Article
Agriculture, Multidisciplinary
Wei Wang, Shan Zhang, Jianhua Wang, Furan Wu, Tao Wang, Gong Xu
Summary: A series of potential novel fungicides were designed and synthesized, with two compounds showing significant antifungal activities against various fungi. These compounds could be promising candidates for the development of new fungicides in crop protection.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Genetics & Heredity
Hui-O Chen, Peng-Chan Lin, Chen-Ruei Liu, Chi-Shiang Wang, Jung-Hsien Chiang
Summary: Developing a biomedical text mining pipeline can help in cancer gene panel discovery. The researchers built a gene term-feature matrix using text-mined co-occurrence features and validated the panel's accuracy. They demonstrated the predictive power of using Text Mining technology for cancer gene prediction.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Kun Li, Yue Zhang, Zeyu Hong, Zhenwu Yu, Xiaoyu Liu, Zhihong Duan, Wei Gao, Liangfu Tang, You Lv, Zhijin Fan
Summary: The development of new fungicides is crucial for protecting crops and achieving sustainable agriculture. In this study, 44 novel coumarin ester derivatives were synthesized and evaluated for their fungicidal activity through in vitro and in vivo bioassays. The results showed that the esterification of 4-(3,4-dichloroisothiazole)-7-hydroxycoumarins resulted in compounds with fungicidal activity comparable to the lead compounds. Density functional theory calculations and 3D-QSAR modeling provided insights into the structure-activity relationship and guided further molecular design.
Article
Chemistry, Multidisciplinary
Hong-Quan Xu, Huan Xiao, Jin-Hui Bu, Yan-Feng Hong, Yu-Hong Liu, Zi-Yue Tao, Shu-Fan Ding, Yi-Tong Xia, E. Wu, Zhen Yan, Wei Zhang, Gong-Xing Chen, Feng Zhu, Lin Tao
Summary: The study introduces a comprehensive database for endophytic microorganism natural products (EMNPD), which aims to meet the increasing demand for data mining and sharing in this field. This database provides a wealth of natural product data and links to other databases, facilitating drug discovery and exploration of bioactive substances.
JOURNAL OF CHEMINFORMATICS
(2023)
Review
Chemistry, Medicinal
Junjie Li, Rui Zhao, Peiran Miao, Fengfeng Xu, Jiahao Chen, Xiaoying Jiang, Zi Hui, Liwei Wang, Renren Bai
Summary: This review provides a comprehensive overview of the diverse anti-inflammatory activities of flavonoids and elucidates the underlying pathways in mediating inflammation. It includes a systematic classification and detailed statistical analysis of flavonoids, related anti-inflammatory targets, and in vitro and in vivo test models. The review aims to provide practical information and potential leads for researchers engaged in natural products and anti-inflammatory drug discovery.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Applied
Manoj Gayke, Hanuman Narode, Rajesh S. Bhosale, Jhillu Singh Yadav
Summary: In this study, we described a novel synthetic strategy for the total synthesis of the harvestmen natural product (4S,5S)-4-hydroxy-gamma-decalactone (minor) using an inexpensive precursor. The synthesis achieved an overall yield of 31% and utilized classical reactions and key steps involving olefin and lactone formation.
NATURAL PRODUCT RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Joachim J. Hug, Nicolas A. Frank, Christine Walt, Petra Senica, Fabian Panter, Rolf Mueller
Summary: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a diverse group of natural products with intriguing modifications, such as the biarylitides. Recent genomic analyses have shown that the biosynthesis of biarylitides only requires a pentapeptide precursor and a modifying cytochrome-P450-dependent enzyme. This discovery expands the biosynthetic scope of RiPPs and highlights the unique biochemistry found in myxobacteria.
Review
Biochemistry & Molecular Biology
Li-Juan Deng, Wei-Qing Deng, Shu-Ran Fan, Min-Feng Chen, Ming Qi, Wen-Yu Lyu, Qi Qi, Amit K. Tiwari, Jia-Xu Chen, Dong-Mei Zhang, Zhe-Sheng Chen
Summary: Abnormal N6-methyladenosine (m6A) modification is closely related to cancer development, and finding targeted anticancer drugs is important. Traditional herbs and computer-synthesized compounds are reasonable sources for these drugs. Artificial intelligence has advantages in discovering m6A-targeting anticancer drugs.
Article
Microbiology
Karolina Subko, Xinhui Wang, Frederik H. Nielsen, Thomas Isbrandt, Charlotte H. Gotfredsen, Maria C. Ramos, Thomas Mackenzie, Francisca Vicente, Olga Genilloud, Jens C. Frisvad, Thomas O. Larsen
Summary: This study presents a method for discovery and design of asperphenamate analogs, resulting in the identification of numerous new analogs from Penicillium astrolabium. The research demonstrates the potential to generate novel analogs by varying amino acid availability and highlights the flexibility of nonribosomal peptide synthetase (NRPS) in filamentous fungi.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Ankur Sarkar, Edward Y. Kim, Taehwan Jang, Akarawin Hongdusit, Hyungjun Kim, Jeong-Mo Choi, Jerome M. Fox
Summary: The study introduces a novel approach to utilize microbial hosts for targeted natural product discovery and biosynthesis, leading to the identification and synthesis of two potential protein tyrosine phosphatase 1B inhibitors for the treatment of diabetes and cancer. The findings demonstrate the scalability and versatility of the method, as well as the potential of using microbes to discover and produce bioactive compounds with unique structures and binding sites.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tristan de Rond, Julia E. Asay, Bradley S. Moore
Summary: A genome-mining approach was developed to discover biochemical transformations through the analysis of co-occurring enzyme domains in a single protein. This methodology successfully identified new enzymatic activities and provided functional annotation for multidomain enzymes.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Wenqin Li, Yi Ding, Huitang Qi, Tian Liu, Qing Yang
Summary: The study found that several phytochemicals can inhibit multiple insect chitinolytic enzymes simultaneously, with predicted interactions with key residues and good insecticidal activity. This research provides a new approach for using a multitarget high-throughput screening strategy to discover natural products as insecticide leads.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biology
Hannah Tabakh, Adelle P. McFarland, Maureen K. Thomason, Alex J. Pollock, Rochelle C. Glover, Shivam A. Zaver, Joshua J. Woodward
Summary: Pathogens encounter various antimicrobial responses during infection, including the ROS burst. The toxic 4-HNE impacts the growth and survival of bacteria, with Listeria monocytogenes inducing gene expression in response to 4-HNE exposure. While Rha1 and Rha2 are not essential for 4-HNE resistance in L. monocytogenes, they can confer resistance to sensitive bacteria in vitro and in host cells.
Article
Chemistry, Applied
Chunxuan Qi, Qingyang Li, Pu Chen, Keyue Wei, Jie Hong, Lele Tang, Hai-Tao Feng, Ben Zhong Tang
Summary: In recent years, aggregation-induced emission luminogens (AIEgens) have been widely used in various fields such as bioimaging, theranostics, organic photoelectronics, and chemo/biosensors. However, the current AIEgens are mostly synthesized organically, which involves complex synthesis routes, high cost, environmental unfriendliness, and poor biocompatibility. Therefore, the exploration of AIEgens from natural products has become an attractive alternative approach. This contribution discovers two natural AIE-active materials, Tangeretin and Nobiletin, which can be extracted from orange peel.
Article
Biochemistry & Molecular Biology
Mary M. LeClair, Zacharie A. Maw, Alyssa L. Grunwald, Joshua R. Kelly, Bradley A. Haltli, Russell G. Kerr, Christopher Cartmell
Summary: Levesquamide A is an anti-tubercular natural product, and additional members of the levesquamide family have been identified using GNPS. Levesquamide B has been structurally elucidated, while the structures of levesquamide C, D, and the other three levesquamides remain ambiguous.
Article
Biochemistry & Molecular Biology
Jeffrey A. van Santen, Ella F. Poynton, Dasha Iskakova, Emily McMann, Tyler A. Alsup, Trevor N. Clark, Claire H. Fergusson, David P. Fewer, Alison H. Hughes, Caitlin A. McCadden, Jonathan Parra, Sylvia Soldatou, Jeffrey D. Rudolf, Elisabeth M-L Janssen, Katherine R. Duncan, Roger G. Linington
Summary: This paper reports the release of a new version of the Natural Products Atlas database, which includes a large number of new compounds and significant upgrades. In addition to adding detailed descriptions of microbial taxa and chemical ontology terms, manual curation and data integration were carried out to improve the user experience.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Kumar Saurav, Alessia Caso, Petra Urajova, Pavel Hrouzek, Germana Esposito, Katerina Delawska, Marketa Macho, Jan Hajek, Jose Cheel, Subhasish Saha, Petra Divoka, Sila Arsin, Kaarina Sivonen, David P. Fewer, Valeria Costantino
Summary: PUW and MIN are structurally homologous cyclic lipopeptides with antifungal and cytotoxic activities, where the variation in fatty acid substitutions influences the cytotoxicity of the compounds. Different substitutions on the fatty acid moiety of PUW/MIN variants lead to varying degrees of cytotoxicity. A 63 kb puwainaphycin biosynthetic gene cluster was identified in the N. harveyana strain UHCC-0300, indicating the presence of specific lipoinitiation mechanisms and enzymes for modifying the fatty acid moiety.
Article
Biology
Maryam Abidizadegan, Jaanika Blomster, David Fewer, Elina Peltomaa
Summary: In recent decades, the demand for natural and sustainable bioproducts has increased. Microalgae, with their industrial potential, have attracted much attention as promising biological resources. This study investigated the effect of light color and species-specific capability of cryptophyte algae to produce biochemical compounds. The results showed that changes in light quality significantly affect the biochemical compositions of cryptophyte algae, and species-specific responses to different light qualities were identified. The study also found that the derived biomolecules from cryptophytes had remarkable antioxidant activity, indicating that cryptophytes could be considered as potential candidates for producing beneficial biochemical compounds.
Article
Biotechnology & Applied Microbiology
Amir Akhgari, Bikash Baral, Arina Koroleva, Vilja Siitonen, David P. Fewer, Charles E. Melancon, Jani Rahkila, Mikko Metsa-Ketela
Summary: This study introduces a reporter-guided metabolic engineering tool based on random mutagenesis, selective pressure, and single-cell sorting for actinomycetes. It enables the identification of high-performing individual cells from mutant populations and has been successfully applied to strain development and drug discovery. The method allows for the activation of silent metabolic pathways and increased yields of proteins and natural products.
METABOLIC ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Sila Arsin, Endrews Delbaje, Jouni Jokela, Matti Wahlsten, Zoe M. Farrar, Perttu Permi, David Fewer
Summary: Two structurally distinct MAAs were identified in the lichen symbiont strain Nostoc sp. UHCC0926, and their biosynthesis in cyanobacteria was found to occur through a branched pathway. The presence of similar gene clusters in other cyanobacterial genomes suggests rapid evolutionary processes leading to chemical diversity in this family of microbial sunscreens.
ACS CHEMICAL BIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Tania Keiko Shishido, Endrews Delbaje, Matti Wahlsten, Inkeri Vuori, Jouni Jokela, Muriel Gugger, Marli F. Fiore, David P. Fewer
Summary: This study reports the isolation of a harmful cyanobacterium (Kamptonema sp. UHCC 0994) from a benthic microbial mat collected in shallow water on the coast of Helsinki. Genome sequencing analysis revealed similarities between this harmful cyanobacterial strain and strains isolated from the Baltic Sea, all of which contain the biosynthetic genes for the production of the harmful compound cylindrospermopsin. These findings suggest that these toxic cyanobacteria may exhibit a tychoplanktic lifestyle in the Baltic Sea and could be a potential source of environmental toxins.
Article
Biodiversity Conservation
Maria Christodoulou, Matti Wahlsten, Kaarina Sivonen
Summary: Cyanobacteria found in both aquatic and terrestrial environments have been extensively studied in Finland, but the diversity of terrestrial rock-inhabiting cyanobacteria is often ignored. In this study, two Pseudanabaena-like cyanobacterial strains were isolated and characterized using a polyphasic approach. Phylogenetic analyses using both 16S rRNA gene and 16S-23S ITS region revealed better resolution of species relationships, and based on these analyses, two new species were described. The study also highlighted the need for taxonomic revision in the poorly studied cyanobacterial genus Pseudanabaena.
Article
Chemistry, Organic
Xiaodan Ouyang, Paul M. D'Agostino, Matti Wahlsten, Endrews Delbaje, Jouni Jokela, Perttu Permi, Greta Gaiani, Antti Poso, Piia Bartos, Tobias A. M. Gulder, Hannu Koistinen, David P. Fewer
Summary: In this study, a comparative bioinformatic analysis was used to identify radiosumin biosynthetic gene clusters in the genomes of 13 filamentous cyanobacteria. The entire biosynthetic gene cluster was captured and expressed in Escherichia coli. High-resolution liquid chromatography-mass spectrometry, nuclear magnetic resonance spectroscopy, and chemical degradation analysis revealed the chemical structure of novel radiosumins produced by cyanobacteria. Radiosumin C was found to inhibit human trypsin isoforms selectively.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Andrea Estefania Carpinteyro Diaz, Lars Herfindal, Heidi Lie Andersen, Torgils Fossen
Summary: This study investigates the natural products of Cryptogramma crispa for the first time, and identifies 15 compounds, including a new compound called 3-malonyl pteroside D. The study finds that these compounds exhibit selective cytotoxic activity against acute myeloid leukemia cells, but not against normal cells.
Article
Chemistry, Multidisciplinary
Claudia Clemente, Nicholas Johnson, Xiaodan Ouyang, Rafael Popin, Sergio Dall'Angelo, Matti Wahlsten, Jouni Jokela, Alessandro Colombano, Brunello Nardone, David P. Fewer, Wael E. Houssen
Summary: The prenyl-D-Arg-containing autum-nalamide A is identified as a member of the cyanobactin family, and the AutF prenyltransferase can target the guanidinium moiety in arginine and homoarginine, making it a useful tool for biotechnological applications.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Organic
L. M. P. Heinila, J. Jokela, M. N. Ahmed, M. Wahlsten, S. Kumar, P. Hrouzek, P. Permi, H. Koistinen, D. P. Fewer, K. Sivonen
Summary: This study reports the discovery of novel natural products called varlaxins, members of the aeruginosin family. The chemical structures of varlaxins 1046A and 1022A were determined, and they were found to strongly inhibit human serine proteases.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)