Pub Date : 2025-01-06eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1504582
Carolina Gómez Vargas, Nora Marta Andrea Ponce, Carlos A Stortz, Eliana Noemi Fissore, Pablo Bonelli, Carlos Mauricio Otálora González, Lía Noemí Gerschenson
The use of green solvents, citric acid (CA), and natural deep eutectic solvents (NADES) for the obtention of pectin from wastes (pulp and peel) of Malus domestica was studied. The NADES used comprised citric acid-glucose-water (N1) or lactic acid-glucose-water (N2). The fractions rich in pectin obtained after exposure to NADES showed lower yield (≈4 g/100 g CA vs. ≈ 11 g/100 g CA), equal to or lower degree of methoxylation (53-71 mol/100 mol CA vs. 73 mol/100 mol CA), equal to or greater content of uronic acid (50-63 g/100 g CA vs. 51 g/100 g CA) than those isolated with CA, and the ones obtained from peel were the most thermally stable. These pectins showed greater linearity, shorter branch lengths, and lower arabinose content than those obtained with CA. The neutral sugars present in the highest concentration in all the isolated fractions were arabinose, xylose, galactose, and rhamnose. Glucose was also detected, probably due to contamination with starch. Their aqueous solutions showed pseudoplastic behavior. The effect of ultrasound assistance was preliminarily evaluated in the production of pectic fractions using N2, observing higher yields (13-18 g/100 g), in general, a higher concentration of uronic acid and a higher degree of methoxylation when compared with the extraction without US. They also showed greater arabinose content (less degradative treatment), lower glucose content (increased purity), and higher rhamnogalacturonan I (RG-I) content. It is known that RG-I is linked to pectin bioactivity and rheological behavior. The green solvent techniques assayed allowed obtaining fractions rich in uronic acid with different chemical, thermochemical, and rheological characteristics. In the case of isolation with NADES, the yield was low, but preliminary tests with ultrasound assistance showed that it is possible to overcome this limitation.
研究了用绿色溶剂柠檬酸(CA)和天然深共晶溶剂(NADES)从海参废(果肉和果皮)中提取果胶的方法。所使用的NADES包括柠檬酸-葡萄糖-水(N1)或乳酸-葡萄糖-水(N2)。NADES处理后得到的果胶含量丰富的组分产率较低(≈4 g/100 g CA vs≈11 g/100 g CA),甲氧基化程度等于或更低(53-71 mol/100 mol CA vs. 73 mol/100 mol CA),醛酸含量等于或更高(50-63 g/100 g CA vs. 51 g/100 g CA),且从果皮中分离得到的组分热稳定性最好。这些果胶的线性度更高,枝长更短,阿拉伯糖含量较低。在所有分离的部分中,阿拉伯糖、木糖、半乳糖和鼠李糖的含量最高。葡萄糖也被检测到,可能是由于淀粉污染。它们的水溶液表现出假塑性行为。初步评价了超声辅助下用N2提取果胶馏分的效果,发现与不加US的提取相比,超声辅助下的产率更高(13 ~ 18 g/100 g),总体而言,脲酸浓度更高,甲氧基化程度更高。它们也显示出更高的阿拉伯糖含量(更少的降解处理),更低的葡萄糖含量(提高纯度)和更高的鼠李糖半乳糖酸I (RG-I)含量。已知RG-I与果胶的生物活性和流变行为有关。绿色溶剂技术可以获得富含不同化学、热化学和流变特性的尿素酸的馏分。在用NADES分离的情况下,产率很低,但在超声辅助下的初步试验表明,有可能克服这一限制。
{"title":"Pectin obtention from agroindustrial wastes of <i>Malus domestica</i> using green solvents (citric acid and natural deep eutectic solvents). Chemical, thermal, and rheological characterization.","authors":"Carolina Gómez Vargas, Nora Marta Andrea Ponce, Carlos A Stortz, Eliana Noemi Fissore, Pablo Bonelli, Carlos Mauricio Otálora González, Lía Noemí Gerschenson","doi":"10.3389/fchem.2024.1504582","DOIUrl":"10.3389/fchem.2024.1504582","url":null,"abstract":"<p><p>The use of green solvents, citric acid (CA), and natural deep eutectic solvents (NADES) for the obtention of pectin from wastes (pulp and peel) of <i>Malus domestica</i> was studied. The NADES used comprised citric acid-glucose-water (N1) or lactic acid-glucose-water (N2). The fractions rich in pectin obtained after exposure to NADES showed lower yield (≈4 g/100 g CA vs. ≈ 11 g/100 g CA), equal to or lower degree of methoxylation (53-71 mol/100 mol CA vs. 73 mol/100 mol CA), equal to or greater content of uronic acid (50-63 g/100 g CA vs. 51 g/100 g CA) than those isolated with CA, and the ones obtained from peel were the most thermally stable. These pectins showed greater linearity, shorter branch lengths, and lower arabinose content than those obtained with CA. The neutral sugars present in the highest concentration in all the isolated fractions were arabinose, xylose, galactose, and rhamnose. Glucose was also detected, probably due to contamination with starch. Their aqueous solutions showed pseudoplastic behavior. The effect of ultrasound assistance was preliminarily evaluated in the production of pectic fractions using N2, observing higher yields (13-18 g/100 g), in general, a higher concentration of uronic acid and a higher degree of methoxylation when compared with the extraction without US. They also showed greater arabinose content (less degradative treatment), lower glucose content (increased purity), and higher rhamnogalacturonan I (RG-I) content. It is known that RG-I is linked to pectin bioactivity and rheological behavior. The green solvent techniques assayed allowed obtaining fractions rich in uronic acid with different chemical, thermochemical, and rheological characteristics. In the case of isolation with NADES, the yield was low, but preliminary tests with ultrasound assistance showed that it is possible to overcome this limitation.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1504582"},"PeriodicalIF":3.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143003098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-06eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1519166
Jingshu Tian, Haichang Zhang
Perovskite solar cells (PVSCs) show remarkable potential due to their high-power conversion efficiencies and scalability. However, challenges related to stability and long-term performance remain significant. Self-assembled monolayers (SAMs) have emerged as a crucial solution, enhancing interfacial properties, facilitating hole extraction, and minimizing non-radiative recombination. This review examines recent advancements in SAMs for PVSCs, focusing on three key areas: anchoring groups and interface engineering, electronic structure modulation as well as band alignment, and stability optimization. We emphasize the role of anchoring groups in reducing defects and improving crystallinity, alongside the ability of SAMs to fine-tune energy levels for more effective hole extraction. Additionally, co-adsorbed SAM strategies was discussed which can enhance the durability of PVSCs against thermal and moisture degradation. Overall, SAMs present a promising avenue for addressing both efficiency and stability challenges in PVSCs, paving the way toward commercial viability. Future research should prioritize long-term environmental durability and the scaling up of SAM applications for industrial implementation.
{"title":"Enhancing efficiency and stability in perovskite solar cells: innovations in self-assembled monolayers.","authors":"Jingshu Tian, Haichang Zhang","doi":"10.3389/fchem.2024.1519166","DOIUrl":"10.3389/fchem.2024.1519166","url":null,"abstract":"<p><p>Perovskite solar cells (PVSCs) show remarkable potential due to their high-power conversion efficiencies and scalability. However, challenges related to stability and long-term performance remain significant. Self-assembled monolayers (SAMs) have emerged as a crucial solution, enhancing interfacial properties, facilitating hole extraction, and minimizing non-radiative recombination. This review examines recent advancements in SAMs for PVSCs, focusing on three key areas: anchoring groups and interface engineering, electronic structure modulation as well as band alignment, and stability optimization. We emphasize the role of anchoring groups in reducing defects and improving crystallinity, alongside the ability of SAMs to fine-tune energy levels for more effective hole extraction. Additionally, co-adsorbed SAM strategies was discussed which can enhance the durability of PVSCs against thermal and moisture degradation. Overall, SAMs present a promising avenue for addressing both efficiency and stability challenges in PVSCs, paving the way toward commercial viability. Future research should prioritize long-term environmental durability and the scaling up of SAM applications for industrial implementation.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1519166"},"PeriodicalIF":3.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Editorial: Green synthesis of metallic and metal oxide nanoparticles with biological applications.","authors":"Renata Katsuko Takayama Kobayashi, Raghvendra Ashok Bohara, Mahendra Rai, Gerson Nakazato","doi":"10.3389/fchem.2024.1546838","DOIUrl":"https://doi.org/10.3389/fchem.2024.1546838","url":null,"abstract":"","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1546838"},"PeriodicalIF":3.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-06eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1516427
Lorena Germán-Ayuso, Rubén Cobos, Leire Lorenzo, Francisca Río, Soraya Prieto-Fernández, Tomás Roncal, José M Cuevas
Within the context of the circular economy, the transformation of agri-food waste or by-products into valuable products is essential to promoting a transition towards more sustainable and efficient utilisation of resources. Whey is a very abundant by-product of dairy manufacturing. Apart from partial reutilisation in animal feed or some food supplements, the sustainable management and disposal of whey still represent significant environmental challenges. In this work, whey is considered a valuable resource for producing high-value products, specifically 2,3-butanediol (2,3-BDO), which was produced through fermentation using the bacterial strain Lactococcus lactis 43103. The described process yielded a >90% purity of 2,3-BDO, which was evaluated as a potential chain extender in the synthesis of bio-based waterborne polyurethane dispersions (PUDs). The incorporation of whey-derived 2,3-BDO led to the development of PUDs with up to 90% bio-based content without detrimental effects on the process or liquid-phase properties. The combination of 100% bio-based polyether polyols with partially renewable L-lysine ethyl ester diisocyanate and whey-derived 2,3-BDO as a chain extender generated totally stable, low-particle-size water dispersions of amorphous polymers characterised by similar structure and molecular weight compared to those of alternative petroleum-based PUDs. These results open up the possibility of incorporating fermentation-derived 2,3-BDO as a totally renewable component in bio-based PUDs as potential sustainable resinous systems for further formulation of water-based coatings or adhesives.
{"title":"Evaluation of 2,3-butanediol derived from whey fermentation as an effective bio-based monomer for waterborne polyurethane dispersions.","authors":"Lorena Germán-Ayuso, Rubén Cobos, Leire Lorenzo, Francisca Río, Soraya Prieto-Fernández, Tomás Roncal, José M Cuevas","doi":"10.3389/fchem.2024.1516427","DOIUrl":"https://doi.org/10.3389/fchem.2024.1516427","url":null,"abstract":"<p><p>Within the context of the circular economy, the transformation of agri-food waste or by-products into valuable products is essential to promoting a transition towards more sustainable and efficient utilisation of resources. Whey is a very abundant by-product of dairy manufacturing. Apart from partial reutilisation in animal feed or some food supplements, the sustainable management and disposal of whey still represent significant environmental challenges. In this work, whey is considered a valuable resource for producing high-value products, specifically 2,3-butanediol (2,3-BDO), which was produced through fermentation using the bacterial strain <i>Lactococcus lactis</i> 43103. The described process yielded a >90% purity of 2,3-BDO, which was evaluated as a potential chain extender in the synthesis of bio-based waterborne polyurethane dispersions (PUDs). The incorporation of whey-derived 2,3-BDO led to the development of PUDs with up to 90% bio-based content without detrimental effects on the process or liquid-phase properties. The combination of 100% bio-based polyether polyols with partially renewable L-lysine ethyl ester diisocyanate and whey-derived 2,3-BDO as a chain extender generated totally stable, low-particle-size water dispersions of amorphous polymers characterised by similar structure and molecular weight compared to those of alternative petroleum-based PUDs. These results open up the possibility of incorporating fermentation-derived 2,3-BDO as a totally renewable component in bio-based PUDs as potential sustainable resinous systems for further formulation of water-based coatings or adhesives.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1516427"},"PeriodicalIF":3.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-06eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1515424
Kevser Kübra Kırboğa, Aman Karim, Ecir Uğur Küçüksille, Mithun Rudrapal, Johra Khan, Raghu Ram Achar, Ekaterina Silina, Natalia Manturova, Victor Stupin
Cannabinoid and stilbenoid compounds derived from Cannabis sativa were screened against eight specific fungal protein targets to identify potential antifungal agents. The proteins investigated included Glycosylphosphatidylinositol (GPI), Enolase, Mannitol-2-dehydrogenase, GMP synthase, Dihydroorotate dehydrogenase (DHODH), Heat shock protein 90 homolog (Hsp90), Chitin Synthase 2 (CaChs2), and Mannitol-1-phosphate 5-dehydrogenase (M1P5DH), all of which play crucial roles in fungal survival and pathogenicity. This research evaluates the binding affinities and interaction profiles of selected cannabinoids and stilbenoids with these eight proteins using molecular docking and molecular dynamics simulations. The ligands with the highest binding affinities were identified, and their pharmacokinetic profiles were analyzed using ADMET analysis. The results indicate that GMP synthase exhibited the highest binding affinity with Cannabistilbene I (-9.1 kcal/mol), suggesting hydrophobic solid interactions and multiple hydrogen bonds. Similarly, Chitin Synthase 2 demonstrated significant binding with Cannabistilbene I (-9.1 kcal/mol). In contrast, ligands such as Cannabinolic acid and 8-hydroxycannabinolic acid exhibited moderate binding affinities, underscoring the variability in interaction strengths among different proteins. Despite promising in silico results, experimental validation is necessary to confirm therapeutic potential. This research lays a crucial foundation for future studies, emphasizing the importance of evaluating binding affinities, pharmacokinetic properties, and multi-target interactions to identify promising antifungal agents.
{"title":"Exploring the antifungal potential of <i>Cannabis sativa</i>-derived stilbenoids and cannabinoids against novel targets through <i>in silico</i> protein interaction profiling.","authors":"Kevser Kübra Kırboğa, Aman Karim, Ecir Uğur Küçüksille, Mithun Rudrapal, Johra Khan, Raghu Ram Achar, Ekaterina Silina, Natalia Manturova, Victor Stupin","doi":"10.3389/fchem.2024.1515424","DOIUrl":"10.3389/fchem.2024.1515424","url":null,"abstract":"<p><p>Cannabinoid and stilbenoid compounds derived from <i>Cannabis sativa</i> were screened against eight specific fungal protein targets to identify potential antifungal agents. The proteins investigated included Glycosylphosphatidylinositol (GPI), Enolase, Mannitol-2-dehydrogenase, GMP synthase, Dihydroorotate dehydrogenase (DHODH), Heat shock protein 90 homolog (Hsp90), Chitin Synthase 2 (CaChs2), and Mannitol-1-phosphate 5-dehydrogenase (M1P5DH), all of which play crucial roles in fungal survival and pathogenicity. This research evaluates the binding affinities and interaction profiles of selected cannabinoids and stilbenoids with these eight proteins using molecular docking and molecular dynamics simulations. The ligands with the highest binding affinities were identified, and their pharmacokinetic profiles were analyzed using ADMET analysis. The results indicate that GMP synthase exhibited the highest binding affinity with Cannabistilbene I (-9.1 kcal/mol), suggesting hydrophobic solid interactions and multiple hydrogen bonds. Similarly, Chitin Synthase 2 demonstrated significant binding with Cannabistilbene I (-9.1 kcal/mol). In contrast, ligands such as Cannabinolic acid and 8-hydroxycannabinolic acid exhibited moderate binding affinities, underscoring the variability in interaction strengths among different proteins. Despite promising <i>in silico</i> results, experimental validation is necessary to confirm therapeutic potential. This research lays a crucial foundation for future studies, emphasizing the importance of evaluating binding affinities, pharmacokinetic properties, and multi-target interactions to identify promising antifungal agents.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1515424"},"PeriodicalIF":3.8,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-03eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1538944
Brij Pal Singh, Pedro Ferreira Santos, Silvia Luna-Suárez, Cristian Jimenez Martínez
{"title":"Editorial: Advances in bioactive peptides and functional properties of foods.","authors":"Brij Pal Singh, Pedro Ferreira Santos, Silvia Luna-Suárez, Cristian Jimenez Martínez","doi":"10.3389/fchem.2024.1538944","DOIUrl":"10.3389/fchem.2024.1538944","url":null,"abstract":"","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1538944"},"PeriodicalIF":3.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-03eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1520586
Junfeng Jiang, Jun Luo, Wenyu Zheng, Jiayi Liu, Hui Jiang, Cuiyun Wu, Hongjin Bai
As an agricultural planting practice, preceding cropping can not only enhance soil fertility and reduce pests and diseases but also boost crop yield and quality. In this study, SZS samples from different preceding cropping areas were selected as research subjects. Phenolic compounds were analyzed using high-performance liquid chromatography (HPLC), and antioxidant activities were assessed based on free radical scavenging effects. Variety differences were explored through chemical pattern recognition, and the spectrum-effect relationship between the fingerprint spectra of SZS and antioxidant activity was investigated using Pearson correlation analysis, grey relational analysis, and other methods. A total of 17 peaks were observed, among which 4 peaks were identified. They are gallic acid, catechin, spinosin, and scutellarin. The 22 SZS samples could be categorized into 3 groups, with cluster analysis and principal component analysis results being largely consistent. Spinosin, a marker compound of SZS, is a crucial contributor to the total antioxidant activity. In conclusion, the spectrum-effect relationship between phenolic compounds and the antioxidant activity of SZS was established, and the main characteristic components affecting antioxidant activity were identified, providing a reference for the quality evaluation of SZS and the development of its products.
{"title":"Establishment of fingerprint of phenolic compounds in <i>Semen Ziziphi Spinosae</i> and study on the spectrum-effect relationship based on different preceding cropping areas.","authors":"Junfeng Jiang, Jun Luo, Wenyu Zheng, Jiayi Liu, Hui Jiang, Cuiyun Wu, Hongjin Bai","doi":"10.3389/fchem.2024.1520586","DOIUrl":"10.3389/fchem.2024.1520586","url":null,"abstract":"<p><p>As an agricultural planting practice, preceding cropping can not only enhance soil fertility and reduce pests and diseases but also boost crop yield and quality. In this study, SZS samples from different preceding cropping areas were selected as research subjects. Phenolic compounds were analyzed using high-performance liquid chromatography (HPLC), and antioxidant activities were assessed based on free radical scavenging effects. Variety differences were explored through chemical pattern recognition, and the spectrum-effect relationship between the fingerprint spectra of SZS and antioxidant activity was investigated using Pearson correlation analysis, grey relational analysis, and other methods. A total of 17 peaks were observed, among which 4 peaks were identified. They are gallic acid, catechin, spinosin, and scutellarin. The 22 SZS samples could be categorized into 3 groups, with cluster analysis and principal component analysis results being largely consistent. Spinosin, a marker compound of SZS, is a crucial contributor to the total antioxidant activity. In conclusion, the spectrum-effect relationship between phenolic compounds and the antioxidant activity of SZS was established, and the main characteristic components affecting antioxidant activity were identified, providing a reference for the quality evaluation of SZS and the development of its products.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1520586"},"PeriodicalIF":3.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-24eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1510029
George Hanson, Joseph Adams, Daveson I B Kepgang, Luke S Zondagh, Lewis Tem Bueh, Andy Asante, Soham A Shirolkar, Maureen Kisaakye, Hem Bondarwad, Olaitan I Awe
Introduction: Dengue Fever continues to pose a global threat due to the widespread distribution of its vector mosquitoes, Aedes aegypti and Aedes albopictus. While the WHO-approved vaccine, Dengvaxia, and antiviral treatments like Balapiravir and Celgosivir are available, challenges such as drug resistance, reduced efficacy, and high treatment costs persist. This study aims to identify novel potential inhibitors of the Dengue virus (DENV) using an integrative drug discovery approach encompassing machine learning and molecular docking techniques.
Method: Utilizing a dataset of 21,250 bioactive compounds from PubChem (AID: 651640), alongside a total of 1,444 descriptors generated using PaDEL, we trained various models such as Support Vector Machine, Random Forest, k-nearest neighbors, Logistic Regression, and Gaussian Naïve Bayes. The top-performing model was used to predict active compounds, followed by molecular docking performed using AutoDock Vina. The detailed interactions, toxicity, stability, and conformational changes of selected compounds were assessed through protein-ligand interaction studies, molecular dynamics (MD) simulations, and binding free energy calculations.
Results: We implemented a robust three-dataset splitting strategy, employing the Logistic Regression algorithm, which achieved an accuracy of 94%. The model successfully predicted 18 known DENV inhibitors, with 11 identified as active, paving the way for further exploration of 2683 new compounds from the ZINC and EANPDB databases. Subsequent molecular docking studies were performed on the NS2B/NS3 protease, an enzyme essential in viral replication. ZINC95485940, ZINC38628344, 2',4'-dihydroxychalcone and ZINC14441502 demonstrated a high binding affinity of -8.1, -8.5, -8.6, and -8.0 kcal/mol, respectively, exhibiting stable interactions with His51, Ser135, Leu128, Pro132, Ser131, Tyr161, and Asp75 within the active site, which are critical residues involved in inhibition. Molecular dynamics simulations coupled with MMPBSA further elucidated the stability, making it a promising candidate for drug development.
Conclusion: Overall, this integrative approach, combining machine learning, molecular docking, and dynamics simulations, highlights the strength and utility of computational tools in drug discovery. It suggests a promising pathway for the rapid identification and development of novel antiviral drugs against DENV. These in silico findings provide a strong foundation for future experimental validations and in-vitro studies aimed at fighting DENV.
{"title":"Machine learning and molecular docking prediction of potential inhibitors against dengue virus.","authors":"George Hanson, Joseph Adams, Daveson I B Kepgang, Luke S Zondagh, Lewis Tem Bueh, Andy Asante, Soham A Shirolkar, Maureen Kisaakye, Hem Bondarwad, Olaitan I Awe","doi":"10.3389/fchem.2024.1510029","DOIUrl":"https://doi.org/10.3389/fchem.2024.1510029","url":null,"abstract":"<p><strong>Introduction: </strong>Dengue Fever continues to pose a global threat due to the widespread distribution of its vector mosquitoes, <i>Aedes aegypti</i> and <i>Aedes albopictus</i>. While the WHO-approved vaccine, Dengvaxia, and antiviral treatments like Balapiravir and Celgosivir are available, challenges such as drug resistance, reduced efficacy, and high treatment costs persist. This study aims to identify novel potential inhibitors of the Dengue virus (DENV) using an integrative drug discovery approach encompassing machine learning and molecular docking techniques.</p><p><strong>Method: </strong>Utilizing a dataset of 21,250 bioactive compounds from PubChem (AID: 651640), alongside a total of 1,444 descriptors generated using PaDEL, we trained various models such as Support Vector Machine, Random Forest, k-nearest neighbors, Logistic Regression, and Gaussian Naïve Bayes. The top-performing model was used to predict active compounds, followed by molecular docking performed using AutoDock Vina. The detailed interactions, toxicity, stability, and conformational changes of selected compounds were assessed through protein-ligand interaction studies, molecular dynamics (MD) simulations, and binding free energy calculations.</p><p><strong>Results: </strong>We implemented a robust three-dataset splitting strategy, employing the Logistic Regression algorithm, which achieved an accuracy of 94%. The model successfully predicted 18 known DENV inhibitors, with 11 identified as active, paving the way for further exploration of 2683 new compounds from the ZINC and EANPDB databases. Subsequent molecular docking studies were performed on the NS2B/NS3 protease, an enzyme essential in viral replication. ZINC95485940, ZINC38628344, 2',4'-dihydroxychalcone and ZINC14441502 demonstrated a high binding affinity of -8.1, -8.5, -8.6, and -8.0 kcal/mol, respectively, exhibiting stable interactions with His51, Ser135, Leu128, Pro132, Ser131, Tyr161, and Asp75 within the active site, which are critical residues involved in inhibition. Molecular dynamics simulations coupled with MMPBSA further elucidated the stability, making it a promising candidate for drug development.</p><p><strong>Conclusion: </strong>Overall, this integrative approach, combining machine learning, molecular docking, and dynamics simulations, highlights the strength and utility of computational tools in drug discovery. It suggests a promising pathway for the rapid identification and development of novel antiviral drugs against DENV. These <i>in silico</i> findings provide a strong foundation for future experimental validations and <i>in-vitro</i> studies aimed at fighting DENV.</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1510029"},"PeriodicalIF":3.8,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11703810/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-24eCollection Date: 2024-01-01DOI: 10.3389/fchem.2024.1539768
Leonardo Lima Fuscaldi, Danielle Vieira Sobral, Ana Claudia Durante, Fernanda Ferreira Mendonça, Ana Cláudia Camargo Miranda, Carla Salgueiro, Silvia Gomez de Castiglia, Lilian Yuri Itaya Yamaga, Marcelo Livorsi da Cunha, Luciana Malavolta, Marycel Figols de Barboza, Jorge Mejia
[This corrects the article DOI: 10.3389/fchem.2023.1271176.].
[这更正了文章DOI: 10.3389/fchem.2023.1271176.]。
{"title":"Corrigendum: Radiochemical and biological assessments of a PSMA-I&S cold kit for fast and inexpensive <sup>99m</sup>Tc-labeling for SPECT imaging and radioguided surgery in prostate cancer.","authors":"Leonardo Lima Fuscaldi, Danielle Vieira Sobral, Ana Claudia Durante, Fernanda Ferreira Mendonça, Ana Cláudia Camargo Miranda, Carla Salgueiro, Silvia Gomez de Castiglia, Lilian Yuri Itaya Yamaga, Marcelo Livorsi da Cunha, Luciana Malavolta, Marycel Figols de Barboza, Jorge Mejia","doi":"10.3389/fchem.2024.1539768","DOIUrl":"https://doi.org/10.3389/fchem.2024.1539768","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fchem.2023.1271176.].</p>","PeriodicalId":12421,"journal":{"name":"Frontiers in Chemistry","volume":"12 ","pages":"1539768"},"PeriodicalIF":3.8,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704264/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}