Finding the needle in the haystack. The dereplication of natural product extracts

Cordell, Geoffrey A.; Shin, Young Geun

doi:10.1351/pac199971061089

Cited by 92 publications

(82 citation statements)

References 9 publications

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“…The advantages of the capillary electrophoresis method are high efficiency of the sample separation; small amounts of the samples to be analyzed, buffers, highly pure and expensive organic solvents; the absence of columns and sorbents; short-term investigation periods [6,7,8].…”

Section: Methodsmentioning

confidence: 99%

The study of amino acid composition of sapropel by the capillary electrophoresis method

Strus

2015

Vìsn. farm.

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Section: Methodsmentioning

confidence: 99%

The study of amino acid composition of sapropel by the capillary electrophoresis method

Strus

2015

Vìsn. farm.

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“…In such cases, the tedious process of complete structure elucidation using a battery of spectrometric tools should be unnecessary. Instead, mass spectrometry alone may be used to quickly 'dereplicate' or identify the known compounds based on molecular weight, fragmentation patterns and elemental composition in combination with natural product database searching [32][33][34][35][36]. Commercially available natural products databases include NAPRA-LERT [37], Scientific & Technical information Network (STN) [38], and the Dictionary of Natural Products [39].…”

Section: Characterization and Dereplication Of Natural Productsmentioning

confidence: 99%

“…Commercially available natural products databases include NAPRA-LERT [37], Scientific & Technical information Network (STN) [38], and the Dictionary of Natural Products [39]. Since some of these databases also contain UV/VIS absorbance data, it is also advantageous to use a photodiode array detector between the HPLC and mass spectrometer to obtain additional spectrometric data during LC-UV-MS dereplication [33,34].…”

Section: Characterization and Dereplication Of Natural Productsmentioning

confidence: 99%

“…Either the active fractions are re-chromatographed using LC-UV-MS for characterization and dereplication, or the entire eluate is analyzed using LC-UV-MS during fractionation. This latter approach was used by Cordell and Shin [33] for the dereplication of an extract of Begonia parviflora that showed cytotoxic activity against human oral epidermoid carcinoma (KB) in cell culture ( Figure 5). The molecular weights of the compounds in the active fractions were compared to molecular weight data for compounds of Begonia sp.…”

Section: Characterization and Dereplication Of Natural Productsmentioning

confidence: 99%

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Analysis and screening of combinatorial libraries using mass spectrometry

Shin

Breemen

2001

Biopharm & Drug Disp

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Mass spectrometry is a highly selective and high throughput analytical technique that is ideally suited for the identification and purity determination of large numbers of compounds prepared using combinatorial chemistry or for the dereplication of natural products. Compounds may be characterized based on molecular weight, elemental composition and structural features based on fragmentation patterns. When coupled to a separation technique such as highperformance liquid chromatography (HPLC) or capillary electrophoresis, mass spectrometric applications may be expanded to include analysis of complex mixtures. However, the slower speed of the separation step reduces the throughput of the analysis. This review concerns the application of mass spectrometry to the characterization of combinatorial libraries and the screening of library and natural product mixtures. Strategies to enhance the throughput of LC-MS are discussed including fast HPLC and parallel LC-MS. Also, mass spectrometry-based screening methods are described including frontal affinity chromatography-mass spectrometry, gel permeation chromatography LC-MS, direct electrospray mass spectrometry of receptor-ligand complexes, affinity chromatography-mass spectrometry, and pulsed ultrafiltration mass spectrometry.

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“…re-discovery of known natural products. 6,7 A method that identifies and eliminates known compounds in the early stages of the natural product discovery process is generally known as dereplication. It plays a key role in phytochemistry and in an effective natural product discovery program.…”

Section: Introductionmentioning

confidence: 99%

Automated molecular formula determination by tandem mass spectrometry (MS/MS)

Jarussophon

Acoca

Gao

et al. 2009

Analyst

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Automated software was developed to analyze the molecular formula of organic molecules and peptides based on high-resolution MS/MS spectroscopic data. The software was validated with 96 compounds including a few small peptides in the mass range of 138-1569 Da containing the elements carbon, hydrogen, nitrogen and oxygen. A Micromass Waters Q-TOF Ultima Global mass spectrometer was used to measure the molecular masses of precursor and fragment ions. Our software assigned correct molecular formulas for 91 compounds, incorrect molecular formulas for 3 compounds, and no molecular formula for 2 compounds. The obtained 95% success rate indicates high reliability of the software. The mass accuracy of the precursor ion and the fragment ions, which is critical for the success of the analysis, was high, i.e. the accuracy and the precision of 850 data were 0.0012 Da and 0.0016 Da, respectively. For the precursor and fragment ions below 500 Da, 60% and 90% of the data showed accuracy within #0.001 Da and #0.002 Da, respectively. The precursor and fragment ions above 500 Da showed slightly lower accuracy, i.e. 40% and 70% of them showed accuracy within #0.001 Da and #0.002 Da, respectively. The molecular formulas of the precursor and the fragments were further used to analyze possible mass spectrometric fragmentation pathways, which would be a powerful tool in structural analysis and identification of small molecules. The method is valuable in the rapid screening and identification of small molecules such as the dereplication of natural products, characterization of drug metabolites, and identification of small peptide fragments in proteomics. The analysis was also extended to compounds that contain a chlorine or bromine atom.

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Finding the needle in the haystack. The dereplication of natural product extracts

Cited by 92 publications

References 9 publications

The study of amino acid composition of sapropel by the capillary electrophoresis method

The study of amino acid composition of sapropel by the capillary electrophoresis method

Analysis and screening of combinatorial libraries using mass spectrometry

Automated molecular formula determination by tandem mass spectrometry (MS/MS)

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