Article
Multidisciplinary Sciences
Martino Bertoni, Miquel Duran-Frigola, Pau Badia-i-Mompel, Eduardo Pauls, Modesto Orozco-Ruiz, Oriol Guitart-Pla, Victor Alcalde, Victor M. Diaz, Antoni Berenguer-Llergo, Isabelle Brun-Heath, Nuria Villegas, Antonio Garcia de Herreros, Patrick Aloy
Summary: Chemical descriptors encode the physicochemical and structural properties of small molecules and are at the core of chemoinformatics. The authors introduce deep neural networks capable of inferring bioactivity signatures for any compound of interest, even with little or no experimental information. Signatures relate to 25 different types of bioactivities and can be used as replacements for chemical descriptors in daily chemoinformatics tasks.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Srijit Seal, Hongbin Yang, Maria-Anna Trapotsi, Satvik Singh, Jordi Carreras-Puigvert, Ola Spjuth, Andreas Bender
Summary: In this study, similarity-based merger models were developed to combine outputs of individual models trained on cell morphology and chemical structure, as well as the structural and morphological similarities of compounds in the test dataset. Logistic regression models were used to apply these similarity-based merger models on predictions and similarities from 177 assays, achieving better performance compared to using structural or cell painting models alone. These results demonstrate that similarity-based merger models combining structure and cell morphology can accurately predict a wide range of biological assay outcomes and expand the applicability domain.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Microbiology
Sonia Coutinho, Vanessa Matos, Natalia Seixas, Hellen Rodrigues, Vanessa B. Paula, Lais Freitas, Teresa Dias, Francisco de Assis Ribeiro Santos, Luis G. Dias, Leticia M. Estevinho
Summary: This study investigated the botanical origin, physicochemical profile, and biological activities of geopropolis from M. scutellaris collected during rainy and dry seasons. The results showed that rainy-season geopropolis had higher phenol and flavonoid content and exhibited superior antioxidant, antimicrobial, and anti-inflammatory activities compared to dry-season geopropolis.
Article
Multidisciplinary Sciences
Sachin Kumar, Yujen Wang, Mohammadhasan Hedayati, Frederik Fleissner, Manuel K. Rausch, Sapun H. Parekh
Summary: This study reveals that mechanical strain-induced structural changes in fibrin affect its biochemistry. Tensile deformation leads to molecular structural transitions of fibrin, reducing the binding ability of tissue plasminogen activator (tPA) and suppressing the biological activity of platelets on mechanically strained fibrin.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Xiaoman Zhao, Yue Kong, Yueshan Ji, Xiulan Xin, Liang Chen, Guang Chen, Changyuan Yu
Summary: In this study, predictive models for TRK inhibitors were constructed using different algorithms. The combination of DNN algorithm and ECFP4 descriptors achieved excellent performance in both dataset divisions. The results demonstrate the strong generalization prediction ability of the DNN algorithm and the importance of feature richness in predicting unknown molecules.
MOLECULAR DIVERSITY
(2023)
Article
Chemistry, Multidisciplinary
Lena Keller, Emilia Oueis, Amninder Kaur, Nasim Safaei, Susanne H. Kirsch, Antonia P. Gunesch, Sibylle Haid, Ulfert Rand, Luka Cicin-Sain, Chengzhang Fu, Joachim Wink, Thomas Pietschmann, Rolf Mueller
Summary: A new strain of actinobacteria, Kibdelosporangium persicum sp. nov., collected from a hot desert in Iran, yielded a novel family of sesquarterpenoids (persicamidines A-E) with remarkable antiviral activity. Extensive NMR analysis revealed a hexacyclic terpenoid molecule with a modified sugar moiety on one side and a unique isourea moiety fused to the terpenoid structure. Persicamidines A-E exhibited potent activity against hCoV-229E and SARS-CoV-2 viruses in the nanomolar range, along with excellent selectivity indices, showing promise as potential drug candidates.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Food Science & Technology
Nelida Nina, Cristina Theoduloz, Hernan Paillan, Felipe Jimenez-Aspee, Katherine Marquez, Katharina Schuster, Laura Becker, Claudia Oellig, Jan Frank, Guillermo Schmeda-Hirschmann
Summary: This study aimed to analyze the chemical composition, antioxidant capacity, and enzyme inhibition effect of secondary metabolites-enriched extracts (SMEE) of thirteen Chilean bean landraces before and after boiling. HPLC-DAD-MS/MS was used to determine the SMEE composition, and various compounds including procyanidins, flavonoids, phenylpropanoids, and saponins were identified. Cooking decreased the total phenolics and saponins content, but certain individual compounds like ferulic acid and soyasaponins Ba and Bb increased. Total phenolics showed a significant correlation with antioxidant activity, and some saponins exhibited a correlation with α-glucosidase inhibition. The findings suggest that bean components may have local activity in the intestine, preventing oxidation of other nutrients and modulating gastrointestinal enzymes.
JOURNAL OF FUNCTIONAL FOODS
(2023)
Article
Chemistry, Multidisciplinary
Kun Jiang, Hongji Yan, Carolin Rickert, Matthias Marczynski, Kajsa Sixtensson, Francisco Vilaplana, Oliver Lieleg, Thomas Crouzier
Summary: The crosslinking architecture of hydrogels affects their bioactivity, with different crosslinking strategies influencing properties such as enzymatic degradation sensitivity and cell response. Modulating the accessibility of binding sites through the choice of crosslinking strategy can alter substrate accessibility to proteases and the pattern of exposed sialic acid residues to macrophages.
ADVANCED FUNCTIONAL MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Seema Dhiman, Johann F. Ulrich, Paul Wienecke, Thomas Wichard, Hans-Dieter Arndt
Summary: Chemical mediators play a crucial role in controlling symbiotic interactions in the environment. This study presents a fully stereoselective total synthesis of (-)-thallusin, a differentiation factor in algae, and shows its potent bioactivity in Ulva mutabilis. SAR investigations suggest that (-)-thallusin triggers different pathways in Ulva that can be separated by chemical editing of the compound structure.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Simon Vlad Luca, Krystyna Skalicka-Wozniak, Cosmin-Teodor Mihai, Adina Catinca Gradinaru, Alexandru Mandici, Nina Ciocarlan, Anca Miron, Ana Clara Aprotosoaie
Summary: This study evaluated the phytochemical profile and potential antimicrobial, antioxidant, and cytotoxic activities of ten Salvia species from Eastern Europe. The results showed that S. officinalis exhibited the highest antimicrobial and antioxidant activities, but no significant cytotoxic effect on human breast carcinoma cells.
Article
Plant Sciences
Mohamed R. Habib, Ahmed A. Hamed, Rasha E. M. Ali, Khaled M. Zayed, Rasha M. Gad El-Karim, Rehab Sabour, Hanaa M. Abu El-Einin, Mosad A. Ghareeb
Summary: This study investigated the chemical profile and biological activities of tissue extracts from Thais savignyi. The ethyl acetate extract showed the highest antioxidant capacity, antibacterial, antibiofilm, antifungal, and cytotoxic activities.
PHARMACEUTICAL BIOLOGY
(2022)
Review
Plant Sciences
Sema Carikci, Turgut Kilic, Ahmet C. Goren, Tuncay Dirmenci, Gulbahar Ozge Alim Toraman, Gulacti Topcu
Summary: This review article evaluates the phytochemical constituents and biological activities of Sideritis species growing in Turkey. The study found that these plants are rich in terpenoids, flavonoids, phenolics, and other secondary metabolites. The Sideritis species exhibit various activities, including antioxidant, antimicrobial, and anti-ulcer/anti-inflammatory activities.
PHARMACEUTICAL BIOLOGY
(2023)
Review
Chemistry, Applied
Ji Kang, Xing Jia, Nifei Wang, Meng Xiao, Shuang Song, Shufen Wu, Zhenjing Li, Shujun Wang, Steve W. Cui, Qingbin Guo
Summary: This review compares the structural characteristics of marine sulfated polysaccharides and summarizes their functional and biological activities, as well as the influence of sulfate groups on their properties. The aim is to provide a deeper understanding of marine SPs for their industrial applications in various fields.
FOOD HYDROCOLLOIDS
(2022)
Article
Food Science & Technology
Diana De Santis, Katya Carbone, Stefania Garzoli, Valentina Laghezza Masci, Giovanni Turchetti
Summary: The extract of Rubus idaeus leaves has strong antioxidant, antibacterial, and cytotoxic activities. Volatile molecules are the main contributors to its biological properties. The extract has great potential for application in the food, cosmetic, and dietary supplement industries.
Article
Chemistry, Medicinal
Maria-Anna Trapotsi, Lewis H. Mervin, Avid M. Afzal, Noe Sturm, Ola Engkvist, Ian P. Barrett, Andreas Bender
Summary: Understanding the mechanism-of-action of compounds and predicting potential drug targets are crucial in small-molecule drug discovery. This study compared chemical and cell morphology information for bioactivity prediction, finding that BMF Macau outperformed RF when image data were used as compound information. Both cell morphology changes and chemical structure information contain valuable information about compound bioactivity, with some targets better predicted by image data and others by fingerprint-based side information.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
