NPASS database update 2023: quantitative natural product activity and species source database for biomedical research.

Quantitative activity and species source data of natural products (NPs) are important for drug discovery, medicinal plant research, and microbial investigations. Activity values of NPs against specific targets are useful for discovering targeted therapeutic agents and investigating the mechanism of medicinal plants. Composition/concentration values of NPs in individual species facilitate the assessments and investigations of the therapeutic quality of herbs and phenotypes of microbes. Here, we describe an update of the NPASS natural product activity and species source database previously featured in NAR. This update includes: (i) new data of ∼95 000 records of the composition/concentration values of ∼1 490 NPs/NP clusters in ∼390 species, (ii) extended data of activity values of ∼43 200 NPs against ∼7 700 targets (∼40% and ∼32% increase, respectively), (iii) extended data of ∼31 600 species sources of ∼94 400 NPs (∼26% and ∼32% increase, respectively), (iv) new species types of ∼440 co-cultured microbes and ∼420 engineered microbes, (v) new data of ∼66 600 NPs without experimental activity values but with estimated activity profiles from the established chemical similarity tool Chemical Checker, (vi) new data of the computed drug-likeness properties and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties for all NPs. NPASS update version is freely accessible at http://bidd.group/NPASS.

Biodegradation of pharmaceuticals in photobioreactors - a systematic literature review.

This work is a systematic review that reports state-of-the-art in removal of pharmaceuticals from water and wastewater by photosynthetic organisms in photobioreactors. The PRISMA protocol-based review of the most recent literature data from the last 10 years (2011-2021) was reported. Articles were searched by the combination of the following keywords: photobioreactor, pharmaceuticals, drugs, hormones, antibiotics, biodegradation, removal, wastewater treatment. The review focuses on original research papers (not reviews), collected in 3 scientific databases: Scopus, Web of Knowledge, PubMed. The review considered the following factors: type of microorganisms, type of micropollutants removed, degradation efficiency and associated products, types of photosynthetic organisms and photobioreactor types. The conclusion from the systematic review is that the main factors that limit widespread pharmaceuticals removal in photobioreactors are high costs and the problem of low efficiency related with low concentrations of pharmaceuticals. The review indicated a need for further research in this area due to increasing amounts of metabolites in the food chain, such as p-aminophenol and estrone, which can cause harm to people and ichthyofauna. Pharmaceuticals removal can be improved by adapting the type of microorganism used to the type of contamination and implementing photoperiods, which increase the removal efficiency of e.g. sulfamethazine by up to 28%. In the future, it is necessary to search for new solutions in terms of the construction of photobioreactors, as well as for more effective species in terms of pharmaceuticals biodegradation that can survive the competition with other strains during water and wastewater treatment.

Comparison of cyclofructan-, cyclodextrin-, and polysaccharide-based chiral stationary phases for the separation of pharmaceuticals.

In this study, cyclofructan (CF)-, cyclodextrin (CD)-, and polysaccharide-based chiral stationary phases (CSPs) were exploited in high-performance liquid chromatography (HPLC) for the chiral separations of different clinically and pharmaceutically important compounds. In particular, R-naphthylethyl carbamate CF6 (RN-CF6), 3,5-dimethylphenyl carbamate CF7 (DMP-CF7), neutral beta cyclodextrin (ß-CD), 3,5-dimethylphenyl carbamate ß-CD (DMP-ß-CD), and cellulose tris-(3,5-dimethylphenylcarbamate) (Cellulose-Tris DMP) columns were utilized under isocratic elution. The performance of these CSPs as chiral separation media was evaluated by use of nine analytes: acidic, basic, and amphiprotic. A possible correlation between the functional groups of these analytes and the chiral-recognition ability of each chiral column was also examined. The enantioseparations were optimized by varying different parameters, such as mobile phase additives, column temperature, and flow rate. Finally, a comparison was made between all CSPs, and it was expressed in terms of resolution (RS), efficiency (N), selectivity (α), retention factors (k1', k2') and analysis time (tR1, tR2). It was observed that RN-CF6 was the most suitable and efficient CSP for the chiral separation of various types of analytes, including acids, primary and tertiary amines, alcohols, and many neutral compounds. It was the only CSP that provided baseline enantioseparation of thyroxine (RS = 1.6) and cetirizine (RS = 2.0).

Electrochemical Oxidation of Different Therapeutic Classes of Pharmaceuticals Using Graphite-PVC Composite Electrode.

This study reports electrochemical treatment of different therapeutic classes of pharmaceuticals (caffeine, prazosin, enalapril, carbamazepine, nifedipine, levonorgestrel, and simvastatin) in a mixture. The electrochemical process was investigated using graphite-PVC anode at different applied voltages (3, 5, and 12 V), initial concentrations of studied pharmaceuticals in aqueous solution (5 and 10 mg/L), and concentrations of sodium chloride (1 and 2 g/L). The % removal of pharmaceuticals increased with the applied voltage, and was found higher than 98% after 50 min of electrolysis at 5 V. Energy consumption ranged between 0.760 and 3.300 Wh/mg using 12 V being the highest value compared to 3 and 5 V. The formation of chlorinated by-products from four selected pharmaceuticals, simvastatin (C11H13Cl3O5, and C10H12Cl4O3), prazosin (C13H12Cl3N5O3 and C10H11Cl4N2O2), carbamazepine and caffeine (C15H11N2O2Cl and C8H9N4O2Cl) was identified and elucidated using liquid chromatography-time of flight mass spectrometry (LC-TOF/MS).

Chiral Nano-Liquid Chromatography and Dispersive Liquid-Liquid Microextraction Applied to the Analysis of Antifungal Drugs in Milk.

A novel chromatographic application in chiral separation by using the nano-LC technique is here reported. The chiral recognition of 12 antifungal drugs was obtained through a 75 µm I.D. fused-silica capillary, which was packed with a CSP-cellulose 3,5-dichlorophenylcarbamate (CDCPC), by means of a lab-made slurry packing procedure. The mobile phase composition and the experimental conditions were optimized in order to find the optimum chiral separation for some selected racemic mixtures of imidazole and triazole derivatives. Some important parameters, such as retention faction, enantioresolution, peak efficiency, and peak shape, were investigated as a function of the mobile phase (pH, water content, type and concentration of both the buffer and the organic modifier, and solvent dilution composition). Within one run lasting 25 min, at a flow rate of approximately 400 nL min-1, eight couples of enantiomers were baseline-resolved and four of them were separated in less than 25 min. The method was then applied to milk samples, which were pretreated using a classical dispersive liquid-liquid microextraction technique preceded by protein precipitation. Finally, the DLLME-nano-LC-UV method was validated in a matrix following the main FDA guidelines for bioanalytical methods.

Review on in vivo profiling of drug metabolites with LC-MS/MS in the past decade.

Metabolite profiling is an indispensable part of drug discovery and development, enabling a comprehensive understanding of the drug's metabolic behavior. Liquid chromatography-mass spectrometry facilitates metabolite profiling by reducing sample complexity and providing high sensitivity. This review discusses the in vivo metabolite profiling involving LC-MS/MS and the utilization of QTOF, QQQ mass analyzers with a particular emphasis on a mass filter. Further, a summary of sample extraction procedures in biological matrices such as plasma, urine, feces, serum and hair as in vivo samples are outlined. toward the end, we present 15 case studies in biological matrices and their LC-MS/MS conditions to understand the metabolic disposition.

The effect of tandem coupling of NicoShell and TeicoShell columns in sub/supercritical fluid chromatography on enantioresolution.

The coupling of columns in sub/supercritical fluid chromatography presents a great opportunity for influencing the separation efficiency and extending the selectivity of the separation system. Combinations of different types of chiral stationary phases could positively affect the enantioresolution if single ones are complementary to each other. In this work, two superficially porous particle (2.7 µm) macrocyclic glycopeptide-based columns, namely TeicoShell and NicoShell, were serially coupled and tested in sub/supercritical fluid chromatography for the first time. The influence of the column arrangement on the enantioseparation of structurally diverse biologically active compounds was examined. The obtained results showed how the column order crucially affected the enantioresolution of compounds tested, but the retention was negligibly affected in most cases. We also demonstrated that single TeicoShell and NicoShell columns are very promising towards the development of highly efficient and fast/ultrafast sub/supercritical fluid chromatography methods for structurally different chiral compounds. The optimized methods for sub-minute enantioselective separation of certain biologically important compounds were proposed.

Application of Experimental Design Methodologies in the Enantioseparation of Pharmaceuticals by Capillary Electrophoresis: A Review.

Chirality is one of the major issues in pharmaceutical research and industry. Capillary electrophoresis (CE) is an interesting alternative to the more frequently used chromatographic techniques in the enantioseparation of pharmaceuticals, and is used for the determination of enantiomeric ratio, enantiomeric purity, and in pharmacokinetic studies. Traditionally, optimization of CE methods is performed using a univariate one factor at a time (OFAT) approach; however, this strategy does not allow for the evaluation of interactions between experimental factors, which may result in ineffective method development and optimization. In the last two decades, Design of Experiments (DoE) has been frequently employed to better understand the multidimensional effects and interactions of the input factors on the output responses of analytical CE methods. DoE can be divided into two types: screening and optimization designs. Furthermore, using Quality by Design (QbD) methodology to develop CE-based enantioselective techniques is becoming increasingly popular. The review presents the current use of DoE methodologies in CE-based enantioresolution method development and provides an overview of DoE applications in the optimization and validation of CE enantioselective procedures in the last 25 years. Moreover, a critical perspective on how different DoE strategies can aid in the optimization of enantioseparation procedures is presented.

On-line solid-phase extraction of pharmaceutical compounds from wastewater treatment plant samples using restricted access media in column-switching liquid chromatography-tandem mass spectrometry.

An on-line solid phase extraction using a lab-made restricted access media (RAM) was developed as sample preparation procedure for determination of the pharmaceutical compounds caffeine (CAF), carbamazepine (CBZ), norfloxacin (NOR), ciprofloxacin (CIP), fluoxetine (FLX) and venlafaxine in wastewater treatment plant samples by liquid chromatography-tandem mass spectrometry (LC-MS/MS). This method is suitable for use in routine of analysis, avoiding cross-contamination and requiring only a small sample volume (50 µL), with minimal handling. The method was validated according to international guidelines. The chromatographic efficiency was evaluated using peak resolution and asymmetry parameters. Carryover was also evaluated, in order to ensure reliability of the analysis and the ability to reuse the cartridge. Satisfactory linearity (r2 > 0.99) was obtained for all the compounds. The intra- and inter-day precision values were lower than 5.79 and 14.1%, respectively. The limits of detection ranged from 0.01 to 3 µg L-1 and the limits of quantification were from 0.1 to 5 µg L-1. The method was applied to 20 environmental wastewater samples, with caffeine being the most widely detected compound, at the highest concentration of 392 µg L-1, while other compounds were detected in fewer samples at lower concentrations (up to 9.60 µg L-1). The lab-made modification is a cheaper option for on-line sample preparation, compared to commercially available on-line SPE cartridges and RAM columns. Moreover, a high-throughput procedure was achieved, with an analysis time of 16 min including sample preparation and chromatographic separation. The same RAM column was applied over 200 injections including method optimization, validation and application in wastewater samples without loss of analytical response.

Development of electrically assisted solvent bar microextraction followed by high performance liquid chromatography for the extraction and quantification of basic drugs in biological samples.

In this study, a new extraction procedure is introduced based on electrically assisted solvent bar microextraction. In the first step, the analytes are transferred from sample solution to the hollow fiber supported organic solvent. After that, with the aid of an electrical field, the analytes migrated into the aqueous extractant. The proposed approach was used to extract the three basic drugs (including lidocaine, diltiazem, and propranolol) from the plasma and urine samples. Under the optimized condition, (the supported organic solvent: 1-octanol, stirring rate: 300 rpm, pH of sample solution: 12.0, salt concentration: 2.0% (w/v), extraction time: 15 min, aqueous extractant: (30 µL, 100 mM HCl), back-extraction time: 2 min, back-extraction voltage: 100 V), the proposed procedure presented wide linearities with coefficients of determination more than 0.992 over a concentration range of 5.0-1000 ng mL-1. The limit of detection was also determined in the range of 0.5 to 5.0 ng mL-1, repeatability (intra-day) was between 3.3 and 11.1% (n = 4), and reproducibility (inter-day) was between 4.3 and 14.6% (n = 4 days). It was indicated that the proposed approach could effectively extract the analytes from the plasma and urine samples, and the relative recoveries were between 90.2 and 105.6%, indicating the validity of this method.

A review on pharmaceuticals removal from waters by single and combined biological, membrane filtration and ultrasound systems.

Contaminants of emerging concern (CEC) such as pharmaceuticals commonly found in urban and industrial wastewater are a potential threat to human health and have negative environmental impact. Most wastewater treatment plants cannot efficiently remove these compounds and therefore, many pharmaceuticals end up in aquatic ecosystems, inducing problems such as toxicity and antibiotic-resistance. This review reports the extent of pharmaceutical removal by individual processes such as bioreactors, advanced oxidation processes and membrane filtration systems, all of which are not 100% efficient and can lead to the direct discharge of pharmaceuticals into water bodies. Also, the importance of understanding biotransformation of pharmaceutical compounds during biological and ultrasound treatment, and its impact on treatment efficacy will be reviewed. Different combinations of the processes above, either as an integrated configuration or in series, will be discussed in terms of their degradation efficiency and scale-up capabilities. The trace quantities of pharmaceutical compounds in wastewater and scale-up issues of ultrasound highlight the importance of membrane filtration as a concentration and volume reduction treatment step for wastewater, which could subsequently be treated by ultrasound.

Current Applications of Magnetic Nanomaterials for Extraction of Mycotoxins, Pesticides, and Pharmaceuticals in Food Commodities.

Environmental pollutants, such as mycotoxins, pesticides, and pharmaceuticals, are a group of contaminates that occur naturally, while others are produced from anthropogenic sources. With increased research on the adverse ecological and human health effects of these pollutants, there is an increasing need to regularly monitor their levels in food and the environment in order to ensure food safety and public health. The application of magnetic nanomaterials in the analyses of these pollutants could be promising and offers numerous advantages relative to conventional techniques. Due to their ability for the selective adsorption, and ease of separation as a result of magnetic susceptibility, surface modification, stability, cost-effectiveness, availability, and biodegradability, these unique magnetic nanomaterials exhibit great achievement in the improvement of the extraction of different analytes in food. On the other hand, conventional methods involve longer extraction procedures and utilize large quantities of environmentally unfriendly organic solvents. This review centers its attention on current applications of magnetic nanomaterials and their modifications in the extraction of pollutants in food commodities.

Design and synthesis of naphthalene-based chiral strong cation exchangers and their application for chiral separation of basic drugs.

In continuation of our efforts to synthesize a highly dedicated strong cation exchanger, we introduce four chiral stationary phases based on a laterally substituted naphthalene core featuring chiral 2-aminocyclohexansulfonic acid as the chiral cation-exchange site. The selectors were modified with two different terminal units, which enabled immobilization to the silica support by thiol-ene radical reaction or azide-yne click chemistry. The chromatographic parameters of these chiral stationary phases were determined using a set of chiral amines, mainly from the family of ß-blocker pharmaceuticals. The chiral stationary phases immobilized by means of click chemistry were found to be superior to those possessing the sulfide linker to the silica support. The chromatographic results and visualization of density functional theory-calculated conformations of the selectors hint at a combination of a steric and electronic effect of the triazole ring in the course of chiral resolution of the target analytes.

Application of a fast and sensitive method for the determination of contaminants of emerging concern in wastewater using a quick, easy, cheap, effective, rugged and safe-based extraction and liquid chromatography coupled to mass spectrometry.

The inefficiency of wastewater treatment plants (WWTPs) to remove contaminants of emerging concern (CECs) leads to their continuous release to the environment. Consequently, CECs are present at low concentrations in the treated wastewater (TWW), producing unpredicted and unwanted effects on living organisms as they are discharged into water receiving bodies. This work presents a fast and reliable method for the determination of CECs in TWW based on the innovative application of a QuEChERS (quick, easy, cheap, effective, rugged and safe) method for water extraction and determination by sensitive liquid chromatography coupled to quadrupole-linear ion trap tandem mass spectrometry (LC-QqLIT-MS/MS). The scope of the proposed QuEChERS-based method allows the monitoring of 107 CECs, including pharmaceuticals (58), antibiotics (16) and pesticides (33). The proposed method was successfully validated in urban TWW at two concentration levels (50 and 500 ng L-1) and it is a feasible alternative to conventional and time-consuming solid-phase extraction (SPE) methodologies. 89% of the CECs presented mean recovery values in the 70-120% range with relative standard deviations (RSDs) always < 20% (intra and inter-day precision), and limits of quantification (LOQs) in the range 5-500 ng L-1 (89% of the compounds showed a LOQ ≤ 50 ng L-1). The applicability of the method was demonstrated by the analysis of urban TWW samples (7 sampling events). In total, 35 CECs (23 pharmaceuticals, 2 antibiotics and 10 pesticides) were detected in the monitored samples with concentrations ranging from 5 to 677 ng L-1.

The effect of water on the large-scale supercritical fluid chromatography purification of two factor XIa active pharmaceutical ingredients.

BMS-962212, a parenteral Factor XIa inhibitor, was scaled-up for toxicity studies. Two steps of supercritical fluid chromatography (SFC) were developed for the chiral resolution of the penultimate and achiral purification of final active pharmaceutical ingredient (API), BMS-962212. A robust SFC process using Chiralcel OD-H with methanol-acetonitrile as modifier in CO2 was established to achieve a stable and uninterrupted operation with reduced mobile phase viscosity and system pressure drop. More than 230 g of the racemic penultimate was chirally resolved to reach >99% chiral purity, ready for final tert-butyl ester deprotection to provide the API. There were a significant number of impurities in BMS-962212 generated from the final step that needed to be removed. In contrast to conventional SFC conditions, an SFC method exploiting water and ammonia as additives in both the mobile phase and sample solution was developed to accomplish purification and desalting (i.e. removing TFA) of the zwitterionic API in one step. Water as an additive eliminated salt precipitation and improved the resolution while ammonia contributed to the desalting, details of which will be discussed in this article. A throughput of 2 g/h was achieved, and >80 g of the crude API was purified. The same strategy was applied to another Factor XIa API (compound A) and its penultimate.

Cinchona-alkaloid-based zwitterionic chiral stationary phases as potential tools for high-performance liquid chromatographic enantioseparation of cationic compounds of pharmaceutical relevance.

Enantiomers of cationic compounds of pharmaceutical relevance, namely tetrahydro-ß-carboline and 1,2,3,4-tetrahydroisoquinoline analogs, were separated by high-performance liquid chromatography. Separations were performed on Cinchona-alkaloid-based zwitterionic ion exchanger type chiral stationary phases applied as cation exchangers using mixtures of methanol and acetonitrile or tetrahydrofuran as bulk solvent components containing triethylammonium acetate or ammonium acetate as organic salt additives. On the zwitterionic ZWIX(+) and ZWIX(-) columns investigated, retention and enantioseparation of the studied basic analytes were influenced by the nature and concentration of the organic components of the mobile phase. The effect of organic salt additives on the retention behavior of the studied analytes can be described by the stoichiometric displacement model related to the counterion concentration. Investigations on the structure-retention relationships were performed applying different mobile phase systems for the two types of cationic analytes. For the thermodynamic characterization, parameters such as changes in standard enthalpy (Δ(ΔH°)), entropy (Δ(ΔS°)), and free energy (Δ(ΔG°)) were calculated on the basis of van't Hoff plots derived from the ln α versus 1/T curves. In most cases, enthalpy-driven enantioseparations were observed, with a consistent dependence of the calculated thermodynamic parameters on the mobile phase composition. Elution sequences of the studied compounds were determined in all cases.

Development of a maleic acid-based material to selectively solid-phase extract basic compounds from environmental samples.

This study presents a novel mixed-mode weak cation-exchange (WCX) material. This material was prepared by means of the functionalization of a mesoporous divinylbenzene (DVB) resin with maleic acid (maleic acid-DVB), which yielded a high carboxylic moiety content resulting in WCX interactions as well as suitable specific surface area for reversed-phase interactions. After the optimization of the solid-phase extraction (SPE) protocol to enhance the selectivity of the sorbent, this material was evaluated as a novel WCX sorbent in the SPE of a group of drugs from environmental water samples. The method is based on SPE followed by liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) with an Orbitrap analyzer, and was validated and applied for the determination of basic drugs in river, effluent and influent wastewater samples. Maleic acid-DVB sorbent yielded suitable recovery rates (57% to 89%) and an acceptable matrix effect (<32%) thanks to the effective washing step included when these environmental waters were loaded through the novel resin. The method was applied to different environmental water samples and some basic drugs were suitably quantified in these environmental samples.

The Use of Dual Cyclodextrin Chiral Selector Systems in the Enantioseparation of Pharmaceuticals by Capillary Electrophoresis: An Overview.

Cyclodextrin (CD) derivatives are the most efficient and frequently used chiral selectors (CSs) in capillary electrophoresis (CE). There are situations when the use of a single CD as CS is not enough to obtain efficient chiral discrimination of the enantiomers; in these cases, sometimes this problem can be resolved using a dual CD system. The use of dual CD systems can often dramatically enhance enantioseparation selectivity and can be applied for the separation of many analytes of pharmaceutical interest for which enantioseparation by CE with another CS systems can be problematic. Usually in a dual CD system an anionic CD is used together with a neutral one, but there are situations when the use of a cationic CD with a neutral one or the use of two neutral CDs or even two ionized CDs can be an efficient solution. In the current review we present general aspects of the use of dual CD systems in the analysis of pharmaceutical substances. Several examples of applications of the use of dual CD systems in the analysis of pharmaceuticals are selected and discussed. Theoretical aspects regarding the separation of enantiomers through simultaneous interaction with the two CSs are also explained. Finally, advantages, disadvantages, potential and new direction in this chiral analysis field are highlighted.

Enhanced Pharmaceutically Active Compounds Productivity from Streptomyces SUK 25: Optimization, Characterization, Mechanism and Techno-Economic Analysis.

The present research aimed to enhance the pharmaceutically active compounds' (PhACs') productivity from Streptomyces SUK 25 in submerged fermentation using response surface methodology (RSM) as a tool for optimization. Besides, the characteristics and mechanism of PhACs against methicillin-resistant Staphylococcus aureus were determined. Further, the techno-economic analysis of PhACs production was estimated. The independent factors include the following: incubation time, pH, temperature, shaker rotation speed, the concentration of glucose, mannitol, and asparagine, although the responses were the dry weight of crude extracts, minimum inhibitory concentration, and inhibition zone and were determined by RSM. The PhACs were characterized using GC-MS and FTIR, while the mechanism of action was determined using gene ontology extracted from DNA microarray data. The results revealed that the best operating parameters for the dry mass crude extracts production were 8.20 mg/L, the minimum inhibitory concentrations (MIC) value was 8.00 µg/mL, and an inhibition zone of 17.60 mm was determined after 12 days, pH 7, temperature 28 °C, shaker rotation speed 120 rpm, 1 g glucose /L, 3 g mannitol/L, and 0.5 g asparagine/L with R2 coefficient value of 0.70. The GC-MS and FTIR spectra confirmed the presence of 21 PhACs, and several functional groups were detected. The gene ontology revealed that 485 genes were upregulated and nine genes were downregulated. The specific and annual operation cost of the production of PhACs was U.S. Dollar (U.S.D) 48.61 per 100 mg compared to U.S.D 164.3/100 mg of the market price, indicating that it is economically cheaper than that at the market price.

Symbioses of Cyanobacteria in Marine Environments: Ecological Insights and Biotechnological Perspectives.

Cyanobacteria are a diversified phylum of nitrogen-fixing, photo-oxygenic bacteria able to colonize a wide array of environments. In addition to their fundamental role as diazotrophs, they produce a plethora of bioactive molecules, often as secondary metabolites, exhibiting various biological and ecological functions to be further investigated. Among all the identified species, cyanobacteria are capable to embrace symbiotic relationships in marine environments with organisms such as protozoans, macroalgae, seagrasses, and sponges, up to ascidians and other invertebrates. These symbioses have been demonstrated to dramatically change the cyanobacteria physiology, inducing the production of usually unexpressed bioactive molecules. Indeed, metabolic changes in cyanobacteria engaged in a symbiotic relationship are triggered by an exchange of infochemicals and activate silenced pathways. Drug discovery studies demonstrated that those molecules have interesting biotechnological perspectives. In this review, we explore the cyanobacterial symbioses in marine environments, considering them not only as diazotrophs but taking into consideration exchanges of infochemicals as well and emphasizing both the chemical ecology of relationship and the candidate biotechnological value for pharmaceutical and nutraceutical applications.