Approaches for natural product detection and structural elucidation using mass spectrometry with high mass accuracy

Natural products (NPs), metabolites produced by bacteria, fungi, plants, and other organisms, have a rich and important history in the treatment of disease. Between 1981 and 2006, 34% of all small-molecule new chemical entities were NPs or natural product derivatives (NPDs), and 17% were synthetic molecules whose pharmacophore was derived from or inspired by an NP [1]. NPs and NPDs have various medicinal uses, ranging from antifungals and antimicrobials to immunosuppressive agents and anticancer therapies. Despite historical and ongoing successes by pharmaceutical companies, bioactivity-based screening that incorporates secondary metabolites in drug-discovery programs has been scaled back over the past two decades. This is due in large part to the rediscovery of known compounds, creating a “dereplication” bottleneck. However, structural approaches such as nuclear magnetic resonance (NMR) and in particular liquid chromatography (LC) coupled with high-resolution mass spectrometry (MS) now offer screening technologies orthogonal to bioassays, with possibilities for streamlined dereplication and detection of multiple compounds from a single strain of bacterium or fungus. LC-MS provides an excellent method for the identification and isolation of new secondary metabolites from complex extracts. Several options and protocols are described subsequently. In MS, different mass analyzers, such as an ion trap, a time-of-flight (TOF), or quadrupole-TOF hybrid instrument, can be coupled to LC. Fourier-transform mass spectrometry (FTMS) instruments have the highest resolution and mass accuracy (Table 8.1) [2] and allow for sequential tandem mass spectrometry (MS/MS) involving gas-phase isolation and ion fragmentation. Generally, electrospray ionization (ESI) has become the ionization mechanism of choice for NP research because of the ease of coupling with LC.