Dereplication Of Known Compounds The Need for Dereplication

Considerable time and effort are required to isolate and characterize NCEs from natural product sources. It has been estimated that, on average, it takes $50,000 and three months to isolate and characterize an active compound from a single natural source [71]. To date, more than 150,000 known compounds have been isolated from nature, and this list expands at a rate of approximately 10,000 per year [72]. As a result, the probability of rediscovering previously isolated compounds steadily increases, and the potential cost associated with reisolating known compounds is high. Consequently, significant effort has been invested to avoid the replicate identification of previously identified compounds from natural product extracts.

This process, commonly termed dereplication, has been defined as "the attempt to determine the occurrence of previously known active compounds in crude extracts as early as possible to minimize the effort lost in their isolation" [43]. Traditionally, dereplication was performed using TLC with bioautographic detection. In this approach, antimicrobial extracts were separated using TLC, and monitored for active compounds with bioautographic detection (i.e., growth inhibition of an organism of interest). The advent of LC with UV/visible (VIS) diode-array detection significantly improved dereplication by providing a combination of high resolution separation with spectroscopic detection. These systems allowed the development of in-house libraries of LC retention times and UV spectra for known actives that could be readily compared to unknowns.

The next step in dereplication is to determine whether actives that do not match internal libraries are, in fact, novel. Several commercial databases have been developed that allow researchers to search for previously discovered natural products using criteria including: taxonomy of the producing organism, bioactivity, molecular formula, molecular weight, substructures, and UV maxima [73]. These databases include: Chapman and Hall's Dictionary of Natural Products, Bioactive Natural Products Database (Berdy), DEREP, Chemical Abstracts Services Registry File (CAS/STN), MARINLIT, and the Marine Natural Products Database (MNP Database), and can provide powerful tools to evaluate the novelty of compounds of interest. Unfortunately, at the dereplication stage, many of the search criteria may not be known. Prior to isolation, generally only the source family or genus and the UV maxima are available for database searching, and often produce long lists of potential matches when used for database searches. One of the most powerful means to narrow these search results is to use molecular weight or molecular formula limits, both of which can be provided by mass spectrometry.

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