RECENT ADVANCEMENTS IN HPLC-NMR AND APPLICATIONS FOR NATURAL PRODUCT PROFILING AND IDENTIFICATION

Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery

Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.

Ultrafast 2D NMR for the analysis of complex mixtures

2D NMR is extensively used in many different fields, and its potential for the study of complex biochemical or chemical mixtures has been widely demonstrated. 2D NMR gives the ability to resolve peaks that overlap in 1D spectra, while providing both structural and quantitative information. However, complex mixtures are often analysed in situations where the data acquisition time is a crucial limitation, due to an ongoing chemical reaction or a moving sample from a hyphenated technique, or to the high-throughput requirement associated with large sample collections. Among the great diversity of available fast 2D methods, ultrafast (or single-scan) 2D NMR is probably the most general and versatile approach for complex mixture analysis. Indeed, ultrafast NMR has undergone an impressive number of methodological developments that have helped turn it into an efficient analytical tool, and numerous applications to the analysis of mixtures have been reported. This review first summarizes the main concepts, features and practical limitations of ultrafast 2D NMR, as well as the methodological developments that improved its analytical potential. Then, a detailed description of the main applications of ultrafast 2D NMR to mixture analysis is given. The two major application fields of ultrafast 2D NMR are first covered, i.e., reaction/process monitoring and metabolomics. Then, the potential of ultrafast 2D NMR for the analysis of hyperpolarized mixtures is described, as well as recent developments in oriented media. This review focuses on high-resolution liquid-state 2D experiments (including benchtop NMR) that include at least one spectroscopic dimension (i.e., 2D spectroscopy and DOSY) but does not cover in depth applications without spectral resolution and/or in inhomogeneous fields.

NMR-based metabolomics and fluxomics: developments and future prospects

Recent NMR developments are acting as game changers for metabolomics and fluxomics – a critical and perspective review.

Development of a Robust and Quantitative High-Throughput Screening Method for Antibiotic Production in Bacterial Libraries

Over the past 30 years, there has been a dramatic rise in the number of infections caused by multidrug-resistant bacteria, which have proliferated due to the misuse and overuse of antibiotics. Over this same time period, however, there has also been a decline in the number of antibiotics with novel mechanisms of action coming to market. Therefore, there is a growing need for an increase in the speed at which new antibiotics are discovered and developed. Natural products produced by bacteria have been and continue to be a robust source of novel antibiotics; however, new and complementary methods for screening large bacterial libraries for novel antibiotic production are needed due to the current agar methods being limited in scope, time consuming, and prone to error. Herein, we describe a rapid, robust, and quantitative high-throughput liquid culture screening method for antibiotic production by bacteria. This method has the ability to screen both mono- and coculture mixtures of bacteria in vitro and be adapted to other phenotypic natural product analyses. Over 260 bacterial species were screened in monoculture, and 38 and 34% were found to produce antibiotics capable of inhibition of Staphylococcus aureus or Escherichia coli, respectively, with 8 and 4% being classified as strong producers (≥30% growth inhibition), respectively. Bacteria found to not produce antibiotics in monoculture were also screened in coculture using an adaptation of this method. Of the more than 270 cocultures screened, 14 and 30% were found to produce antibiotics capable of inhibition of S. aureus or E. coli, respectively. Of those bacteria found to produce antibiotics in monoculture, 43 bacteria were subjected to 16S rRNA sequencing and found to be majority Pseudomonas (37%), Serratia (19%), and Bacillus (14%) bacteria, but two novel producers, Herbaspirillum and Kluyvera, were also found.

Two-dimensional nuclear magnetic resonance spectroscopy with a microfluidic diamond quantum sensor

Quantum sensors based on nitrogen-vacancy centers in diamond have emerged as a promising detection modality for nuclear magnetic resonance (NMR) spectroscopy owing to their micrometer-scale detection volume and noninductive-based detection. A remaining challenge is to realize sufficiently high spectral resolution and concentration sensitivity for multidimensional NMR analysis of picoliter sample volumes. Here, we address this challenge by spatially separating the polarization and detection phases of the experiment in a microfluidic platform. We realize a spectral resolution of 0.65 ± 0.05 Hz, an order-of-magnitude improvement over previous diamond NMR studies. We use the platform to perform two-dimensional correlation spectroscopy of liquid analytes within an effective ∼40-picoliter detection volume. The use of diamond quantum sensors as in-line microfluidic NMR detectors is a major step toward applications in mass-limited chemical analysis and single-cell biology.

Absolute Configuration Determination of Retroflexanone Using the Advanced Mosher Method and Application of HPLC-NMR

The absolute configuration of retroflexanone (1) and a closely related phlorogluinol (2) was established using the advanced Mosher method and by application of HPLC-NMR. HPLC-NMR permitted a small scale Mosher method analysis to be carried out on these unstable phloroglucinols.

Recent advances and applications of experimental technologies in marine natural product research

Marine natural products are a rich source of novel and biologically active compounds. The number of identified marine natural compounds has grown 20% over the last five years from 2009 to 2013. Several challenges, including sample collection and structure elucidation, have limited the development of this research field. Nonetheless, new approaches, such as sampling strategies for organisms from extreme ocean environments, nanoscale NMR and computational chemistry for structural determination, are now available to overcome the barriers. In this review, we highlight the experimental technology innovations in the field of marine natural products, which in our view will lead to the development of many new drugs in the future.

Limit of detection studies for application to natural product identification using high performance liquid chromatography coupled to nuclear magnetic resonance spectroscopy

In the pursuit of new natural products, the demand to rapidly identify compounds present, in ever decreasing amounts, in complex crude extracts has become a limiting factor. Despite improvements in HPLC-NMR hardware and pulse sequences, no extensive limit of detection (LOD) investigations have been reported for the acquisition of 2D NMR spectroscopic experiments acquired through HPLC-NMR. In this study the LOD for five key 1D and 2D NMR spectroscopic experiments have been established, using two reference compounds, including the on-flow (WET 1D proton), stop-flow (WET1D proton), gCOSY, HSQCAD and gHMBCAD NMR experiments. The LOD for all of the NMR experiments were within the range of 700ng to 1mg for the set of fixed experimental parameters implemented. For principle components in a complex multi-component mixture, this would allow for in situ compound identification. HPLC-NMR analysis was employed to investigate the principle components present in a marine brown alga crude extract, Cystophora subfarcinata.

Chemical dereplication of marine actinomycetes by liquid chromatography-high resolution mass spectrometry profiling and statistical analysis

Discovery of novel bioactive metabolites from marine bacteria is becoming increasingly challenging, and the development of novel approaches to improve the efficiency of early steps in the microbial drug discovery process is therefore of interest. For example, current protocols for the taxonomic dereplication of microbial strains generally use molecular tools which do not take into consideration the ability of these selected bacteria to produce secondary metabolites. As the identification of novel chemical entities is one of the key elements driving drug discovery programs, this study reports a novel methodology to dereplicate microbial strains by a metabolomics approach using liquid chromatography-high resolution mass spectrometry (LC-HRMS). In order to process large and complex three dimensional LC-HRMS datasets, the reported method uses a bucketing and presence-absence standardization strategy in addition to statistical analysis tools including principal component analysis (PCA) and cluster analysis. From a closely related group of Streptomyces isolated from geographically varied environments, we demonstrated that grouping bacteria according to the chemical diversity of produced metabolites is reproducible and provides greatly improved resolution for the discrimination of microbial strains compared to current molecular dereplication techniques. Importantly, this method provides the ability to identify putative novel chemical entities as natural product discovery leads.

HPLC-NMR revisited: using time-slice high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance with database-assisted dereplication

Time-based trapping of chromatographically separated compounds onto solid-phase extraction (SPE) cartridges and subsequent elution to NMR tubes was done to emulate the function of HPLC-NMR for dereplication purposes. Sufficient mass sensitivity was obtained by use of a state-of-the-art HPLC-SPE-NMR system with a cryogenically cooled probe head, designed for 1.7 mm NMR tubes. The resulting (1)H NMR spectra (600 MHz) were evaluated against a database of previously acquired and prepared spectra. The in-house-developed matching algorithm, based on partitioning of the spectra and allowing for changes in the chemical shifts, is described. Two mixtures of natural products were used to test the approach: an extract of Carthamus oxyacantha (wild safflower), containing an array of spiro compounds, and an extract of the endophytic fungus Penicillum namyslowski, containing griseofulvin and analogues. The database matching of the resulting spectra positively identified expected compounds, while the number of false positives was few and easily recognized.

Application of HPLC-NMR in the identification of plocamenone and isoplocamenone from the marine red alga Plocamium angustum

A combination of on-line HPLC-NMR and off-line chemical investigations has resulted in the identification of the previously reported polyhalogenated monoterpene plocamenone, together with the new structural analogue isoplocamenone from the crude extract of the marine alga Plocamium angustum. On-flow and stop-flow HPLC-NMR analyses (including the acquisition of WET 2D NMR spectra) rapidly assisted in the identification of the major component plocamenone and in the partial identification of its unstable double bond isomer isoplocamenone. Conventional off-line isolation and structural characterization techniques were employed to unequivocally confirm both structures, leading to a structural revision for plocamenone, as well as to obtain sufficient quantities for biological testing.

Phytochemical profile of aerial parts and roots of Wachendorfia thyrsiflora L. studied by LC-DAD-SPE-NMR

Hyphenated liquid chromatography - diode array detection - solid phase extraction - nuclear magnetic resonance spectroscopy (LC-DAD-SPE-NMR) was used to investigate the phytochemical composition of aerial parts and roots of Wachendorfia thyrsiflora (Haemodoraceae). Eleven phenylphenalenones and related compounds were identified in the aerial parts of the plant, ten compounds were found in the roots, and four additional compounds occurred in both plant parts. Twelve compounds are previously unreported natural products including five alkaloids (phenylbenzoisoquinolinones) are described here for the first time. In the work presented here, phenylphenalenones with an intact C(19) core structure were found only in the roots. Oxa analogs with a C(18)O scaffold occurred both in the roots and in the aerial plant parts, while most of the aza analogs with a C(18)N scaffold were detected in the aerial plant parts. This distribution pattern suggests that phenylphenalenones form in the roots, then the intact C(19) skeleton is converted into oxa analogs in the roots, translocated into the leaves and further reacted with amines or amino acids to form aza analogs (phenylbenzoisoquinolin-1,6-dione alkaloids).

A historical overview of natural products in drug discovery

Historically, natural products have been used since ancient times and in folklore for the treatment of many diseases and illnesses. Classical natural product chemistry methodologies enabled a vast array of bioactive secondary metabolites from terrestrial and marine sources to be discovered. Many of these natural products have gone on to become current drug candidates. This brief review aims to highlight historically significant bioactive marine and terrestrial natural products, their use in folklore and dereplication techniques to rapidly facilitate their discovery. Furthermore a discussion of how natural product chemistry has resulted in the identification of many drug candidates; the application of advanced hyphenated spectroscopic techniques to aid in their discovery, the future of natural product chemistry and finally adopting metabolomic profiling and dereplication approaches for the comprehensive study of natural product extracts will be discussed.