Genome mining methods to discover bioactive natural products.

Covering: 2016 to 2021With genetic information available for hundreds of thousands of organisms in publicly accessible databases, scientists have an unprecedented opportunity to meticulously survey the diversity and inner workings of life. The natural product research community has harnessed this breadth of sequence information to mine microbes, plants, and animals for biosynthetic enzymes capable of producing bioactive compounds. Several orthogonal genome mining strategies have been developed in recent years to target specific chemical features or biological properties of bioactive molecules using biosynthetic, resistance, or transporter proteins. These "biosynthetic hooks" allow researchers to query for biosynthetic gene clusters with a high probability of encoding previously undiscovered, bioactive compounds. This review highlights recent case studies that feature orthogonal approaches that exploit genomic information to specifically discover bioactive natural products and their gene clusters.

A method to assess glyphosate, glufosinate and aminomethylphosphonic acid in soil and earthworms.

A new sensitive and selective analytical methodology to quantify glyphosate (GLY), aminomethylphosphonic acid (AMPA), and glufosinate (GLU) in both soil and earthworms (Allolobophora chlorotica) was developed. The extraction and purification methods were optimized. The samples were extracted with various aqueous solutions (HNO3, H2O, KOH and borate buffer) and derivatized with 9-Fluorenylmethyl chloroformate (FMOCCl). To optimize the extraction step, a method to remove the excess FMOCCl was applied based on liquid-liquid extraction with diethyl ether. The purification of derivatized extracts was carried out using XLB solid phase extraction (SPE) cartridges before internal standard quantification by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS). The elution step was optimized to obtain the best recoveries possible, which was with acidic methanol (1% formic acid) (67% for GLY, 70% for GLU and 65% for AMPA). The extraction and purification method followed by analysis of the two herbicides and AMPA in soils using LC/MS/MS determined limit of quantification (LOQ) values of 0.030 µg g - 1 for GLY, 0.025 µg g - 1 for AMPA and 0.020 µg g - 1 for GLU . For earthworms, LOQ were 0.23 µg g - 1 for GLY, 0.20 µg g - 1 for AMPA and 0.12 µg g - 1 for GLU. . The developed method was applied to determine these compounds in natural soils and earthworms.

One-step purification/extraction method to access glyphosate, glufosinate, and their metabolites in natural waters.

A new green method for trace level quantification of four herbicides, glyphosate (GLYP), glufosinate (GLUF), and their main metabolites, aminomethylphosphonic acid (AMPA) and 3-(methyl-phosphinico)-propionic acid (MPPA), was developed. The purification step without any derivatization was conducted by solid-phase extraction using Chelex-100 resin in the Fe (III) form, followed by elution with 5% NH4OH. The four analytes were quantified by ultra-high-performance liquid chromatography coupled to tandem mass spectrometry. The developed extraction method was validated on five fresh and sea water matrices with mean recoveries ranging from 80.1% to 109.4% (relative standard deviation < 20%). The extraction conditions were evaluated and certified for the high applicability of the extraction method too. The limits of detection (ng/L) in the five water matrices were in ranges 0.70 - 4.0, 2.4 - 3.9, 1.8 - 4.7, and 1.6 - 4.0 for GLYP, AMPA, GLUF, and MPPA, respectively. The method was successfully applied to detect the four compounds in surface waters sampled along the Red River Delta region in July 2019. The highest concentrations were detected at 565, 1,330, 234, and 871 ng/L for GLYP, AMPA, GLUF, and MPPA, respectively. These results showed the potential capacity of this new method for convenient monitoring of herbicides and their metabolites in the diverse natural water system.

Determination of glyphosate and AMPA in oat products for the selection of candidate reference materials.

The use of reference materials (RMs) is critical for validating and testing the accuracy of analytical protocols. The National Institute of Standards and Technology (NIST) is in initial stages of developing a glyphosate in oats RM. The first aim of this study was to optimize and validate a robust method for the extraction and analysis of glyphosate and aminomethylphosphonic acid (AMPA). The optimized method was used to screen thirteen commercially available oat products to identify candidate RMs. Glyphosate was detected in all samples, with the highest glyphosate mass fraction of 1100 ng/g; lower levels were measured in grains from organic agriculture. AMPA was quantified in nine samples up to 40 ng/g. The findings of this study led to the identification of candidate RMs, with "high" and "low" glyphosate levels. A preliminary stability study determined that glyphosate is stable in oat material at room temperature for six months.

Genome Mining Reveals the Phosphonoalamide Natural Products and a New Route in Phosphonic Acid Biosynthesis.

Phosphonic acid natural products have potent inhibitory activities that have led to their application as antibiotics. Recent studies uncovered large collections of gene clusters encoding for unknown phosphonic acids across microbial genomes. However, our limited understanding of their metabolism presents a significant challenge toward accurately informing the discovery of new bioactive compounds directly from sequence information alone. Here, we use genome mining to identify a family of gene clusters encoding a conserved branch point unknown to bacterial phosphonic acid biosynthesis. The products of this gene cluster family are the phosphonoalamides, four new phosphonopeptides with l-phosphonoalanine as the common headgroup. Phosphonoalanine and phosphonoalamide A are antibacterials, with strongest inhibition observed against strains of Bacillus and Escherichia coli. Heterologous expression identified the gene required for transamination of phosphonopyruvate to phosphonoalanine, a new route for bacterial phosphonic acids encoded within genomes of diverse microbes. These results expand our knowledge of phosphonic acid diversity and pathways for their biosynthesis.

Analysis of degradation products of nerve agents via post-pentafluorobenzylation liquid chromatography-tandem mass spectrometry.

In the work reported here, a screening procedure was developed for the detection and identification of RMPAs (nerve agent degradation products) after pentafluorobenzylation using liquid chromatography-tandem mass spectrometry (LC-MS/MS). With this method, all RMPAs, including highly hydrophilic types such as methylphosphonic acid (MPA) and ethyl methylphosphonic acid (EMPA), were sufficiently retained in commonly used reversed-phase columns (retention times: 15.7 and 11.0 min.), and the presence of RMPAs was determined more efficiently than with the conventional direct LC-MS/MS method. The detection limits of RMPAs using this approach (<33 ng) were mostly superior to those observed with direct LC-MS/MS (<74 ng) and gas chromatography-mass spectrometry (GC-MS) after pentafluorobenzylation (<1.1 µg). The applicability of newly developed method toward real samples was evaluated via recovery tests involving urine/serum and wipe tests on various surfaces.

Fungal synthesis of chiral phosphonic synthetic platform - Scope and limitations of the method.

Chiral hydroxyphosphonates due to their wide range of biological properties are industrially important chemicals. Chemical synthesis of their optical isomers is expensive, time consuming and not friendly to the environment, so biotransformations are under consideration. Among others, these compounds act as enzymes inhibitors. This makes the bioconversions of phosphonates, especially scaling experiments, hard to perform. Biocatalysis is one of the methods that can be applied in synthesis of optically pure compounds. To increase the efficiency of the process with whole cell biocatalysts, it is essential to ensure optimal reaction conditions that minimize cellular stress and can enhance the metabolic activity of cells. The present investigation focuses on the scaling up of the kinetic resolution of racemic mixture of 2-butyryloxy-2-(ethoxy-P-phenylphosphinyl)acetic acid, applying free and immobilized form of the fungal biocatalysts and two operation systems: shake flask and recirculated fixed-bed batch reactor. Protocols of effective mycelium immobilization on polyurethane foams were set for T. purpurogenus IAFB 2512, F. oxysporum, P. commune. The best results of biotransformation were obtained with the immobilized P. commune in the column recirculated fixed-bed batch reactor. The conversion reaches 56% (maximal for the kinetic process) and the enantiomeric enrichment of the isomers mixture ranges between 82 and 93% (93% for ester of RP,R conformation). All biocatalysts exhibit SP-preference toward tested compound, what is essential because of importance of the phosphorus atom chirality for its biological activity.

Novel peptidyl α-aminoalkylphosphonates as inhibitors of hepatitis C virus NS3/4A protease.

Herein, we describe the synthesis and application of novel phosphonic inhibitors designed to target the NS3/4A protease, which is crucial for the life cycle of hepatitis C virus. We examined the inhibitory potency of our synthesized compounds against two genotypes (1a and 1b) of NS3/4A protease and four mutant strains of HCV. The most potent inhibitors displayed k2/KI values of 79 850 M-1s-1 and 60 850 M-1s-1 against genotype 1a and 1b protease, respectively. Further in vitro evaluation of the most potent inhibitors revealed that vastly reduced HCV replication. Cellular toxicity, plasma stability, reactivity with selected human proteases as well the stability of inhibitor-protease complex and its intracellular availability are also discussed.

Occurrence of the herbicide glyphosate and its metabolite AMPA in surface waters in Switzerland determined with on-line solid phase extraction LC-MS/MS.

Glyphosate is currently one of the most important herbicides worldwide. Its unique properties provide for a wide range of uses in agriculture but also in non-agricultural areas. At the same time, its zwitterionic nature prevents the inclusion in multi-residue analytical methods for environmental monitoring. Consequently, despite its extensive use, data on occurrence of glyphosate in the aquatic environment is still scarce. Based on existing methods, we developed a simplified procedure for the determination of glyphosate and its main metabolite aminomethylphosphonic acid (AMPA) in water samples using derivatization with fluorenylmethyl chloroformate FMOC-Cl, combined with on-line solid phase extraction and liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection. This method was extensively tested on over 1000 samples of surface water, groundwater, and treated wastewater and proved to be simple, sensitive, and reliable. Limits of quantification of 0.005 µg/L were routinely achieved. Glyphosate and AMPA were detected in the vast majority of stream water samples in the area of Zurich, Switzerland, with median concentrations of 0.11 and 0.20 µg/L and 95th percentile concentrations of 2.1 and 2.6 µg/L, respectively. Stream water data and data from treated wastewater indicated that non-agricultural uses may significantly contribute to the overall loads of glyphosate and AMPA in surface waters. In the investigated groundwater samples, selected specifically because they had shown presence of other herbicides in previous monitoring programs, glyphosate and AMPA were generally not detected, except for two monitoring sites in Karst aquifers, indicating that these compounds show much less tendency for leaching.

A novel pretreatment method combining sealing technique with direct injection technique applied for improving biosafety.

AIM: People today have a stronger interest in the risk of biosafety in clinical bioanalysis. A safe, simple, effective method of preparation is needed urgently. METHODOLOGY/RESULTS: To improve biosafety of clinical analysis, we used antiviral drugs of adefovir and tenofovir as model drugs and developed a safe pretreatment method combining sealing technique with direct injection technique. The inter- and intraday precision (RSD %) of the method were <4%, and the extraction recoveries ranged from 99.4 to 100.7%. Meanwhile, the results showed that standard solution could be used to prepare calibration curve instead of spiking plasma, acquiring more accuracy result. CONCLUSION/DISCUSSION: Compared with traditional methods, the novel method not only improved biosecurity of the pretreatment method significantly, but also achieved several advantages including higher precision, favorable sensitivity and satisfactory recovery. With these highly practical and desirable characteristics, the novel method may become a feasible platform in bioanalysis.

Estimation of apparent binding constant of complexes of selected acyclic nucleoside phosphonates with ß-cyclodextrin by affinity capillary electrophoresis.

Affinity capillary electrophoresis (ACE) has been applied to estimation of apparent binding constant of complexes of (R,S)-enantiomers of selected acyclic nucleoside phosphonates (ANPs) with chiral selector ß-cyclodextrin (ßCD) in aqueous alkaline medium. The noncovalent interactions of five pairs of (R,S)-enantiomers of ANPs-based antiviral drugs and their derivatives with ßCD were investigated in the background electrolyte (BGE) composed of 35 or 50 mM sodium tetraborate, pH 10.0, and containing variable concentration (0-25 mM) of ßCD. The apparent binding constants of the complexes of (R,S)-enantiomers of ANPs with ßCD were estimated from the dependence of effective electrophoretic mobilities of (R,S)-enantiomers of ANPs (measured simultaneously by ACE at constant reference temperature 25°C inside the capillary) on the concentration of ßCD in the BGE using different nonlinear and linear calculation methodologies. Nonlinear regression analysis provided more precise and accurate values of the binding constants and a higher correlation coefficient as compared to the regression analysis of the three linearized plots of the effective mobility dependence on ßCD concentration in the BGE. The complexes of (R,S)-enantiomers of ANPs with ßCD have been found to be relatively weak - their apparent binding constants determined by the nonlinear regression analysis were in the range 13.3-46.4 L/mol whereas the values from the linearized plots spanned the interval 12.3-55.2 L/mol.

Analysis of glyphosate and aminomethylphosphonic acid in leaves from Coffea arabica using high performance liquid chromatography with quadrupole mass spectrometry detection.

Glyphosate is a commonly applied herbicide in coffee plantations. Because of its non-selective mode of action it can damage the crop exposed through spray drift. Therefore, it is of interest to study glyphosate fate in coffee plants. The aim of this study was to develop an analytical method for accurate and precise quantification of glyphosate and its main metabolite aminomethylphosphonic acid (AMPA) at trace levels in coffee leaves using liquid chromatography with single-quadrupole mass spectrometry detection. The method is based on a two-step solid phase extraction (SPE) with an intermediate derivatization reaction using 9-fluorenylmethylchloroformate (FMOC). An isotope dilution method was used to account for matrix effects and to enhance the confidence in analyte identification. The limit of quantification (LOQ) for glyphosate and AMPA in coffee leaves was 41 and 111 µg kg(-1) dry weight, respectively. For the method optimization a design of experiments (DOE) approach was used. The sample clean-up procedure can be simplified for the analysis of less challenging matrices, for laboratories having a tandem mass spectrometry detector and for cases in which quantification limits above 0.1 mg kg(-1) are acceptable, which is often the case for glyphosate. The method is robust, possesses high identification confidence, while being suitable for most commercial and academic laboratories. All leaf samples from five coffee fields analyzed (n=21) contained glyphosate, while AMPA was absent. The simplified clean-up procedure was successfully validated for coffee leaves, rice, black beans and river water.

Water-compatible molecularly imprinted polymer as a sorbent for the selective extraction and purification of adefovir from human serum and urine.

A molecularly imprinted polymer has been synthesized to specifically extract adefovir, an antiviral drug, from serum and urine by dispersive solid-phase extraction before high-performance liquid chromatography with UV analysis. The imprinted polymers were prepared by bulk polymerization by a noncovalent imprinting method that involved the use of adefovir (template molecule) and functional monomer (methacrylic acid) complex prior to polymerization, ethylene glycol dimethacrylate as cross-linker, and chloroform as porogen. Molecular recognition properties, binding capacity, and selectivity of the molecularly imprinted polymers were evaluated and the results show that the obtained polymers have high specific retention and enrichment for adefovir in aqueous medium. The new imprinted polymer was utilized as a molecular sorbent for the separation of adefovir from human serum and urine. The serum and urine extraction of adefovir by the molecularly imprinted polymer followed by high-performance liquid chromatography showed a linear calibration curve in the range of 20-100 µg/L with excellent precisions (2.5 and 2.8% for 50 µg/L), respectively. The limit of detection and limit of quantization were determined in serum (7.62 and 15.1 µg/L), and urine (5.45 and 16 µg/L). The recoveries for serum and urine samples were found to be 88.2-93.5 and 84.3-90.2%, respectively.

Phosphonate removal from discharged circulating cooling water using iron-carbon micro-electrolysis.

Phosphonate is a commonly used corrosion and scale inhibitor for a circulating cooling water (CCW) system. Its discharge could cause eutrophication of receiving waters. The iron-carbon (Fe/C) micro-electrolysis technology was used to degrade and remove phosphonate from discharged CCW. The influences of initial pH, Fe/C ratio (FCR) and temperature on phosphonate removal were investigated in a series of batch tests and optimized by response surface methodology. The quadratic model of phosphonate removal was obtained with satisfactory degrees of fitness. The optimum conditions with total phosphorus removal efficiency of 95% were obtained at pH 7.0, FCR of 1.25, and temperature of 45 °C. The phosphonate removal mechanisms were also studied. Phosphonate removal occurred predominantly via two consecutive reactive phases: the degradation of phosphonate complexes (Ca-phosphonate) and the precipitation of Fe/C micro-electrolysis products (PO4(3-), Ca²âº and Fe³âº).

Rapid and efficient filtration-based procedure for separation and safe analysis of CBRN mixed samples.

Separating CBRN mixed samples that contain both chemical and biological warfare agents (CB mixed sample) in liquid and solid matrices remains a very challenging issue. Parameters were set up to assess the performance of a simple filtration-based method first optimized on separate C- and B-agents, and then assessed on a model of CB mixed sample. In this model, MS2 bacteriophage, Autographa californica nuclear polyhedrosis baculovirus (AcNPV), Bacillus atrophaeus and Bacillus subtilis spores were used as biological agent simulants whereas ethyl methylphosphonic acid (EMPA) and pinacolyl methylphophonic acid (PMPA) were used as VX and soman (GD) nerve agent surrogates, respectively. Nanoseparation centrifugal devices with various pore size cut-off (30 kD up to 0.45 µm) and three RNA extraction methods (Invisorb, EZ1 and Nuclisens) were compared. RNA (MS2) and DNA (AcNPV) quantification was carried out by means of specific and sensitive quantitative real-time PCRs (qPCR). Liquid chromatography coupled to time-of-flight mass spectrometry (LC/TOFMS) methods was used for quantifying EMPA and PMPA. Culture methods and qPCR demonstrated that membranes with a 30 kD cut-off retain more than 99.99% of biological agents (MS2, AcNPV, Bacillus Atrophaeus and Bacillus subtilis spores) tested separately. A rapid and reliable separation of CB mixed sample models (MS2/PEG-400 and MS2/EMPA/PMPA) contained in simple liquid or complex matrices such as sand and soil was also successfully achieved on a 30 kD filter with more than 99.99% retention of MS2 on the filter membrane, and up to 99% of PEG-400, EMPA and PMPA recovery in the filtrate. The whole separation process turnaround-time (TAT) was less than 10 minutes. The filtration method appears to be rapid, versatile and extremely efficient. The separation method developed in this work constitutes therefore a useful model for further evaluating and comparing additional separation alternative procedures for a safe handling and preparation of CB mixed samples.

Cyanohydrin phosphonate natural product from Streptomyces regensis.

Streptomyces regensis strain WC-3744 was identified as a potential phosphonic acid producer in a large-scale screen of microorganisms for the presence of the pepM gene, which encodes the key phosphonate biosynthetic enzyme phosphoenolpyruvate phosphonomutase. (31)P NMR revealed the presence of several unidentified phosphonates in spent medium after growth of S. regensis. These compounds were purified and structurally characterized via extensive 1D and 2D NMR spectroscopic and mass spectrometric analyses. Three new phosphonic acid metabolites, whose structures were confirmed by comparison to chemically synthesized standards, were observed: (2-acetamidoethyl)phosphonic acid (1), (2-acetamido-1-hydroxyethyl)phosphonic (3), and a novel cyanohydrin-containing phosphonate, (cyano(hydroxy)methyl)phosphonic acid (4). The gene cluster responsible for synthesis of these molecules was also identified from the draft genome sequence of S. regensis, laying the groundwork for future investigations into the metabolic pathway leading to this unusual natural product.

Trace analysis of mono-, di-, tri-substituted polyfluoroalkyl phosphates and perfluorinated phosphonic acids in sewage sludge by high performance liquid chromatography tandem mass spectrometry.

A new method using ultrasonic extraction and solid phase extraction (SPE) clean-up pretreatments was developed for the analysis of mono-, di- and tri-substituted polyfluoroalkyl phosphates (abbreviated as mono-PAPs, di-PAPs and tri-PAPs) and perfluorinated phosphonic acids (PFPAs) in sludge from wastewater treatment plants (WWTPs). For the ultrasonic extraction of three mono-PAPs, three di-PAPs and three PFPAs in sludge samples, a mixture of tetrahydrofuran/acetic acid (1:1, v/v) was found to be the most suitable extraction solvent. The subsequently optimized clean-up and enrichment procedures were carried out with weak anion exchange (WAX) cartridges in-line coupled with graphitized carbon black (ENVI-Carb) tubes. Two tri-PAPs were ultrasonically extracted by acetonitrile/tetrahydrofuran (1:1, v/v) and cleaned by mixed-mode anion exchange (MAX) in-line coupled with ENVI-Carb cartridges. The analytes were analyzed by optimized high performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) method either in negative or positive ionization mode. The method quantification limits (MQLs) of the 11 analytes in sludge ranged from 0.6 to 5.1 ng/g, meanwhile the total recoveries of the pretreatment varied from 24% (6:2 mono-PAP) to 107% (PFDPA). The method was successfully applied to analyze 16 sewage sludge samples collected from seven provinces in China, and two mono-PAPs were identified with concentrations ranging from

Electro-driven extraction across a polymer inclusion membrane in a flow-through cell.

A flow-through arrangement for electrodriven extraction across a polymer inclusion membrane was developed. Sample introduction into the donor chamber was continuous, while the acceptor solution was stagnant. By adjustment of the total volume of the donor solution pumped through the cell the best compromise between enrichment factor and extraction time can be set. The enriched extract was analyzed by capillary electrophoresis with contactless conductivity detection. Membranes of 20µm thickness were employed which consisted of 60% cellulose triacetate as base polymer, 20% o-nitrophenyl octyl ether as plasticizer, and 20% Aliquat 336. By passing through 10mL of sample at a flow rate of 1mL/min the model analytes glyphosate (a common herbicide) and its major metabolite aminomethylphosphonic acid could be transported from the aqueous donor solution to the aqueous acceptor solution with efficiencies >87% in 10min at an applied voltage of 1500V. Enrichment factors of 87 and 95 and limits of detection down to 43 and 64pg/mL were obtained for glyphosate and aminomethylphosphonic acid, respectively. The intra- and interday reproducibilities for the extraction of the two compounds from spiked river water were about 6 and 7% respectively when new membranes were used for each experiment. For consecutive extractions of batches of river water with a single piece of membrane a deterioration of recovery by about 16% (after 20 runs) was noted, an effect not observed with purely aqueous standards.

On-line solid phase extraction-liquid chromatography-mass spectrometry for trace determination of nerve agent degradation products in water samples.

Three primary nerve agent degradation products (ethyl-, isopropyl- and pinacolyl methylphosphonic acid) have been determined in water samples using on-line solid phase extraction-liquid chromatography and mass spectrometry (SPE-LC-MS) with electrospray ionisation. Porous graphitic carbon was employed for analyte enrichment followed by hydrophilic interaction chromatography. Diethylphosphate was applied as internal standard for quantitative determination of the alkyl methylphosphonic acids (AMPAs). By treating the samples with strong cation-exhange columns on Ba, Ag and H form, the major inorganic anions in water were removed by precipitation prior to the SPE-LC-MS determination. The AMPAs could be determined in tap water with limits of detection of 0.01-0.07 µg L(-1) with the [M-H](-) ions extracted at an accuracy of ±5 mDa. The within and between assay precisions at analyte concentrations of 5 µg L(-1) were 2-3%, and 5-9% relative standard deviation, respectively. The developed method was employed for determination of the AMPAs in three natural waters and a simulated waste water sample, spiked at 5 µg L(-1). Recoveries of ethyl-, isopropyl- and pinacolyl methylphosphonic acid were 80-91%, 92-103% and 99-106%, respectively, proving the applicability of the technique for natural waters of various origins.