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Ayres LB, Gomez FJV, Silva MF, Linton JR, Garcia CD. Predicting the formation of NADES using a transformer-based model. Sci Rep 2024; 14:2715. [PMID: 38388549 PMCID: PMC10883925 DOI: 10.1038/s41598-022-27106-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/26/2022] [Indexed: 02/24/2024] Open
Abstract
The application of natural deep eutectic solvents (NADES) in the pharmaceutical, agricultural, and food industries represents one of the fastest growing fields of green chemistry, as these mixtures can potentially replace traditional organic solvents. These advances are, however, limited by the development of new NADES which is today, almost exclusively empirically driven and often derivative from known mixtures. To overcome this limitation, we propose the use of a transformer-based machine learning approach. Here, the transformer-based neural network model was first pre-trained to recognize chemical patterns from SMILES representations (unlabeled general chemical data) and then fine-tuned to recognize the patterns in strings that lead to the formation of either stable NADES or simple mixtures of compounds not leading to the formation of stable NADES (binary classification). Because this strategy was adapted from language learning, it allows the use of relatively small datasets and relatively low computational resources. The resulting algorithm is capable of predicting the formation of multiple new stable eutectic mixtures (n = 337) from a general database of natural compounds. More importantly, the system is also able to predict the components and molar ratios needed to render NADES with new molecules (not present in the training database), an aspect that was validated using previously reported NADES as well as by developing multiple novel solvents containing ibuprofen. We believe this strategy has the potential to transform the screening process for NADES as well as the pharmaceutical industry, streamlining the use of bioactive compounds as functional components of liquid formulations, rather than simple solutes.
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Affiliation(s)
- Lucas B Ayres
- Department of Chemistry, Clemson University, 211 S. Palmetto Blvd, Clemson, SC, 29634, USA
| | - Federico J V Gomez
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza (IBAM-CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Maria Fernanda Silva
- Facultad de Ciencias Agrarias, Instituto de Biología Agrícola de Mendoza (IBAM-CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Jeb R Linton
- Department of Chemistry, Clemson University, 211 S. Palmetto Blvd, Clemson, SC, 29634, USA
- IBM Cloud, Armonk, NY, 10504, USA
| | - Carlos D Garcia
- Department of Chemistry, Clemson University, 211 S. Palmetto Blvd, Clemson, SC, 29634, USA.
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Nigdelioglu Dolanbay S, Şirin S, Aslim B. Cocktail of three isoquinoline alkaloids derived from Glaucium grandiflorum Boiss. & A. Huet subsp. refractum (Nábelek) Mory inhibits the production of LPS-induced ROS, pro-inflammatory cytokines, and mediators through the down-regulation of p38 MAPK in BV-2 cells. Fitoterapia 2023; 170:105652. [PMID: 37595642 DOI: 10.1016/j.fitote.2023.105652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/09/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Glaucium grandiflorum extracts have traditionally been used to treat brain-related disorders. G. grandiflorum extracts also exhibited inhibitory effects on cholinesterase enzymes, as well as antigenotoxic activity. However, no research has been done on the effect of G. grandiflorum alkaloid extracts on the anti-oxidative and anti-inflammatory mechanisms. In this study we aimed to evaluate the anti-oxidative and anti-inflammatory activities of the alkaloid extract obtained from G. grandiflorum as well as the mechanisms responsible for their neuroprotective effects in neuronal damage caused by LPS in BV2 cells. We used LC-MS/MS and 1H, 13C NMR analysis to determine the presence of major alkaloids (allocryptopine, tetrahydropalmatine, and tetrahydroberberine N-oxide (trans-cannadine-N-oxide) in the alkaloid extracts. We used flow cytometry to study the alkaloid extracts' effects on ROS production; we also employed qRT-PCR and Western Blot to analyze the effects of oxidative stress and inflammation-related genes and proteins. ROS production within the cell was inhibited by chloroform alkaloid extract (CAE). There occurred marked CAE-induced reductions in IL-1β, Cox-2, and iNOS mRNA expressions. We also observed marked reductions in IL-6 and TNF-α mRNA expressions with methanol alkaloid extract (MAE). CAE effectively suppressed IL-1β and iNOS protein levels, especially as in qRT-PCR studies, while MAE effectively reduced IL-6 and TNF-α protein levels. Additionally, MAE was found to be prominent in suppressing the levels of Cox-2 protein, unlike qRT-PCR studies. According to our study findings, oxidative stress brought about by inflammation was suppressed by alkaloid extracts from G. grandiflorum which can be attributed to their suppressor effects on the pro-inflammatory cytokines-mediators, and p38 MAPK. As a result, a drug active substance that suppresses oxidative stress and inflammation has been brought to the neuropharmacological field.
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Affiliation(s)
| | - Seda Şirin
- Gazi University, Faculty of Science, Department of Biology, 06500, Teknikokullar, Ankara, Turkey
| | - Belma Aslim
- Gazi University, Faculty of Science, Department of Biology, 06500, Teknikokullar, Ankara, Turkey
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Hu J, Peng D, Huang X, Wang N, Liu B, Di D, Liu J, Qu Q, Pei D. COSMO-SAC and QSPR combined models: A flexible and reliable strategy for screening the extraction efficiency of deep eutectic solvents. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2023.123699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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Li D. Natural deep eutectic solvents in phytonutrient extraction and other applications. FRONTIERS IN PLANT SCIENCE 2022; 13:1004332. [PMID: 36212381 PMCID: PMC9533057 DOI: 10.3389/fpls.2022.1004332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/18/2022] [Indexed: 06/16/2023]
Abstract
Natural deep eutectic solvents (NaDESs) are considered a new type of green solvent with attractive application prospects in many fields because of their simple preparation, low cost, environmental friendliness, low volatility, high solvency capacity, designable structure, and easy biodegradability. Due to their biocompatibility, they are safe to use and are particularly suitable for natural product applications. In recent years, NaDESs have been used to extract phytonutrients (e.g., flavonoids, saponins, polysaccharides, alkaloids, quinones, phenolic acids, volatile oils, etc.) to improve their solubility, stability, and bioavailability. This review is intended to summarize and discuss recent progress in the field of natural products related to materials and preparation methods, physicochemical properties, enhancing extraction and separation, increasing solubility, improving stability and bioavailability, facilitating oral absorption of phytonutrients, and finally, highlighting the challenge for future work.
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Bragagnolo FS, Socas-Rodríguez B, Mendiola JA, Cifuentes A, Funari CS, Ibáñez E. Pressurized natural deep eutectic solvents: An alternative approach to agro-soy by-products. Front Nutr 2022; 9:953169. [PMID: 36159477 PMCID: PMC9493435 DOI: 10.3389/fnut.2022.953169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Soybeans are mainly used for food and biodiesel production. It is estimated that soy crops worldwide will leave about 651 million metric tons of branches, leaves, pods, and roots on the ground post-harvesting in 2022/23. These by-products might serve as largely available and cheap source of high added-value metabolites, such as flavonoids, isoflavonoids, and other phenolic compounds. This work aimed to explore green approaches based on the use of pressurized and gas expanded-liquid extraction combined with natural deep eutectic solvents (NADESs) to achieve phenolic-rich extracts from soy by-products. The total phenolic and flavonoid contents of the generated extracts were quantified and compared with conventional solvents and techniques. Pressurized liquid extraction (PLE) with choline chloride/citric acid/water (1:1:11 – molar ratio) at 120°C, 100 bar, and 20 min, resulted in an optimized condition to generate phenolic and flavonoid-rich fractions of soy by-products. The individual parts of soy were extracted under these conditions, with their metabolic profile obtained by UHPLC-ESI-QToF-MS/MS and potential antioxidant properties by ROS scavenging capacity. Extracts of soy roots presented the highest antioxidant capacity (207.48 ± 40.23 mg AA/g), three times higher than soybean extracts (68.96 ± 12.30). Furthermore, Hansen solubility parameters (HSPs) were applied to select natural hydrophobic deep eutectic solvents (NaHDES) as substituents for n-heptane to defat soybeans. Extractions applying NaHDES candidates achieved a similar yield and chromatography profile (GC-QToF-MS) to n-heptane extracts.
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Affiliation(s)
- Felipe Sanchez Bragagnolo
- Green Biotech Network, School of Agricultural Sciences, São Paulo State University, Botucatu, Brazil
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC-UAM, Madrid, Spain
| | | | - Jose A. Mendiola
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC-UAM, Madrid, Spain
| | - Alejandro Cifuentes
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC-UAM, Madrid, Spain
| | - Cristiano Soleo Funari
- Green Biotech Network, School of Agricultural Sciences, São Paulo State University, Botucatu, Brazil
| | - Elena Ibáñez
- Laboratory of Foodomics, Institute of Food Science Research, CIAL, CSIC-UAM, Madrid, Spain
- *Correspondence: Elena Ibáñez,
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Strzemski M, Dresler S, Podkościelna B, Skic K, Sowa I, Załuski D, Verpoorte R, Zielińska S, Krawczyk P, Wójciak M. Effectiveness of Volatile Natural Deep Eutectic Solvents (VNADESs) for the Green Extraction of Chelidonium majus Isoquinoline Alkaloids. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092815. [PMID: 35566166 PMCID: PMC9101032 DOI: 10.3390/molecules27092815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
The Chelidonium majus plant is rich in biologically active isoquinoline alkaloids. These alkaline polar compounds are isolated from raw materials with the use of acidified water or methanol; next, after alkalisation of the extract, they are extracted using chloroform or dichloromethane. This procedure requires the use of toxic solvents. The present study assessed the possibility of using volatile natural deep eutectic solvents (VNADESs) for the efficient and environmentally friendly extraction of Chelidonium alkaloids. The roots and herb of the plant were subjected three times to extraction with various menthol, thymol, and camphor mixtures and with water and methanol (acidified and nonacidified). It has been shown that alkaloids can be efficiently isolated using menthol–camphor and menthol–thymol mixtures. In comparison with the extraction with acidified methanol, the use of appropriate VNADESs formulations yielded higher amounts of protopine (by 16%), chelidonine (35%), berberine (76%), chelerythrine (12%), and coptisine (180%). Sanguinarine extraction efficiency was at the same level. Additionally, the values of the contact angles of the raw materials treated with the tested solvents were assessed, and higher wetting dynamics were observed in the case of VNADESs when compared with water. These results suggest that VNADESs can be used for the efficient and environmentally friendly extraction of Chelidonium alkaloids.
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Affiliation(s)
- Maciej Strzemski
- Department of Analytical Chemistry, Medical University of Lublin, 20-093 Lublin, Poland; (S.D.); (I.S.)
- Correspondence: (M.S.); (M.W.)
| | - Sławomir Dresler
- Department of Analytical Chemistry, Medical University of Lublin, 20-093 Lublin, Poland; (S.D.); (I.S.)
- Department of Plant Physiology and Biophysics, Institute of Biological Science, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Beata Podkościelna
- Faculty of Chemistry, Institute of Chemistry, Maria Curie-Skłodowska University, 20-031 Lublin, Poland;
| | - Kamil Skic
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland;
| | - Ireneusz Sowa
- Department of Analytical Chemistry, Medical University of Lublin, 20-093 Lublin, Poland; (S.D.); (I.S.)
| | - Daniel Załuski
- Department of Pharmaceutical Botany and Pharmacognosy, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094 Bydgoszcz, Poland;
| | - Rob Verpoorte
- Natural Products Laboratory, Institute of Biology, Leiden University, 2300RA Leiden, The Netherlands;
| | - Sylwia Zielińska
- Department of Pharmaceutical Biology and Biotechnology, Division of Pharmaceutical Biotechnology, Wroclaw Medical University, 50-556 Wroclaw, Poland;
| | - Paweł Krawczyk
- Immunology and Genetics Laboratory, Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Magdalena Wójciak
- Department of Analytical Chemistry, Medical University of Lublin, 20-093 Lublin, Poland; (S.D.); (I.S.)
- Correspondence: (M.S.); (M.W.)
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