Prediction of Natural Product Classes Using Machine Learning and 13C NMR Spectroscopic Data

2020 ◽  
Vol 60 (7) ◽  
pp. 3376-3386 ◽  
Author(s):  
Saúl H. Martínez-Treviño ◽  
Víctor Uc-Cetina ◽  
María A. Fernández-Herrera ◽  
Gabriel Merino
Keyword(s):  
Machine Learning ◽  
Natural Product ◽  
13C Nmr ◽  
Spectroscopic Data

Discrimination of olive oils based on the olive cultivar origin by machine learning employing the fusion of emission and absorption spectroscopic data

Food Control ◽  
2021 ◽  
pp. 108318
Author(s):  
Dimitrios Stefas ◽  
Nikolaos Gyftokostas ◽  
Panagiotis Kourelias ◽  
Eleni Nanou ◽  
Vasileios Kokkinos ◽  
...  
Keyword(s):  
Machine Learning ◽  
Spectroscopic Data ◽  
Olive Cultivar ◽  
Olive Oils

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

Molecules ◽  
2021 ◽  
Vol 26 (3) ◽  
pp. 637
Author(s):  
Mariacaterina Lianza ◽  
Ritchy Leroy ◽  
Carine Machado Rodrigues ◽  
Nicolas Borie ◽  
Charlotte Sayagh ◽  
...  
Keyword(s):  
Natural Product ◽  
Spectroscopic Data ◽  
Preliminary Test ◽  
Rapid Identification ◽  
Molecular Structures ◽  
Data Sources ◽  
Test Case ◽  
The Andes ◽  
Spectroscopic Signatures ◽  
Product Chemistry

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.

scholarly journals Antimicrobial Coumarins from the Stem Bark of Afraegle paniculata

2010 ◽  
Vol 5 (4) ◽  
pp. 1934578X1000500 ◽  
Author(s):  
Valerie Beatrice Tsassi ◽  
Hidayat Hussain ◽  
Bouberte Yemele Meffo ◽  
Simeon F. Kouam ◽  
Etienne Dongo ◽  
...  
Keyword(s):  
Natural Product ◽  
Dimethyl Ether ◽  
Spectroscopic Data ◽  
2D Nmr ◽  
Stem Bark

Eight compounds were isolated from the stem bark of the plant Afraegle paniculata. One of them, a dimethyl ether of S-trans-marmin (1), is reported as a new natural product. The structures were determined by comprehensive analyses of their 1D and 2D NMR spectroscopic and HREIMS data. The remaining seven known compounds, identified by comparing their spectroscopic data with those reported in the literature, were S-trans-marmin (2), psoralene (3), bergaptene (4), imperatorin (5), 2-(4-hydroxy-3,5-dimethoxyphenyl)-3-hydroxymethyl-2,3-dihydro-1,4,5-trioxaphenanthren-6-one (6), xanthoxyletin (7), and β-sitosterol glucopyranoside. Preliminary studies indicated that compounds 2, 3, 5, and 7 showed potent antibacterial, fungicidal, and algicidal properties, while 6 showed only moderate algicidal property.

scholarly journals Structure Elucidation of an Pentacyclic Triterpenoid and Phenolic from Steam Bark of Vitex Pubescens Vahl

2019 ◽  
Vol 1 (1) ◽  
pp. 68-74
Author(s):  
Lenny Anwar
Keyword(s):  
1H Nmr ◽  
13C Nmr ◽  
Betulinic Acid ◽  
Spectroscopic Data ◽  
Structure Elucidation ◽  
Stem Bark ◽  
Hydroxybenzoic Acid ◽  
Pentacyclic Triterpenoid ◽  
Reported Data ◽  
First Time

Pentacyclic triterpenoid, betulinic acid (1) and phenolic, p-hydroxybenzoic acid (2), had been isolated for the first time from the stem bark of Vitex pubescens Vahl. The structure of compounds 1 and 2 was determined based on the interpretation of spectroscopic data including UV, IR, NMR (1H-NMR, 13C-NMR, HMQC, HMBC, COSY) and MS, as well as by comparison with those reported data.

scholarly journals Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

2020 ◽  
Vol 295 (44) ◽  
pp. 14826-14839
Author(s):  
Serina L. Robinson ◽  
Barbara R. Terlouw ◽  
Megan D. Smith ◽  
Sacha J. Pidot ◽  
Timothy P. Stinear ◽  
...  
Keyword(s):  
Machine Learning ◽  
Natural Product ◽  
Global Analysis ◽  
Gene Clusters ◽  
Divergent Evolution ◽  
Acid Activation ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Predictive Tool ◽  
Wide Range

Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.

scholarly journals Machine learning of two-dimensional spectroscopic data

2019 ◽  
Vol 520 ◽  
pp. 52-60 ◽  
Author(s):  
Mirta Rodríguez ◽  
Tobias Kramer
Keyword(s):  
Machine Learning ◽  
Spectroscopic Data ◽  
Two Dimensional

13C NMR spectroscopic data for glutinol and derivatives

1994 ◽  
Vol 32 (6) ◽  
pp. 378-379 ◽  
Author(s):  
Roberto Sigfrido Gallegos Olea ◽  
Luce Maria Brandão Torres ◽  
Luiz Carlos Roque ◽  
Nidia Franca Roque
Keyword(s):  
13C Nmr ◽  
Spectroscopic Data

Design of Natural‐Product‐Inspired Multitarget Ligands by Machine Learning

ChemMedChem ◽  
2019 ◽  
Vol 14 (12) ◽  
pp. 1129-1134 ◽  
Author(s):  
Francesca Grisoni ◽  
Daniel Merk ◽  
Lukas Friedrich ◽  
Gisbert Schneider
Keyword(s):  
Machine Learning ◽  
Natural Product

scholarly journals Functionalized 1,3-Thiazolidin-4-Ones from 2-Oxo-Acenaphthoquinylidene- and [2.2]Paracyclophanylidene-Thiosemicarbazones

Molecules ◽  
2019 ◽  
Vol 24 (17) ◽  
pp. 3069 ◽  
Author(s):  
Ashraf A. Aly ◽  
Nasr K. Mohamed ◽  
Alaa A. Hassan ◽  
Kamal M. El-Shaieb ◽  
Maysa M. Makhlouf ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Elemental Analysis ◽  
13C Nmr ◽  
Spectroscopic Data ◽  
Complex Structure ◽  
2D Nmr ◽  
Efficient Tool ◽  
X Ray ◽  
Dialkyl Acetylenedicarboxylates ◽  
Allyl Derivative

The reactions of dialkyl acetylenedicarboxylates with various 2-oxo-acenaphthoquinylidene- and 4-acetyl[2.2]paracyclophanylidene-thiosemicarbazones were investigated. Using simple experimental procedures, 1,3-Thiazolidin-4-ones derived from acenaphthequinone or [2.2]paracyclophane were obtained as major products in good yields. In the case of allyl derivative of acenaphthoquinylidene-thiosemicarbazones, a complex structure of tetramethyl 5-(2-(((Z,E)-N-allyl-N′-(2-oxoacenaphthylen-1(2H)-ylidene)carbamohydrazonoyl)thio)-1,2,3-tris-(methoxycarbonyl)-cyclopropyl)-4-methoxy-7-oxabicyclo[2.2.1]hepta-2,5-diene-1,2,3,6-tetracarboxylate was formed. Single crystal X-ray analysis was used as an efficient tool to confirm the structure of the synthesized compounds as well as different spectroscopic data (1H-NMR, 13C-NMR, 2D-NMR, mass spectrometry and elemental analysis). The mechanism of the obtained products was discussed.

ChemInform Abstract: Calculation of the σR-Constants of Tetrazole Groups from 13C-NMR Spectroscopic Data of Vinyltetrazoles.

ChemInform ◽  
1987 ◽  
Vol 18 (37) ◽  
Author(s):  
O. A. IVASHKEVICH ◽  
P. N. GAPONIK ◽  
V. N. NUMENKO
Keyword(s):  
13C Nmr ◽  
Spectroscopic Data
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