High-Resolution MS, MS/MS, and UV Database of Fungal Secondary Metabolites as a Dereplication Protocol for Bioactive Natural Products

Abstract

A major problem in the discovery of new biologically active compounds from natural products is the re-isolation of known compounds. Such re-isolations waste time and resources, distracting chemists from more promising leads. To address this problem, dereplication strategies are needed that enable crude extracts to be screened for the presence of known compounds before isolation efforts are initiated. In a project to identify anticancer drug leads from filamentous fungi, a significant dereplication challenge arises, as the taxonomy of the source materials are rarely known, and, thus, the literature cannot be probed to identify likely known compounds. An ultra-performance liquid chromatography-photodiode array-high-resolution tandem mass spectrometric (UPLC-PDA-HRMS-MS/MS) method was developed for dereplication of fungal secondary metabolites in crude culture extracts. A database was constructed by recording HRMS and MS/MS spectra of fungal metabolites, utilizing both positive- and negative-ionization modes. Additional details, such as UV-absorption maxima and retention times, were also recorded. Small-scale cultures that showed cytotoxic activities were dereplicated before engaging in the scale-up or purification processes. Using these methods, approximately 50% of the cytotoxic extracts could be eliminated from further study after the confident identification of known compounds. The specific attributes of this dereplication methodology include a focus on bioactive secondary metabolites from fungi, the use of a 10-min chromatographic method, and the inclusion of both HRMS and MS/MS data.

Chemoinformatic Expedition of the Chemical Space of Fungal Products

“…Based on previous studies and as part of our continued effort to quantify the chemical diversity of fungal isolates [6], herein we expand the analysis to a larger set of 207 compounds described by our group [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] that represent twice the size of the dataset analyzed in 2012. In the current analysis, we employed molecular fingerprints as distinct molecular representations not analyzed in the previous study; also we emphasized the evaluation of molecular complexity that may have a significant impact in drug discovery endeavors, since this feature has been associated with target selectivity (and potential toxicity).…”

“…The largest fragments were kept, duplicates in each dataset were removed and all molecules with molecular weight (MW) over 1000 were excluded. The in-house library of fungal metabolites with 207 compounds (referred to hereafter as 'FUNGI') [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] was compared with the following five reference collections: 2249 compounds based on the Flavor and Extract Manufacturers Association of the United States GRAS list, updated to GRAS 27 (hereafter referred to as 'GRAS') [24,30]; FDA drugs obtained from DrugBank [31] containing: 76 drugs approved to treat cancer (hereafter referred to as 'FDA-ONC') and 1399 nononcological drugs (hereafter referred to as 'FDA-NONC'); 713 drugs in clinical trials reported by the Therapeutic Target Database [32] (hereafter referred to as 'CLINIC'); and 850 compounds from a commercial collection focused on epigenetic targets, available at Selleckchem (hereafter referred to as 'GENERAL') [33]. Supplementary Table 1 summarizes the number of duplicate molecules found in the initial datasets.…”

Larvicidal Activity of Beauveria bassiana Extracts against Aedes aegypti and Identification of Beauvericins

“…Moreover, the product ion spectra allowed the comparison of the compounds fragmentation profile to the data found in the literature (Table 1). 24,25,[40][41][42][43][44] The electrospray ionization tandem mass spectra (ESI-MS/MS) and fragmentation mechanism proposal for beauvericin A or F are depicted in Figures 4 and 5, Larvicidal Activity of Beauveria bassiana Extracts against Aedes aegypti and Identification of Beauvericins J. Braz. Chem.…”

A Strategy for the Rapid Identification of Fungal Metabolites and the Discovery of the Antiviral Activity of Pyrenocine a and Harzianopyridone

“…This is particularly true when dereplication of secondary metabolites in extracts of biological matrixes is unfeasible by high-resolution and high--throughput chromatography-spectroscopy hyphenated tools, such as HPLC-HRMS, HPLC-NMR and related techniques. [3][4][5][6][7] Data obtained from joint UV, LRMS and 1 H NMR analyses only, and sometimes 13 C NMR, can be used in querying databases such as the Dictionary of Natural Products (DNP), Antimarin, MarinLit, and Molecular Networking, as an effective combination for the rapid identification of known structures. 8,9 The rapid identification of secondary metabolites enables further assessment of structures of interest, particularly of unprecedentedly bioactive known compounds.…”