total quantity of the bacteria was calculated under the microscope in Goryaev chamber, the number of viable cells was determined in luminescence microscope after staining by an array of fluorescent dyes, the quantity of CFU/ml was evaluated by method of seeding into the respective solid or semi-liquid cultivation medium.

RESULTS

Juxtaposition of the specified parameter values allowed to establish that in lyophilized preparations of colibacterin with expired shelf life the amount of viable but not forming colonies (uncultivable forms) cells varied from 4.13 to 99.73% depending on date of production. For bifidumbacterin with unexpired shelf life live cells constituted 95.45 and 70.73%. The amount of viable bifidobacteria forming colonies was on the level of 100 and 50%, respectively. In bifidopreparations micro colonies that may possibly be formed spontaneously by awakened uncultivable forms were noted. A possibility of growth stimulation of these cells by 1 and 10% aminopeptide was shown.

CONCLUSION

The presence of uncultivable forms in lyophilized preparations of probiotics was proven experimentally.

Fiber-optic trap-on-a-chip platform for probing low refractive index contrast biomaterials

Dual-beam fiber trapping is a versatile technique for manipulating microparticles. We fabricate and evaluate the performance of a compact trap-on-a-chip design and demonstrate, for what we believe is the first time, trapping of low-contrast (m<1.005) lipid vesicles in solution. Counterpropagating fibers are fixed along the chip channel, and we calibrate the trap by optically displacing polystyrene microspheres from the trap center. Measured scattering forces are ~30-49 pN from each beam. Stable trapping and reversible deformation of lipid vesicles is demonstrated under femtonewton trapping forces. This chip has applications in probing a variety of soft biomaterials, such as biological cells, lipid membranes, and protein assemblies.

Preparation and application of reversed phase Chromatorotor for the isolation of natural products by centrifugal preparative chromatography

A method of preparation of rotors with a reversed phase (RP) solid silica gel sorbent layer has been developed for centrifugal preparative chromatography (CPC), also known as rotational planar chromatography (RPC). The rotors consist of binder free RP solid SiO2 layers of different thicknesses packed between two supported circular glass discs and can be used in any appropriate device for centrifugal chromatography, like Chromatotron and CycloGraph. Polar and /or semi-polar compounds with close R(f) values, as well as extracts and column fractions were separated and/or purified in a preparative and/or semi-preparative scale using the RP rotors, eluted with mixtures of aqueous-based solvents. We herein report three examples of its application, using RP Chromatorotors, for the isolation of the diastereoisomeric alkaloids banistenosides I and II from Banisteriopsis caapi, saponins III and IV from Fagonia cretica, and the sesquiterpenes artemisinin (V) and artemisinic acid (VI) from Artemisia annua.

NMR spectroscopy: structure elucidation of cycloelatanene A: a natural product case study

The structure elucidation of new secondary metabolites derived from marine and terrestrial sources is frequently a challenging task. The hurdles include the ability to isolate stable secondary metabolites of sufficient purity that are often present in <0.5 % of the dry weight of the sample. This usually involves a minimum of several chromatographic purification steps. The second issue is the stability of the compound isolated. It must always be assumed when dealing with the isolation of natural products that the compound may rapidly degrade during and/or after the isolation, due to sensitivity to light, air oxidation, and/or temperature. In this way, precautions need to be taken, as much as possible to avoid any such chemical inter-conversions and/or degradations. Immediately after purification, the next step is to rapidly acquire all analytical spectroscopic data in order to complete the characterization of the isolated secondary metabolite(s), prior to any possible decomposition. The final hurdle in this multiple step process, especially in the acquisition of the NMR spectroscopic and other analytical data (mass spectra, infrared and ultra-violet spectra, optical rotation, etc.), is to assemble the structural moieties/units in an effort to complete the structure elucidation. Often ambiguity with the elucidation of the final structure remains when structural fragments identified are difficult to piece together on the basis of the HMBC NMR correlations or when the relative configuration cannot be unequivocally identified on the basis of NOE NMR enhancements observed. Herein, we describe the methodology used to carry out the structure elucidation of a new C16 chamigrene, cycloelatanene A (5) which was isolated from the southern Australian marine alga Laurencia elata (Rhodomelaceae). The general approach and principles used in the structure determination of this compound can be applied to the structure elucidation of other small molecular weight compounds derived from either natural or synthetic sources.

Metabolomics and dereplication strategies in natural products

Metabolomic methods can be utilized to screen diverse biological sources of potentially novel and sustainable sources of antibiotics and pharmacologically-active drugs. Dereplication studies by high resolution Fourier transform mass spectrometry coupled to liquid chromatography (LC-HRFTMS) and nuclear magnetic resonance (NMR) spectroscopy can establish the chemical profile of endophytic and/or endozoic microbial extracts and their plant or animal sources. Identifying the compounds of interest at an early stage will aid in the isolation of the bioactive components. Therefore metabolite profiling is important for functional genomics and in the search for new pharmacologically active compounds. Using the tools of metabolomics through the employment of LC-HRFTMS as well as high resolution NMR will be a very efficient approach. Metabolomic profiling has found its application in screening extracts of macroorganisms as well as in the isolation and cultivation of suspected microbial producers of bioactive natural products.Metabolomics is being applied to identify and biotechnologically optimize the production of pharmacologically active secondary metabolites. The links between metabolome evolution during optimization and processing factors can be identified through metabolomics. Information obtained from a metabolomics dataset can efficiently establish cultivation and production processes at a small scale which will be finally scaled up to a fermenter system, while maintaining or enhancing synthesis of the desired compounds. MZmine (BMC Bioinformatics 11:395-399, 2010; http://mzmine.sourceforge.net/download.shtml ) and SIEVE ( http://www.vastscientific.com/resources/index.html ; Rapid Commun Mass Spectrom 22:1912-1918, 2008) softwares are utilized to perform differential analysis of sample populations to find significant expressed features of complex biomarkers between parameter variables. Metabolomes are identified with the aid of existing high resolution MS and NMR records from online or in-house databases like AntiMarin, a merger database of Antibase (Laatsch H. Antibase Version 4.0 - The Natural Compound Identifier. Wiley-VCH Verlag GmbH & Co. KGaA, 2012) for microbial secondary metabolites as well as higher fungi and MarinLit for marine natural products (Blunt J. MarinLit. University of Canterbury, New Zealand, 2012). This is further validated through available reference standards and NMR experiments. Metabolomics has become a powerful tool in systems biology which allows us to gain insights into the potential of natural isolates for synthesis of significant quantities of promising new agents and allows us to manipulate the environment within fermentation systems in a rational manner to select a desired metabolome.

Evaluation of relative isotopic abundance measurements in a quadrupole time-of-flight mass spectrometer for elemental composition determination of natural products in traditional Chinese medicine

The relative isotopic abundance (RIA) measurement errors of a quadrupole time-of-flight (Q-ToF) instrument incorporating analog-to-digital converter detectors were systemically evaluated by stochastically collecting about 200 data in positive ion mass spectrometry (MS) mode. Errors varied with peak intensities at definite spectral acquisition rates but were very close, even if peak intensities changed sharply at different spectral acquisition rates with the same concentration. Intensity thresholds were systematically defined at 1 Hz of spectral acquisition rates. RIA measurement errors were also evaluated using peak area. It seemed that peak area was better adapted for the high-intensity ions while peak intensity was suited for very low-intensity ions. Several known compounds were selected for RIA measurements for product ions in tandem mass spectropmetry (MS/MS) mode. An extract of a representative traditional Chinese medicinal, Paederia scandens was analyzed with high-performance liquid chromatography-electrospray ionization-QToF-MS/MS. The unique elemental compositions of some compounds could not be identified even with exact masses and MS/MS spectra of measured and reference compounds. RIA errors, especially of (M+2)M(-1), provided vital information for determining the elemental composition.

Pharmacologically prospective antibiotic agents and their sources: a marine microbial perspective

Marine microbes have been a storehouse of bioactive metabolites with tremendous potential as drug candidates. Marine microorganism derived secondary metabolites (chemical compounds/peptides) are considered to be a burning area of research since recent past. Many of such compounds have been proven to be anti-bacterial, anti-fungal, anti-algal, anti-HIV, anti-helminthic, anti-protozoan, anti-tumor and anti-allergic agents. Marine bacteria and fungi have been reported to be the producers of such compounds owing to their defense mechanisms and metabolic by products. Although the number of natural products isolated from these classes of marine microbial flora is large, a limited number of such compounds reach the clinical trial and even less number of them get approved as a drug. Here we discuss the recent studies on the isolation, characterization and the pharmacological significances of anti-bacterial, anti-fungal and anti-infective agents of marine microbial origin. Further, the clinical status of such compounds has also been discussed in comparison with those derived from their terrestrial counterparts.

Analysis of biologically active peptides using two-dimensional HPLC-CE

High-performance liquid chromatography (HPLC) is a technique most frequently used for the assessment of biologically active peptides. Owing to the ionic character of these compounds, they may also be separated and assayed using capillary electrophoresis (CE), which offers very high efficiency, short analysis time and low consumption of reagents, and is used increasingly more often. The paper describes the combination of HPLC and CE in order to increase the efficiency of the separation of complex mixture of peptides (active substance and its related impurities). The developed two-dimensional HPLC-CE technique was employed for the analysis of the impurities of octreotide, a cyclic octapeptide used in therapy. Because distinct separation mechanisms are used, the two-dimensional technique ensures higher separation efficiency and a more comprehensive impurity profile of the medicinal product than either of the techniques used separately.

[Construction and application of natural products LC-MS-DS]

To overcome the defects of current research methods of natural products, an LC-MS-DS that consisted of more than 600 natural products was constructed with HPLC-ESI-IT-MS/MS. The database searching results of LC-MS-DS were validated to be reliable, which indicated that LC-MS-DS could be successfully applied for the effective identification and target isolation of natural products. The study will provide an effective method for fast identification and efficient isolation of natural products.

Detection of bioactive exometabolites produced by the filamentous marine cyanobacterium Geitlerinema sp

Marine cyanobacteria are noted for their ability to excrete metabolites with biotic properties. This paper focuses on such exometabolites obtained from the culture of the marine filamentous cyanobacterium Geitlerinema sp. strain, their purification and subsequent analyses. By this means the recoveries of the active compounds, a prerequisite for properly determining their concentration, are quantified here for the first time. We demonstrate a new procedure using Amberlite XAD-1180 resin in combination with the eluent isopropanol for extraction of the culture media and gas chromatography as simplified chemical analysis. This procedure reduced necessary bacteria cultivation time (from 150 to 21 days) at low volumes of culture media (300 mL) required for identification of two selected bioactive compounds: 4,4'-dihydroxybiphenyl and harmane.

Natural product studies of U.S. endangered plants: volatile components of Lindera melissifolia (Lauraceae) repel mosquitoes and ticks

The number of endangered plant species in the U.S. is significant, yet studies aimed towards utilizing these plants are limited. Ticks and mosquitoes are vectors of significant pathogenic diseases of humans. Repellents are critical means of personal protection against biting arthropods and disease transmission. The essential oil and solvent extracts from Lindera melissifolia (Walt.) Blume (Lauraceae) (pondberry) drupes were gathered and analyzed by GC and GC-MS. The essential oil obtained from this endangered plant showed a significant dose dependent repellency of ticks and a moderate mosquito repellent effect while the subsequent hexanes extract was completely ineffective. Fractional freezing enriched the tick repellent components of the essential oil. Several known tick repellent components were recognized by the GC-MS comparison of the resulting fractions and β-caryophyllene, α-humulene, germacrene D and β-elemene warrant evaluations for tick repellency. Identifying pondberry as a potential renewable source for a broad spectrum repellent supports efforts to conserve similar U.S. endangered or threatened plant species.

Rapid isolation and identification of minor natural products by LC-MS, LC-SPE-NMR and ECD: isoflavanones, biflavanones and bisdihydrocoumarins from Ormocarpum kirkii

The combination of the hyphenated techniques LC-MS and LC-SPE-NMR constitutes a powerful platform for the rapid isolation and identification of minor components from natural sources. Electronic circular dichroism (ECD) is a useful tool to determine the absolute configuration of small quantities of chiral molecules. In order to search for minor constituents present in an Ormocarpum kirkii extract, these techniques were applied for the separation and structure elucidation of a series of isoflavanones, biflavanones and biscoumarins. After optimization of chromatographic conditions and subsequent isolation, MS and 1D and 2D NMR data were collected. Experimental and calculated ECD spectra were used in conjunction with NMR data to confirm the absolute configuration of these compounds. Eight compounds were identified for the first time and six have been previously reported. The present approach offers a strategy for accelerating research on natural products.

A review of the chemistry of the genus Crataegus

Since the 1800s, natural health products that contain hawthorn (Crataegus spp.) have been used in North America for the treatment of heart problems such as hypertension, angina, arrhythmia, and congestive heart failure. Traditionally, Native American tribes used hawthorn (Crataegus spp.) to treat gastrointestinal ailments and heart problems, and consumed the fruit as food. Hawthorn also has a long history of use in Europe and China for food, and in traditional medicine. Investigations of Crataegus spp. typically focus on the identification and quantification of flavonoids and anthocyanins, which have been shown to have pharmacological activity. The main flavonoids found in Crataegus spp. are hyperoside, vitexin, and additional glycosylated derivatives of these compounds. Reviewed herein are the botany, ethnobotany, and traditional use of hawthorn while focusing on the phytochemicals that have been reported in Crataegus species, and the variation in the described chemistry between individual species.

Analysis and purification of bioactive natural products: the AnaPurNa study

Based on a meta-analysis of data mined from almost 2000 publications on bioactive natural products (NPs) from >80000 pages of 13 different journals published in 1998-1999, 2004-2005, and 2009-2010, the aim of this systematic review is to provide both a survey of the status quo and a perspective for analytical methodology used for isolation and purity assessment of bioactive NPs. The study provides numerical measures of the common means of sourcing NPs, the chromatographic methodology employed for NP purification, and the role of spectroscopy and purity assessment in NP characterization. A link is proposed between the observed use of various analytical methodologies, the challenges posed by the complexity of metabolomes, and the inescapable residual complexity of purified NPs and their biological assessment. The data provide inspiration for the development of innovative methods for NP analysis as a means of advancing the role of naturally occurring compounds as a viable source of biologically active agents with relevance for human health and global benefit.

Microbial strain prioritization using metabolomics tools for the discovery of natural products

Natural products profoundly impact many research areas, including medicine, organic chemistry, and cell biology. However, discovery of new natural products suffers from a lack of high throughput analytical techniques capable of identifying structural novelty in the face of a high degree of chemical redundancy. Methods to select bacterial strains for drug discovery have historically been based on phenotypic qualities or genetic differences and have not been based on laboratory production of secondary metabolites. Therefore, untargeted LC/MS-based secondary metabolomics was evaluated to rapidly and efficiently analyze marine-derived bacterial natural products using LC/MS-principal component analysis (PCA). A major goal of this work was to demonstrate that LC/MS-PCA was effective for strain prioritization in a drug discovery program. As proof of concept, we evaluated LC/MS-PCA for strain selection to support drug discovery, for the discovery of unique natural products, and for rapid assessment of regulation of natural product production.

Determination of natural pyrethrins by liquid chromatography-electron ionisation-mass spectrometry

INTRODUCTION

Pyrethrum extract is a mixture of six insecticidal compounds from the flower heads of Chrysanthemum cinerariaefolium L.. Since they only have low to moderate mammalian toxicity they can be used as natural insecticides in agriculture or to develop low cost and safe dermatological formulations. Because of the thermal instability of pyrethrins, analytical methods based on liquid chromatography (LC) are preferred over those based on gas chromatography (GC). A few applications using LC with mass spectrometry detection are presented in the literature. Current protocols for their characterisation by LC rely on the use of less sophisticated detectors such as UV detection.

OBJECTIVE

To develop the first liquid chromatography-electron ionisation-mass spectrometry (LC-EI-MS) method for pyrethrins detection and quantitation in pyrethrum extracts.

METHODOLOGY

A commercial pyrethrum extract and various samples of flower heads from C. cinerariaefolium L. were investigated using reversed-phase nano-liquid chromatography coupled to direct electron ionisation-mass spectrometry (nanoLC-direct EI-MS). The eluted compounds were identified through searches of the US National Institute of Standards and Technology (NIST) library, exploiting the direct EI capability to produce high quality EI mass spectra.

RESULTS

The method demonstrated satisfactory sensitivity (limit of detection (LOD) range: 0.04-0.38 mg/g), linearity (R² range: 0.9740-0.9983) and precision (RSD% range: 4-13%) for the quantitation of the natural pyrethrins in extracts from C. cinerariaefolium L.

CONCLUSION

The nanoLC-direct EI-MS technique can be a useful tool for the detection of pyrethrins.

Universal quantification of structurally diverse natural products using an evaporative light scattering detector

A lack of good methods for absolute quantification of natural products has limited the accuracy of high-throughput screening. Many currently used methods for quantification are either too slow or not amenable to the structural diversity of natural products. Recent developments in low-temperature evaporative light scattering detectors (ELSD-LT) have overcome several historical limitations of ELSDs, including analyte decomposition and low sensitivity. Primarily, ELSDs have been used for relative quantification and detection of compounds that lack a UV chromophore. In this study, we employ an ELSD-LT for absolute quantification of natural products. Calibration curves were constructed using a weighted least-squares analysis for a diverse set of natural products and other compounds. An average calibration curve was evaluated for the "universal" quantification of natural products. Optimization of ELSD-LT hardware and parameters improved sensitivity and throughput and established the utility of ELSD-LT for quantification of large natural product libraries.