Discovery of highly insecticidal synthetic spinosyn mimics - CAMD enabled de novo design simplifying a complex natural product

Simplifying complex natural products: Computer modeling-based design leads to highly insecticidal, chemically simpler synthetic mimics of the spinosyn natural products that are active in the field. © 2018 Society of Chemical Industry.

Occurrence of halogenated natural products in highly consumed fish from polluted and unpolluted tropical bays in SE Brazil

Natural compounds from the metabolism of marine organisms have been detected at high concentrations in environmental samples which are not the producers of these compounds. These natural substances are known as halogenated natural products (HNPs). HNPs are possibly toxic halogenated compounds analogous to POPs that may bioaccumulate and biomagnify along the food web and pose a further risk to human and environmental health. The present study analyzed the occurrence of HNPs in the edible muscle of the three most consumed commercial fish species in the state of Rio de Janeiro: sardine (Sardinella brasiliensis), whitemouth croaker (Micropogonias furnieri) and mullet (Mugil liza) from the highly polluted Guanabara Bay (GB) and the less polluted Ilha Grande Bay (IGB). The analytical steps included Soxhlet extraction, clean-up step and injection in a gas chromatography system coupled to a mass spectrometer operated in the electron-capture negative ion mode (GC/ECNI-MS). The compounds 2,4,6-TBP, 2,4,6-TBA, MHC-1, Q1, 6-MeO-BDE 47 and 2'-MeO-BDE 68 were found in the analyzed fish from both studied areas. Q1, 6-MeO-BDE 47 and 2'-MeO-BDE 68 showed the highest concentrations in samples. Q1 concentrations in the sardines from IGB were higher than the sardines from GB (p < 0.05) and higher than the other IGB species (p < 0.05). The differences found among the species may be related to their characteristic habitat and diet. It is noteworthy that most of these compounds do not have any toxicological reference value. Moreover, the HNPs are being detected in species of low trophic level and since this study has worked only with commercial species, these fish may be considered as a source for human exposure to these natural compounds.

Virtual screening of natural anti-filarial compounds against glutathione-S-transferase of Brugia malayi and Wuchereria bancrofti

Glutathione-S-transferase also referred as GST is one of the major detoxification enzymes in parasitic helminths. The crucial role played by GST in various chronic infections has been well reported. The dependence of nematodes on detoxification enzymes to maintain their survival within the host established the crucial role of GST in filariasis and other related diseases. Hence, this well-established role of GST in filariasis along with its greater nonhomology with its human counterpart makes it an important therapeutic drug target. Here in this study, we have tried to explore the inhibitory potential of some of the well-reported natural ant-filarial compounds against the GST from Wuchereria bancrofti (W.bancrofti) and Brugia malayi (B.malayi). In silico virtual screening, approach was used to screen the selected natural compounds against GST from W.bancrofti and B.malayi. On the basis of our results, here we are reporting some of the natural compounds which were found to be very effective against GSTs. Along with we have also revealed the characteristic of the active site of BmGST and WbGST and the role of important active site residues involve in the binding of natural compounds within the active site of GSTs. This information will oped doors for using natural compounds as anti-filarial therapy and will also be helpful for future drug discovery.

Transcriptomics and proteomics analyses of anti-cancer mechanisms of TR35-An active fraction from Xinjiang Bactrian camel milk in esophageal carcinoma cell

BACKGROUND & AIMS

The aim of the paper is to investigate the effect of the active fraction extracted from the Xinjiang Bactrian camel whey on the human cancer cells using an in vitro and in vivo model of human carcinoma of the esophagus.

METHODS AND RESULTS

Our results demonstrated that an antitumor active fraction, TR35, isolated from Xinjiang Bactrian camel milk could significantly inhibit Eca109 cell proliferation and induce its apoptosis (indicated by MTT assay, Annexin V-FITC Apoptosis Detection, and caspase-3 activity). Moreover, we found that TR35 could inhibit the growth of xenografted tumor in nude mice without loss in body weight. Furthermore, we used RNA-Seq and 2-DE combined Mass Spectrometry analysis to identify differentially expressed RNA and protein markers of apoptosis and necrosis. Compared with untreated Eca109 cells, a total of 405 differentially expressed genes and 55 differentially expressed proteins were identified in TR35 treated Eca109 cells. KEGG analysis uncovered signaling pathways closely associated with cancer inhibition that were enriched in the TR35-treated cells.

CONCLUSIONS

These results might implicate that downregulation of specific proteins identified in this study may be the cause of this tumor growth inhibition. This study sheds light on the potential therapeutic advantages based on the historical anti-cancer activities of camel milk.

Increasing Metabolic Diversity in Marine Sponges Extracts by Controlling Extraction Parameters

Metabolomics has become an important tool in the search for bioactive compounds from natural sources, with the recent inclusion of marine organisms. Of the several steps performed in metabolomics studies, the extraction process is a crucial step-one which has been overlooked for a long time. In the presented study, a pressurized liquid extraction system was used to investigate the effect of extraction parameters such as pressure, temperature, number of cycles, and solvent polarity on the chemical diversity of the extract obtained from the marine sponge, Xestospongia. For this, a full factorial design (2⁴) was performed using a chemical diversity index, which was found to be a suitable tool to determine the efficiency of the extraction process, as the response variable. This index was calculated using a logarithmic transformation of ¹H NMR signals. Three factors (number of cycles, temperature, and solvent polarity) and two interactions were found to affect the chemical diversity of the obtained extracts significantly. Two individual factors (temperature and solvent polarity) were selected for further study on their influence on sponge metabolites using orthogonal partial least square (OPLS) modeling. Based on the results, the groups of compounds that were most influenced by these parameters were determined, and it was concluded that ethanol as the extraction solvent together with low temperatures were the conditions that provided a higher chemical diversity in the extract.

Dereplication of microbial metabolites through database search of mass spectra

Natural products have traditionally been rich sources for drug discovery. In order to clear the road toward the discovery of unknown natural products, biologists need dereplication strategies that identify known ones. Here we report DEREPLICATOR+, an algorithm that improves on the previous approaches for identifying peptidic natural products, and extends them for identification of polyketides, terpenes, benzenoids, alkaloids, flavonoids, and other classes of natural products. We show that DEREPLICATOR+ can search all spectra in the recently launched Global Natural Products Social molecular network and identify an order of magnitude more natural products than previous dereplication efforts. We further demonstrate that DEREPLICATOR+ enables cross-validation of genome-mining and peptidogenomics/glycogenomics results.

Exploring bioactive peptides from bacterial secretomes using PepSAVI-MS: identification and characterization of Bac-21 from Enterococcus faecalis pPD1

As current methods for antibiotic drug discovery are being outpaced by the rise of antimicrobial resistance, new methods and innovative technologies are necessary to replenish our dwindling arsenal of antimicrobial agents. To this end, we developed the PepSAVI-MS pipeline to expedite the search for natural product bioactive peptides. Herein we demonstrate expansion of PepSAVI-MS for the discovery of bacterial-sourced bioactive peptides through identification of the bacteriocin Bac-21 from Enterococcus faecalis pPD1. Minor pipeline modifications including implementation of bacteria-infused agar diffusion assays and optional digestion of peptide libraries highlight the versatility and wide adaptability of the PepSAVI-MS pipeline. Additionally, we have experimentally validated the primary protein sequence of the active, mature Bac-21 peptide for the first time and have confirmed its identity with respect to primary sequence and post-translational processing. Successful application of PepSAVI-MS to bacterial secretomes as demonstrated herein establishes proof-of-principle for use in novel microbial bioactive peptide discovery.

Integrated analytical assets aid botanical authenticity and adulteration management

This article reviews and develops a perspective for the meaning of authenticity in the context of quality assessment of botanical materials and the challenges associated with discerning adulterations vs. contaminations vs. impurities. Authentic botanicals are by definition non-adulterated, a mutually exclusive relationship that is confirmed through the application of a multilayered set of analytical methods designed to validate the (chemo)taxonomic identity of a botanical and certify that it is devoid of any adulteration. In practice, the ever-increasing sophistication in the process of intentional adulteration, as well as the growing number of botanicals entering the market, altogether necessitate a constant adaptation and reinforcement of authentication methods with new approaches, especially new technologies. This article summarizes the set of analytical methods - classical and contemporary - that can be employed in the authentication of botanicals. Particular emphasis is placed on the application of untargeted metabolomics and chemometrics. An NMR-based untargeted metabolomic model is proposed as a rapid, systematic, and complementary screening for the discrimination of authentic vs. potentially adulterated botanicals. Such analytical model can help advance the evaluation of botanical integrity in natural product research.

Pharmacological studies of Adhatoda vasica and Calotropis procera as resource of bio-active compounds for various diseases

Adhatoda vasica and Calotropis procera species were investigated as a resource for new diverse pharmacological agents including B complex, individual total phenolic compounds and antioxidants for curing and treatments of many infectious diseases in human through advanced analytical methods. These plants are abundant in Khyber Pukhtoon Khawa, Pakistan as well as in all over the world and famous for their unique medicinal importance. These herbaceous species are so far used for animals curing while current exploration of these species showed that these species are a precious resource of various compounds which can be employed in the formation of different drugs. The results showed that the leaf and flower extracts of Adhatoda vasica and leaf extract of Calotropis procera contained higher contents of bioactive compounds. The chemical analysis of the samples resulted in higher values of total phenolic compounds (71.32mg GAE/g), total antioxidants (651% DPPH inhibition), the enzyme catalase (4716µg/g), ash content (16.72%) and pH values in the Calotropis procera, whereas the total carotenoids (1987mg/100g), the enzymes, superoxide dismutase (4566µg/g) and peroxidase (1322μg/g) were higher in leaves of Adhatoda vasica. The flower extract of the Adhatoda vasica was rich in the flavonoids (0.87mg/100g) and organic matter (89.99%) as compared to Calotropis procera. The obtained data for each parameter was interpreted by applying Complete Randomized Design (CRD) along with factorial arrangements. The mean comparison was performed using LSD test at 5% probability level. The presence of these phytochemicals may lead to the conclusion that these herbal plants have the potential for formation of new drugs and can be used as herbal medicine for treatment of different cancer and viral diseases. These compounds are also useful in the treatment of the tumor.

Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research

Imaging mass spectrometry (IMS) has recently established itself in the field of "spatial metabolomics." Merging the sensitivity and fast screening of high-throughput mass spectrometry with spatial and temporal chemical information, IMS visualizes the production, location, and distribution of metabolites in intact biological models. Since metabolite profiling and morphological features are combined in single images, IMS offers an unmatched chemical detail on complex biological and microbiological systems. Thus, IMS-type "spatial metabolomics" emerges as a powerful and complementary approach to genomics, transcriptomics, and classical metabolomics studies. In this review, we summarize the current state-of-the-art IMS methods with a strong focus on desorption electrospray ionization (DESI)-IMS. DESI-IMS utilizes the original principle of electrospray ionization, but in this case solvent droplets are rastered and desorbed directly on the sample surface. The rapid and minimally destructive DESI-IMS chemical screening is achieved at ambient conditions and enables the accurate view of molecules in tissues at the µm-scale resolution. DESI-IMS analysis does not require complex sample preparation and allows repeated measurements on samples from different biological sources, including microorganisms, plants, and animals. Thanks to its easy workflow and versatility, DESI-IMS has successfully been applied to many different research fields, such as clinical analysis, cancer research, environmental sciences, microbiology, chemical ecology, and drug discovery. Herein we discuss the present applications of DESI-IMS in natural product research.

Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery

The therapeutic properties of plants have been recognised since time immemorial. Many pathological conditions have been treated using plant-derived medicines. These medicines are used as concoctions or concentrated plant extracts without isolation of active compounds. Modern medicine however, requires the isolation and purification of one or two active compounds. There are however a lot of global health challenges with diseases such as cancer, degenerative diseases, HIV/AIDS and diabetes, of which modern medicine is struggling to provide cures. Many times the isolation of "active compound" has made the compound ineffective. Drug discovery is a multidimensional problem requiring several parameters of both natural and synthetic compounds such as safety, pharmacokinetics and efficacy to be evaluated during drug candidate selection. The advent of latest technologies that enhance drug design hypotheses such as Artificial Intelligence, the use of 'organ-on chip' and microfluidics technologies, means that automation has become part of drug discovery. This has resulted in increased speed in drug discovery and evaluation of the safety, pharmacokinetics and efficacy of candidate compounds whilst allowing novel ways of drug design and synthesis based on natural compounds. Recent advances in analytical and computational techniques have opened new avenues to process complex natural products and to use their structures to derive new and innovative drugs. Indeed, we are in the era of computational molecular design, as applied to natural products. Predictive computational softwares have contributed to the discovery of molecular targets of natural products and their derivatives. In future the use of quantum computing, computational softwares and databases in modelling molecular interactions and predicting features and parameters needed for drug development, such as pharmacokinetic and pharmacodynamics, will result in few false positive leads in drug development. This review discusses plant-based natural product drug discovery and how innovative technologies play a role in next-generation drug discovery.

Quality markers of animal medicinal materials: Correlative analysis of musk reveals distinct metabolic changes induced by multiple factors

BACKGROUND

Common farming environmental elements, such as longitude, latitude, and altitude, and physiological conditions, such as age and body weight, are thought to influence medicinal animal homeostasis and material quality by altering endocrine functions for primary and secondary metabolite formation. However, the currently available methods for evaluating complex components of traditional Chinese animal medicines have insufficient sensitivity and specificity.

PURPOSE

Characterizing the primary/secondary metabolomes of medicinal animals is essential for understanding their material basis, controlling product quality, and reflecting on distribution interactions. Therefore, this study aimed to screen ecological- and physiological-related metabolites in captive Moschus berezovskii throughout the collection period based on the quality marker (Q-marker) concept.

STUDY DESIGN AND METHODS

Fifty-one musk deer samples from 12 different distribution farms ranging in age from 2 to 11 years were enrolled. Differentially expressed musk metabolites were assessed via chromatography-tandem mass spectrometry technologies. A metabolome that mapped connections among these factors was established using chemometric and topological calculations.

RESULTS

Statistical analysis revealed that muscone, cis-9-hexadecenal, antioxidant 2264, prasterone-3-sulfate, androstan-17-one, and 1,2-benzenedicarboxylic acid showed significantly altered expression. Partial least squares (PLS) regression analysis of qualified data for these 6 secondary metabolites (active components) demonstrated that age is the most important factor underlying the varying levels of muscone, androstan-17-one and 1,2-benzenedicarboxylic acid. Furthermore, weight was the most important factor for cis-9-hexadecenal, longitude was important for antioxidant 2264, latitude was important for prasterone-3-sulfate, and altitude was important for antioxidant 2264, androstan-17-one and 1,2-benzenedicarboxylic. Metabolite analysis within the MetaboAnalyst (MetPA) suite showed that 18 candidate biomarker metabolites were screened, including allantoin, glycine, serine, creatine, alanine, taurine, lactate, 2-oxoglutarate (2-OG), fumarate, proline, xanthine, cytosine, carnitine, arginine, threonine, aspartate, and urea. Metabolic network analysis showed 4 important pathways that were involved: arginine and proline metabolism, the urea cycle, aspartate metabolism, and glycine, serine and threonine metabolism.

CONCLUSION

Using this combined metabolomic and chemometric approach, this study was successful in screening Q-markers for musk quality control and provided new insights into correlations among "ecological & physiological factors→Q-markers→metabolites", which potentially provides crucial information for musk breeding and material quality control.

Experience with host cell protein impurities in biopharmaceuticals

In the 40-year history of biopharmaceuticals, there have been a few cases where the final products contained residual host cell protein (HCP) impurities at levels high enough to be of concern. This article summarizes the industry experience in these cases where HCP impurities have been presented in public forums and/or published. Regulatory guidance on HCP impurities is limited to advising that products be as pure as practical, with no specified numerical limit because the risk associated with HCP exposure often depends on the clinical setting (route of administration, dose, indication, patient population) and the particular impurity. While the overall safety and purity track record of the industry is excellent, these examples illustrate several important lessons learned about the kinds of HCPs that co-purify with products (e.g., product homologs, and HCPs that react with product), and the kinds of clinical consequences of HCP impurities (e.g., direct biological activity, immunogenicity, adjuvant). The literature on industry experience with HCP impurities is scattered, and this review draws in to one reference documented examples where the data have been presented in meetings, patents, product inserts, or press releases, in addition to peer-reviewed journal articles. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:828-837, 2018.

Supercritical Fluid Chromatography in Natural Product Analysis - An Update

The wide chemical diversity of natural products has challenged analysts all over the world and has been a driving force for the development of innovative technologies since decades. In the last years, supercritical fluid chromatography (SFC) has finally emerged from the shadow of liquid chromatography (LC) and gas chromatography (GC) and has become a powerful tool in modern natural product analysis. Whereas in the past the technique had mainly been restricted to a small group of nonpolar compounds, it has largely expanded its suitability in the last years and has demonstrated possibilities without boundaries. This mini-review, focused on the latest applications, provides a brief update on the current status of SFC in natural product analysis with the aim to demonstrate its applicability for both polar and nonpolar plant constituents. The approaches cover the whole range of polarity, including carotenoids, flavonoids, water-unstable ginkgolides, and even highly polar triterpene saponins with several sugar residues.

Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra

Motivation

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI) facilitates the analysis of large organic molecules. However, the complexity of biological samples and MALDI data acquisition leads to high levels of variation, making reliable quantification of samples difficult. We present a new analysis approach that we believe is well-suited to the properties of MALDI mass spectra, based upon an Independent Component Analysis derived for Poisson sampled data. Simple analyses have been limited to studying small numbers of mass peaks, via peak ratios, which is known to be inefficient. Conventional PCA and ICA methods have also been applied, which extract correlations between any number of peaks, but we argue makes inappropriate assumptions regarding data noise, i.e. uniform and Gaussian.

Results

We provide evidence that the Gaussian assumption is incorrect, motivating the need for our Poisson approach. The method is demonstrated by making proportion measurements from lipid-rich binary mixtures of lamb brain and liver, and also goat and cow milk. These allow our measurements and error predictions to be compared to ground truth.

Availability and implementation

Software is available via the open source image analysis system TINA Vision, www.tina-vision.net.

Contact

paul.tar@manchester.ac.uk.

Supplementary information

Supplementary data are available at Bioinformatics online.

Quantifying orientational regeneration of injured neurons by natural product concentration gradients in a 3D microfluidic device

Regeneration of injured neurons in complicated three-dimensional (3D) microenvironments is a key approach for treating neurodegenerative diseases. Microfluidics provides a versatile tool to recapitulate cellular microenvironments in vitro, but it still remains a big challenge to construct a microfluidic platform incorporating extracellular matrix (ECM) structures and highly controlled 3D gradients of soluble factors to study the regeneration of injured neurons. In this work, we developed a microfluidic device which can provide multiple adjustable gradients in a 3D ECM to investigate the regeneration of injured central nervous system (CNS) neurons in response to natural small molecules. With interconnecting but independently controlled central channels, asymmetrically designed side channels and a series of microgrooves connecting the central channels, spatially and temporally controlled 3D biochemical gradients can be generated inside collagen hydrogel in the central channels. This allows quantitative analysis of guided axon growth and the orientational regeneration of injured dopaminergic neurons by 3D chemical gradients of three natural molecules. This study demonstrates a promising microfluidic platform for the generation of highly controlled 3D biochemical gradients in an ECM to quantitatively study neuronal responses, thereby potentially facilitating drug screening and optimization of treatment protocols for neurodegenerative diseases.

Collision induced unfolding of isolated proteins in the gas phase: past, present, and future

Rapidly characterizing the three-dimensional structures of proteins and the multimeric machines they form remains one of the great challenges facing modern biological and medical sciences. Ion mobility-mass spectrometry based techniques are playing an expanding role in characterizing these functional complexes, especially in drug discovery and development workflows. Despite this expansion, ion mobility-mass spectrometry faces many challenges, especially in the context of detecting small differences in protein tertiary structure that bear functional consequences. Collision induced unfolding is an ion mobility-mass spectrometry method that enables the rapid differentiation of subtly-different protein isoforms based on their unfolding patterns and stabilities. In this review, we summarize the modern implementation of such gas-phase unfolding experiments and provide an overview of recent developments in both methods and applications.

Optimization and validation of reverse phase HPLC method for qualitative and quantitative assessment of polyphenols in seaweed

A simple reverse phase-high performance liquid chromatography (RP-HPLC) coupled to a diode array detector (DAD) and negative ion electrospray mass spectrometer (ESI-MS) method was developed for simultaneous identification and quantification of phenolic antioxidants in seaweed. The proposed method was validated in terms of linearity, limits of detection (LOD), limits of quantification (LOQ), recovery and intermediate precision. The calibration curves were linear with correlation coefficient ranging from 0.9909 to 0.9997 while the values of LOD (0.26-0.82mg/L), LOQ (0.77-2.50mg/L), recovery (≥97.2%) and precision in terms of retention time (%RSD ≤2.27) and peak area (% RSD ≤5.11) were satisfactory. Brown seaweed Himanthalia elongata used in this study was extracted with 60% methanol and the crude extract was cleaned with SPE (Solid Phase Extraction) cartridge. HPLC-DAD-MS/MS analysis of the SPE fraction allowed the identification of 7 phenolic compounds comprising phlorotannins, hydroxybenzoic acid, hydroxycinnamic acid and flavonols subclasses of polyphenols. Quantitative analysis of these compounds revealed the presence of phloroglucinol (394.1±4.33μg/g), gallic acid (96.3±3.12μg/g), chlorogenic acid (38.8±1.94μg/g), caffeic acid (44.4±2.72μg/g), ferulic acid (17.6±0.85μg/g), myricetin (8.6±0.85μg/g) and quercetin (4.2±0.15μg/g), in the extract. The SPE fraction were tested for antioxidant capacity which were significantly (P <0.05) higher (EC50; 14.5±0.57mg/g) than the ascorbic acid (EC50; 35.8±0.59mg/g) and the crude extract (EC50; 46.3±0.48mg/g). The occurrence of all these phenolic antioxidant compounds in H. elongata extract suggested that the developed method is sensitive enough and reproducible and could be used for qualitative and quantitative assessment of polyphenols in seaweed.

Anti-Trypanosoma, anti-Leishmania and cytotoxic activities of natural products from Psidium brownianum Mart. ex DC. and Psidium guajava var. Pomifera analysed by LC-MS

Neglected diseases are those that are prevalent in developing countries, even with a rich biodiversity. These diseases still persist because of the lack of scientific studies, government negligence or failures of the public health system. This study aims to identify the composition of extracts and fractions from Psidium brownianum and Psidium guajava through LC-MS, to evaluate its in vitro anti-parasitic and cytotoxic activity against Trypanosoma cruzi, Leishmania brasiliensis and L. infantum epismastigote and promastigote forms, as well as mammalian cells. The results showed the presence of chemical constituents in the two Psidium species as quercetin, myricetin and gallic acid derivatives. The P. brownianum extract and fractions showed low toxicity at all tested concentrations and all samples were effective at the concentration of 1000μg/mL against the parasites, with the extract being the most efficient against the L. infantum promastigote form. The ethanolic extract, and the flavonoid and tannic fractions, from P. guajava showed low toxicity for the fibroblasts. All samples showed effectiveness at the highest concentration tested and the extract was more effective against the promastigote forms tested. The results showed that the species Psidium brownianum and Psidium guajava demonstrated an anti-parasitic activity against the T. cruzi, L. brasiliensis and L. infantum parasite cell lines indicating these species as an alternative therapy given their efficacy in the in vitro assays performed, opening the possibility for new biological studies to further this knowledge through in vivo assays.

Qualitative and quantitative characterization of protein biotherapeutics with liquid chromatography mass spectrometry

In the last decade, the advancement of liquid chromatography mass spectrometry (LC/MS) techniques has enabled their broad application in protein characterization, both quantitatively and qualitatively. Owing to certain important merits of LC/MS techniques (e.g., high selectivity, flexibility, and rapid method development), LC/MS assays are often deemed as preferable alternatives to conventional methods (e.g., ligand-binding assays) for the analysis of protein biotherapeutics. At the discovery and development stages, LC/MS is generally employed for two purposes absolute quantification of protein biotherapeutics in biological samples and qualitative characterization of proteins. For absolute quantification of a target protein in bio-matrices, recent work has led to improvements in the efficiency of LC/MS method development, sample treatment, enrichment and digestion, and high-performance low-flow-LC separation. These advances have enhanced analytical sensitivity, specificity, and robustness. As to qualitative analysis, a range of techniques have been developed to characterize intramolecular disulfide bonds, glycosylation, charge variants, primary sequence heterogeneity, and the drug-to-antibody ratio of antibody drug conjugate (ADC), which has enabled a refined ability to assess product quality. In this review, we will focus on the discussion of technical challenges and strategies of LC/MS-based quantification and characterization of biotherapeutics, with the emphasis on the analysis of antibody-based biotherapeutics such as monoclonal antibodies (mAbs) and ADCs. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:734-754, 2017.

Photo-affinity labelling and biochemical analyses identify the target of trypanocidal simplified natural product analogues

Current drugs to treat African sleeping sickness are inadequate and new therapies are urgently required. As part of a medicinal chemistry programme based upon the simplification of acetogenin-type ether scaffolds, we previously reported the promising trypanocidal activity of compound 1, a bis-tetrahydropyran 1,4-triazole (B-THP-T) inhibitor. This study aims to identify the protein target(s) of this class of compound in Trypanosoma brucei to understand its mode of action and aid further structural optimisation. We used compound 3, a diazirine- and alkyne-containing bi-functional photo-affinity probe analogue of our lead B-THP-T, compound 1, to identify potential targets of our lead compound in the procyclic form T. brucei. Bi-functional compound 3 was UV cross-linked to its target(s) in vivo and biotin affinity or Cy5.5 reporter tags were subsequently appended by Cu(II)-catalysed azide-alkyne cycloaddition. The biotinylated protein adducts were isolated with streptavidin affinity beads and subsequent LC-MSMS identified the FoF1-ATP synthase (mitochondrial complex V) as a potential target. This target identification was confirmed using various different approaches. We show that (i) compound 1 decreases cellular ATP levels (ii) by inhibiting oxidative phosphorylation (iii) at the FoF1-ATP synthase. Furthermore, the use of GFP-PTP-tagged subunits of the FoF1-ATP synthase, shows that our compounds bind specifically to both the α- and β-subunits of the ATP synthase. The FoF1-ATP synthase is a target of our simplified acetogenin-type analogues. This mitochondrial complex is essential in both procyclic and bloodstream forms of T. brucei and its identification as our target will enable further inhibitor optimisation towards future drug discovery. Furthermore, the photo-affinity labeling technique described here can be readily applied to other drugs of unknown targets to identify their modes of action and facilitate more broadly therapeutic drug design in any pathogen or disease model.

Nanofluidic device for continuous multiparameter quality assurance of biologics

Process analytical technology (PAT) is critical for the manufacture of high-quality biologics as it enables continuous, real-time and on-line/at-line monitoring during biomanufacturing processes. The conventional analytical tools currently used have many restrictions to realizing the PAT of current and future biomanufacturing. Here we describe a nanofluidic device for the continuous monitoring of biologics' purity and bioactivity with high sensitivity, resolution and speed. Periodic and angled nanofilter arrays served as the molecular sieve structures to conduct a continuous size-based analysis of biologics. A multiparameter quality monitoring of three separate commercial biologic samples within 50 minutes has been demonstrated, with 20 µl of sample consumption, inclusive of dead volume in the reservoirs. Additionally, a proof-of-concept prototype system, which integrates an on-line sample-preparation system and the nanofluidic device, was demonstrated for at-line monitoring. Thus, the system is ideal for on-site monitoring, and the real-time quality assurance of biologics throughout the biomanufacturing processes.

Quantitative LC/ESI-SRM/MS of antibody biopharmaceuticals: use of a homologous antibody as an internal standard and three-step method development

Monoclonal antibody-based therapeutic agents (antibody drugs) have attracted considerable attention as a new type of drug. Concomitantly, the use of quantitative approaches for characterizing antibody drugs, such as liquid chromatography (LC)-mass spectrometry (MS), has increased. Generally, selective quantification of antibody drugs is done using unique peptides from variable regions (V _H and V _L) as surrogate peptides. Further, numerous internal standards (ISs) such as stable isotope-labeled (SIL)-intact proteins and SIL-surrogate peptides are used. However, developing LC-MS methodology for characterizing antibody drugs is time-consuming and costly. Therefore, LC-MS is difficult to apply for this purpose, particularly during the drug discovery stage when numerous candidates must be evaluated. Here, we demonstrate an efficient approach to developing a quantitative LC/electrospray ionization (ESI)-selected reaction monitoring (SRM)/MS method for characterizing antibody drugs. The approach consists of the following features: (i) standard peptides or SIL-IS are not required; (ii) a peptide from the homologous monoclonal antibody serves as an IS; (iii) method development is monitored using a spiked plasma sample and one quantitative MS analysis; and (iv) three predicted SRM assays are performed to optimize quantitative SRM conditions such as transition, collision energy, and declustering potential values. Using this strategy, we developed quantitative SRM methods for infliximab, alemtuzumab, and bevacizumab with sufficient precision (<20%)/accuracy (<±20%) for use in the drug discovery stage. We have also demonstrated that choosing a higher homologous peptide pair (from analyte mAb/IS mAb) is necessary to obtain the sufficient precision and accuracy. Graphical abstract ᅟ.

qNMR for profiling the production of fungal secondary metabolites

Analysis of complex mixtures is a common challenge in natural products research. Quantitative nuclear magnetic resonance spectroscopy offers analysis of complex mixtures at early stages and with benefits that are orthogonal to more common methods of quantitation, including ultraviolet absorption spectroscopy and mass spectrometry. Several experiments were conducted to construct a methodology for use in analysis of extracts of fungal cultures. A broadly applicable method was sought for analysis of both pure and complex samples through use of an externally calibrated method. This method has the benefit of not contaminating valuable samples with the calibrant, and it passed scrutiny for line fitting and reproducibility. The method was implemented to measure the yield of griseofulvin and dechlorogriseofulvin from three fungal isolates. An isolate of Xylaria cubensis (coded MSX48662) was found to biosynthesize griseofulvin in the greatest yield, 149 ± 8 mg per fermentation, and was selected for further supply experiments. Copyright © 2016 John Wiley & Sons, Ltd.