The Three Pillars of Natural Product Dereplication. Alkaloids from the Bulbs of Urceolina peruviana (C. Presl) J.F. Macbr. as a Preliminary Test Case

Abstract

The role and importance of the identification of natural products are discussed in the perspective of the study of secondary metabolites. The rapid identification of already reported compounds, or structural dereplication, is recognized as a key element in natural product chemistry. The biological taxonomy of metabolite producing organisms, the knowledge of metabolite molecular structures, and the availability of metabolite spectroscopic signatures are considered as the three pillars of structural dereplication. The role and the construction of databases is illustrated by references to the KNApSAcK, UNPD, CSEARCH, and COCONUT databases, and by the importance of calculated taxonomic and spectroscopic data as substitutes for missing or lost original ones. Two NMR-based tools, the PNMRNP database that derives from UNPD, and KnapsackSearch, a database generator that provides taxonomically focused libraries of compounds, are proposed to the community of natural product chemists. The study of the alkaloids from Urceolina peruviana, a plant from the Andes used in traditional medicine for antibacterial and anticancer actions, has given the opportunity to test different approaches to dereplication, favoring the use of publicly available data sources.

Metabolit Sekunder dari Kulit Batang Kalesi (Sphatolobus Ferrogenus) Serta Uji Inhibitor Enzim A-Glukosinade

“…Spektrum yang telah didapatkan kemudian dibandingkan dengan spektrum dari sigmasterol yang telah diisolasi dari tanaman akar slatri (Doni Eko Saputra et al, 2014) pada Tabel 2 di bawah ini. (Lianza et al, 2021). Jadi karena perbedaan antara senyawa isolat dengan tersebut dapat disimpulkan bahwa senyawa isolat tersebut adalah gliseril monostearate dan sigmasterol (Gambar 2).…”

Taxonomy-Focused Natural Product Databases for Carbon-13 NMR-Based Dereplication

“…The dereplication of NPs relies on NP DBs containing structural, taxonomic and spectroscopic data [19]. Merging spectroscopic and biological taxonomy data offers a way to reduce, possibly to one, the number of annotations for a given compound.…”

“…This communication reports a way to create a database related to a given taxon with included data for dereplication through 13 C NMR spectroscopy. A similar approach, KnapsackSearch [19], was reported, resorting to the internet to access the KNApSAcK DB [20]. The current approach, called CNMR_Predict, relies on the LOTUS DB as a structure provider by the possibility it offers to carry out searches according to taxonomy and to easily export the result of searches [6].…”

Taxonomy-focused Natural Product Databases for Carbon-13 NMR-based Dereplication

“…[8,13] The analytical technique being either MS or NMR or both, dereplication of NPs relies on NP DBs containing structural, taxonomic and spectroscopic data. [14] Merging spectroscopic and biological taxonomy data offers a way to reduce, possibly to on e, the number of annotations for a given compound. Restricting the set of candidate structures for dereplication to the chemical entities produced by the organisms that are taxonomically related to the one under study finds its justification in the co -evolution of species and of the compounds they produce to establish relationships with their environment.…”

“…A similar approach, KnapsackSearch, was reported, resorting on the internet access to the KNApSAcK DB (knapsackfamily.com). [14] The current approach, called CNMRPredict, relies on the LOTUS DB as structure provider by the possibility it offers to carry out searches according to taxonomy and to easily export the result of searches. [5] CNMRPredict also relies on the Advanced Chemistry Development, Inc. (ACD/Labs) CNMR Predictor and DB software (version 2020.1.0) for high-quality 13 shifts for its use with the DerepCrude software.…”