Molecular Pharmacognosy
The ultimate goal of the research in 'selection methods' will be to fuse the maps for navigating evolutionary space - phylogenies - and those for navigating natural products chemical space - chemography - to proved a firm basis for the selection process in working with natural products chemistry.
Phylogenies, hypotheses of evolutionary relationships, has during the last 20 years emerged as one of the powerful concepts ever in life-sciences, with regard to their explanatory power.
One of the greatest advantages of phylogenies as compared to the older synoptical arrangements, is that it enables also a predictive perspective. This option originates from the properties of the phylogeny itself - as the groupings observed are formed by shared, derived, characters these allow themselves to be interpreted from the tree.
Although the overwhelming majority of phylogenetic hypotheses suggested today have their basis in molecular data such as vast stretches of nucleotide sequence data, virtually any type of hierarchically structured data can be used - such as e.g. biosynthesis schemes, chemographic, or even ecological data.
In 2001 Oprea and Gottfries suggested the term chemography, in resemblance to geography, as the art of navigating in chemical space. The concept chemical space is often used instead of multi-dimensional descriptor space. Navigation in chemical space could be compared to making a real space trip, but without a rocket. In chemical space stars and planets constitute of chemical compounds positioned based on their properties, where similar compounds are grouped together.
We have therefore developing an expanded chemical space map tuned for natural products research - http://chemgps.bmc.uu.se. The chemical compounds in Nature are very diverse and many times extremely complex and different from "normal" drug-like compounds. Therefore ChemGPS-NP will have core structures with a focus on natural products and even more extreme satellites than the original ChemGPS. This is to ensure that the natural products under study do not end up as outliers when predicted with the model.
These are some aspect of what we attempt to explore and utilize in the selection of study objects in search for bioactive compounds, their origins, evolution, and distribution.
Group members at UU and focus area 2016.08.24
Principal Investigators
Anders Backlund, Prof. - chemography & phylogeny
Christina Wedén, Dr. - fungi & fungal compounds
Cecilia Alsmark, Dr. - bioinformatics, LGT
Muaaz Alajlani, Dr. - TB & ChemGPS-NP
PhD students
Msc Elisabet Vikeved - LGT, Leishmania
Msc Kuei-Hung ’Momo’ Lai 賴奎宏 - bioactive compounds from fungi
Msc Astrid Henz - chemography & phylogeny
Msc Lu Yang 杨璐 - TCM bioactivity interpretation
Msc Åke Strese - LGT, Trichomonas on paternal leave
External collaborators
Thierry Kogej, Dr. - AstraZeneca R&D
Johan Gottfries, Prof. - Gothenburg University
Previous members and thesis focus
Josefin Rosén, Dr. - chemography, 2009
Catarina Ekenäs, Dr. - ethnobotany, 2008
Sonny Larsson, Dr. - phylogenies, 2007
Petra Lindholm, Dr. - screening, 2005
Publications
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Anti-inflammatory and Antiphytopathogenic Fungal Activity of 2,3-seco-Tirucallane Triterpenoids Meliadubins A and B from Melia dubia Cav. Barks with ChemGPS-NP and In Silico Prediction.
(2023). ACS Omega, . vol. 8, ss. 37116-37127 DOI -
Stability Study of Alpinia galanga Constituents and Investigation of Their Membrane Permeability by ChemGPS-NP and the Parallel Artificial Membrane Permeability Assay.
(2022). Pharmaceutics, . vol. 14 DOI -
In vitro and in silico evaluation of Ononis isoflavonoids as molecules targeting the central nervous system.
(2022). PLOS ONE, . vol. 17 DOI -
Decoding Multiple Biofunctions of Maca on Its Anti-allergic, Anti-inflammatory, Anti-thrombotic, and Pro-angiogenic Activities.
(2021). Journal of Agricultural and Food Chemistry, . vol. 69, ss. 11856-11866 DOI -
Survival and growth of saprotrophic and mycorrhizal fungi in recalcitrant amine, amide and ammonium containing media.
(2021). PLOS ONE, vol. 16 DOI -
Bisabolane sesquiterpenes from the leaves of Lindera benzoin reduce prostaglandin E2 formation in A549 cells.
(2020). Phytochemistry Letters, . vol. 38, ss. 6-11 DOI -
Evaluating Antimycobacterial Screening Schemes Using Chemical Global Positioning System-Natural Product Analysis.
(2020). Molecules, . vol. 25 DOI -
Revisiting the phylogeny of Dipsacales: New insights from phylogenomic analyses of complete plastomic sequences.
(2020). Journal of Systematics and Evolution, vol. 58, ss. 103-117 DOI -
Bisabolane sesquiterpenes from the leaves of Lindera benzoin reduce prostaglandin E2 formation in A549 cells.
Phytochemistry Letters -
Structural classification and scaffold diversity of sesquiterpene lactones in the angiosperms.
Phytochemistry -
Charting Angiosperm Chemistry: Evolutionary Perspective on Specialized Metabolites Reflected in Chemical Property Space.
(2019). Journal of Natural Products, vol. 82, ss. 798-812 DOI -
Briaviolides K-N, New Briarane-Type Diterpenoids from Cultured Octocoral Briareum violaceum.
(2018). Marine Drugs, . vol. 16 DOI -
Predicting the mechanism of action of antituberculosis agents using chemical global positioning system - natural product.
(2016). Planta Medica, vol. 82 DOI -
Bioactivity mapping of chemical property space - possible applications in natural products research.
(2016). Planta Medica, vol. 82 DOI -
Phylogenetic relationships through the lens of chemoinformatic methods.
(2016). Planta Medica, vol. 82 DOI -
Antileukemic sesterterpenoids from a marine sponge, Luffariella sp..
(2016). Planta Medica, vol. 82 DOI -
Mapping metabolic pathways in chemical property space paves the way for new leishmanicidals.
(2016). Planta Medica, . vol. 82 DOI -
Screening of compounds of Evernia prunastri (L.) for their antiproliferative activity in glioblastoma cells.
(2016). Planta Medica, . vol. 82 DOI -
Predicting inhibitors of HSP27 phosphorylation using ChemGPS-NP.
(2016). Planta Medica, vol. 82 DOI -
35 Years of Marine Natural Product Research in Sweden: Cool Molecules and Models from Cold Waters..
(2017). Progress in molecular and subcellular biology, vol. 55, ss. 1-34 DOI -
Tribelaceae.
(2016). I K. Kubitzki, J. Kadereit, and V. Bittrich (red.) The Families and Genera of Vascular Plants, . ss. 377-379 DOI -
Columelliaceae.
(2016). I K. Kubitzki, J. Kadereit, and V. Bittrich (red.) The Families and Genera of Vascular Plants, . ss. 141-144 DOI -
Adoxaceae.
(2016). I K. Kubitzki, J. Kadereit, and V. Bittrich (red.) The Families and Genera of Vascular Plants, . ss. 19-29 DOI -
Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets (Viola).
(2017). Frontiers in Plant Science, vol. 8 DOI -
Spasmolytic Mechanism of Aqueous Licorice Extract on Oxytocin-Induced Uterine Contraction through Inhibiting the Phosphorylation of Heat Shock Protein 27.
(2017). Molecules, . vol. 22 DOI -
Anti-allergic Hydroxy Fatty Acids from Typhonium blumei Explored through ChemGPS-NP.
(2017). Frontiers in Pharmacology, . vol. 8 DOI -
Cytotoxic Lanostanoids from Poria cocos.
(2016). Journal of natural products (Print), vol. 79, ss. 2805-2813 DOI -
Anti-Dengue Virus Constituents from Formosan Zoanthid Palythoa mutuki.
(2016). Marine Drugs, vol. 14 DOI -
The Dynamics of Lateral Gene Transfer in Genus Leishmania - A Route for Adaptation and Species Diversification.
(2016). PLoS Neglected Tropical Diseases, vol. 10 DOI -
"Ligand fishing" in chemical space reveals new potential leishmanicidals.
(2015). Planta Medica, vol. 81, ss. 1420-1420 -
Antileukemic lanostanoids from Poria cocos.
(2015). Planta Medica, vol. 81, ss. 1418-1418 -
Charting biological activity in chemical property space using ChemGPS-NP.
(2015). Planta Medica, vol. 81, ss. 1413-1413 -
"Ligand fishing" in chemical space reveals new potential leishmanicidals.
(2015). Planta Medica, vol. 81, ss. 1473-1473 -
Antileukemic lanostanoids from Poria cocos.
(2015). Planta Medica, vol. 81, ss. 1453-1453 -
Challenges to get axenic cultures of Trichomonas spp.: A new approach in eradication of contaminants and maintenance of laboratory microbiological cultures.
(2015). Journal of Microbiological Methods, vol. 118, ss. 25-30 DOI -
Investigating Pharmacological Similarity by Charting Chemical Space.
(2015). Journal of Chemical Information and Modeling, vol. 55, ss. 2375-2390 DOI -
Impulse Lecture: The odd fellow - Benefits of anomaly.
(2014). Planta Medica, vol. 80, ss. 1373-1374 -
A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes.
(2014). BMC Evolutionary Biology, vol. 14, ss. 119- DOI -
In silico comparison of marine, terrestrial and synthetic compounds using ChemGPS-NP for navigating chemical space.
(2013). Phytochemistry Reviews, vol. 12, ss. 449-457 DOI -
Microbial diversity of Alcyonium digitatum.
(2013). Phytochemistry Reviews, vol. 12, ss. 531-542 DOI -
Novel Trisubstituted Harmine Derivatives with Original in Vitro Anticancer Activity.
(2012). Journal of Medicinal Chemistry, vol. 55, ss. 6489-6501 DOI -
Synthesis and Biological Evaluation of Phenanthrenes as Cytotoxic Agents with Pharmacophore Modeling and ChemGPS-NP Prediction as Topo II Inhibitors.
(2012). PLOS ONE, vol. 7, ss. e37897- DOI -
The edible truffle Choiromyces venosus and its use in Sweden.
(2009). Acta Botanica Yunnanica, vol. 31, ss. 94-96 -
Topical chemical space in relation to biological space.
(2010). I L. Mander & H.-W. Lui (red.) Comprehensive Natural Products II, Oxford: Elsevier. ss. 47-79 DOI -
Chemography and Phylogeny: navigating chemical and evolutionary space.
(2006). Planta Medica, vol. 72, ss. 972-972 DOI -
Natural products in modern life science.
(2010). Phytochemistry Reviews, vol. 9, ss. 279-301 DOI -
Regarding the putative identity of a moth (Thaumetopoea spp.) allergen.
(2009). Allergy. European Journal of Allergy and Clinical Immunology, vol. 64, ss. 493-493 DOI -
Klum collection anteckningsbok.
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Teoribildning öppnar nya fält för naturproduktsforskning.
(2008). Läkemedelsvärlden, ss. 31 31- -
Phylogeny and chemography.
(2008). Planta Medica, . vol. 74, ss. SL64- DOI -
Modern pharmacognosy: Connecting biology and chemistry.
(2007). Pure and Applied Chemistry, vol. 79, ss. 763-774 DOI -
Expanding the ChemGPS chemical space with natural products.
(2005). Journal of natural products (Print), vol. 68, ss. 985-991 DOI -
Structure and function of Rubisco.
(2008). Plant physiology and biochemistry (Paris), vol. 46, ss. 275-291 DOI -
ChemGPS-NPweb A tool tuned for navigation in biologically relevant chemical space.
(2008). Embnet.news, vol. 14, ss. 6-9 -
Reappraising a decade old explanatory model for pharmacognosy.
(2008). Phytochemistry Letters, vol. 1, ss. 131-134 DOI -
Screening for Anti-Inflammatory Activity of 12 Arnica (Asteraceae) Species Assessed by Inhibition of NF-κB and Release of Human Neutrophil Elastase.
(2008). Planta Medica, vol. 74, ss. 1789-1794 DOI -
Novel chemical space exploration via natural products.
(2009). Journal of Medicinal Chemistry, vol. 52, ss. 1953-1962 DOI -
ChemGPS-NP mapping of chemical compounds for prediction of anticancer mode of action.
(2009). QSAR & combinatorial science (Print), vol. 28, ss. 436-446 DOI -
ChemGPS-NPweb: chemical space navigation online.
(2009). Journal of Computer-Aided Molecular Design, vol. 23, ss. 253-259 DOI -
Phylogenetic implications of an expanded valepotriate distribution in the Valerianaceae.
(1998). Biochemical Systematics and Ecology, . vol. 26, ss. 309-335 -
Phylogeny of the Asterales sensu late based on rbcL sequences with particular reference to the Goodeniaceae.
(1996). Plant Systematics and Evolution, . vol. 199, ss. 217-242 -
Pollen morphology and the systematic position of Triplostegia (Dipsacales).
(1997). Taxon, . vol. 46, ss. 21-31 -
Phylogeny of the Asteridae s. str. based on rbcL sequences, with particular reference to the Dipsacales.
(1997). Plant Systematics and Evolution, . vol. 207, ss. 225-254 -
The floral development and floral anatomy of Chrysosplenium alternifolium, an unusual member of the Saxifragaceae.
(1998). Journal of plant research, . vol. 111, ss. 573-580 -
An ordinal classification for the families of flowering plants.
(1998). ANNALS OF THE MISSOURI BOTANICAL GARDEN, . vol. 85, ss. 531-553 -
To be or not to be - principles of classification and monotypic plant families.
(1998). Taxon, . vol. 47, ss. 391-400 -
Diervillaceae and Linnaeaceae, two new families of caprifolioids.
(1998). Taxon, . vol. 47, ss. 657-661 -
Primary and 3-D modelled structures of two cyclotides from Viola odorata.
(2003). Phytochemistry, vol. 64, ss. 135-142 DOI -
Dipsacales (Honeysuckle).
(2002). I Encyclopedia of Life Sciences . DOI -
Building a computerized herbal substance register for imnplementation and use in the whole world health organisation international drug monitoring programme.
(2002). Drug information journal, vol. 36, ss. 839-854 -
Origin of the cyathium-bearing Euphorbieae (Euphorbiaceae): phylogenetic study based on morphological characters.
(2002). Botanical bulletin of Academia Sinica, vol. 43, ss. 57-62 -
A neutrophil multitarget functional bioassay to detect anti-inflammatory natural products.
(2002). Journal of natural products (Print), vol. 65, ss. 32-41 DOI -
First crystal structure of Rubisco from a green alga, Chlamydomonas reinhardtii.
(2001). Journal of Biological Chemistry, vol. 276, ss. 48159-48164 DOI -
Nothofagus biogeography revisited with special emphasis on the enigmatic distribution of subgenus Brassospora in New Caledonia.
(2001). Cladistics, vol. 17, ss. 28-47 DOI -
Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences.
(2000). Kew bulletin, vol. 55, ss. 257-309 -
ChemGPS-NP: tuned for navigation in biologically relevant chemical space.
(2007). Journal of natural products (Print), vol. 70, ss. 789-794 DOI -
Secondary chemistry and ribosomal DNA data congruencies in Arnica (Asteraceae).
(2009). Cladistics, vol. 25, ss. 78-92 DOI -
Anti-inflammatory activity of extracts from Arnica (Asteraceae) species assessed by inhibition of NF-κB and release of human neutrophil elastase.
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Delineating small plant polypeptides: with a proposal on their classification and circumscription.
(2012). -
Screening for small cytotoxic peptides in Loranthaceae and Santalaceae.
(2012). -
Comparison of extraction methods for alkaline thionins from mistletoes.
(2012). -
Chemosystematic value of cyclopeptide alkaloids from Heisteria nitida (Olacaceae).
(2005). Biochemical Systematics and Ecology, vol. 33, ss. 831-839 DOI -
The population of the hypogeous fungus Tuber aestivum syn T. uncinatum on the island of Gotland.
(2004). Mycorrhiza, vol. 14, ss. 19-23 DOI -
Bioassay-guided isolation of a cytotoxic quinolizidine alkaloid from Nuphar luteum.
Chemistry and Biodiversity -
Selective cytotoxicity evaluation in anticancer drug screening of fractionated plant extracts.
(2002). Journal of Biomolecular Screening, vol. 7, ss. 333-340 DOI -
Cyclotides: a novel type of cytotoxic agents.
(2002). Molecular Cancer Therapeutics, vol. 1, ss. 365-369
Last modified: 2022-12-16