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Exploring Evolutionary and Chemical Space Using Chemoinformatic Tools and Traditional Methods in Pharmacognosy

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Exploring Evolutionary and Chemical Space Using Chemoinformatic Tools and Traditional Methods in Pharmacognosy Digital Comprehensive Summaries of Uppsala Dissertations Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy 282 from the Faculty of Pharmacy 282 Exploring evolutionary Exploring evolutionary and chemical space using and chemical space using chemoinformatic tools chemoinformatic tools and traditional methods in and traditional methods in pharmacognosy pharmacognosy ASTRID HENZ RYEN ASTRID HENZ RYEN ACTA ACTA UNIVERSITATIS UNIVERSITATIS UPSALIENSIS ISSN 1651-6192 UPSALIENSIS ISSN 1651-6192 UPPSALA ISBN 978-91-513-0843-2 UPPSALA ISBN 978-91-513-0843-2 2020 urn:nbn:se:uu:diva-399068 2020 urn:nbn:se:uu:diva-399068 Dissertation presented at Uppsala University to be publicly examined in C4:305, BMC, Dissertation presented at Uppsala University to be publicly examined in C4:305, BMC, Husargatan 3, Uppsala, Friday, 14 February 2020 at 09:15 for the degree of Doctor of Husargatan 3, Uppsala, Friday, 14 February 2020 at 09:15 for the degree of Doctor of Philosophy (Faculty of Pharmacy). The examination will be conducted in English. Faculty Philosophy (Faculty of Pharmacy). The examination will be conducted in English. Faculty examiner: Associate Professor Fernando B. Da Costa (School of Pharmaceutical Sciences of examiner: Associate Professor Fernando B. Da Costa (School of Pharmaceutical Sciences of Ribeiraõ Preto, University of Saõ Paulo). Ribeiraõ Preto, University of Saõ Paulo). Abstract Abstract Henz Ryen, A. 2020. Exploring evolutionary and chemical space using chemoinformatic Henz Ryen, A. 2020. Exploring evolutionary and chemical space using chemoinformatic tools and traditional methods in pharmacognosy. Digital Comprehensive Summaries of tools and traditional methods in pharmacognosy. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy 282. 80 pp. Uppsala: Acta Universitatis Uppsala Dissertations from the Faculty of Pharmacy 282. 80 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0843-2. Upsaliensis. ISBN 978-91-513-0843-2. The number of new drugs coming to the market is declining while interest in lead discovery from The number of new drugs coming to the market is declining while interest in lead discovery from natural resources is seeing a revival. Although methods for isolation and identification of natural natural resources is seeing a revival. Although methods for isolation and identification of natural products have advanced tremendously, methods for selection of potential leads have fallen products have advanced tremendously, methods for selection of potential leads have fallen behind. As part of the Marie Curie ITN “MedPlant: Phylogenetic exploration of medicinal behind. As part of the Marie Curie ITN “MedPlant: Phylogenetic exploration of medicinal plant diversity” this thesis contributed to the exploration of chemical diversity in angiosperms plant diversity” this thesis contributed to the exploration of chemical diversity in angiosperms and the development of new tools to analyze and define the chemical potential of a plant. and the development of new tools to analyze and define the chemical potential of a plant. In Paper I, it was demonstrated that physicochemical properties of selected specialized In Paper I, it was demonstrated that physicochemical properties of selected specialized metabolites change in different plant groups. Changes in properties were assessed using metabolites change in different plant groups. Changes in properties were assessed using ChemGPS-NP and diversity was quantified by calculating the volume occupied by the ChemGPS-NP and diversity was quantified by calculating the volume occupied by the compounds in chemical space. By discussing the results against the background of possible compounds in chemical space. By discussing the results against the background of possible underlying evolutionary mechanisms, it was concluded that evolutionary processes are reflected underlying evolutionary mechanisms, it was concluded that evolutionary processes are reflected in chemical property space. These results hold great value for further studies on the evolution in chemical property space. These results hold great value for further studies on the evolution of chemical diversity and biochemical traits in plants. The methods developed can be used e.g. of chemical diversity and biochemical traits in plants. The methods developed can be used e.g. to define and predict the chemical diversity of related taxa, providing a strategy for a guided to define and predict the chemical diversity of related taxa, providing a strategy for a guided plant selection in search for new drug leads. plant selection in search for new drug leads. In Paper II, the scaffold and molecular diversity of over 5,200 sesquiterpene lactones (STLs) In Paper II, the scaffold and molecular diversity of over 5,200 sesquiterpene lactones (STLs) was investigated, using different chemoinformatic tools. Quantity and distribution of skeleton was investigated, using different chemoinformatic tools. Quantity and distribution of skeleton classes was determined and it was shown that different plant families possess specific sets classes was determined and it was shown that different plant families possess specific sets of molecular frameworks, with considerable variation in their frequency. Clustering analysis of molecular frameworks, with considerable variation in their frequency. Clustering analysis enabled qualitative division of STLs into smaller groups with similar structural features, enabled qualitative division of STLs into smaller groups with similar structural features, pointing out the differentiation of various plant groups. Including the study results, the dataset pointing out the differentiation of various plant groups. Including the study results, the dataset offers a compelling resource for chemosystematics, natural product research and drug lead offers a compelling resource for chemosystematics, natural product research and drug lead discovery focused on STLs. It provides the basis for phylogenetic implementations due to the discovery focused on STLs. It provides the basis for phylogenetic implementations due to the detailed taxonomic annotation. Since STLs display a source for new drugs, it is of high value detailed taxonomic annotation. Since STLs display a source for new drugs, it is of high value for a guided search for plant derived drug leads. for a guided search for plant derived drug leads. In Paper III, Lindera benzoin was subjected to phytochemical and pharmacological In Paper III, Lindera benzoin was subjected to phytochemical and pharmacological investigations. Phytochemical investigations led to the isolation of three new sesquiterpenes. investigations. Phytochemical investigations led to the isolation of three new sesquiterpenes. As Native American tribes used this shrub for various medicinal purposes, e.g. cold remedy or As Native American tribes used this shrub for various medicinal purposes, e.g. cold remedy or diaphoretic, the isolated compounds were evaluated in vitro for their anti-inflammatory activity. diaphoretic, the isolated compounds were evaluated in vitro for their anti-inflammatory activity. In cellular assays, they reduced pro-inflammatory prostaglandin E2 production in A549 cells in In cellular assays, they reduced pro-inflammatory prostaglandin E2 production in A549 cells in a dose-dependent manner, which may rationalize the traditional use of this plant. a dose-dependent manner, which may rationalize the traditional use of this plant. Keywords: angiosperm chemistry, physicochemical properties of plant specialized Keywords: angiosperm chemistry, physicochemical properties of plant specialized metabolites, chemical diversity, chemical space, sesquiterpene lactones, scaffold diversity, metabolites, chemical diversity, chemical space, sesquiterpene lactones, scaffold diversity, molecular framework, cluster analysis, ECFP6, Lindera benzoin, sesquiterpenes, anti- molecular framework, cluster analysis, ECFP6, Lindera benzoin, sesquiterpenes, anti- inflammatory inflammatory Astrid Henz Ryen, Department of Medicinal Chemistry, Farmakognosi, Box 574, Uppsala Astrid Henz Ryen, Department of Medicinal Chemistry, Farmakognosi, Box 574, Uppsala University, SE-751 23 Uppsala, Sweden. University, SE-751 23 Uppsala, Sweden. © Astrid Henz Ryen 2020 © Astrid Henz Ryen 2020 ISSN 1651-6192 ISSN 1651-6192 ISBN 978-91-513-0843-2 ISBN 978-91-513-0843-2 urn:nbn:se:uu:diva-399068 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-399068) urn:nbn:se:uu:diva-399068 (http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-399068) Was ist blau und liegt unterm Pilz? Schlumpfkacke. List of Papers This thesis is based on the following papers, which are referred to in the text by their Roman numerals. I Henz Ryen A., Backlund A. (2019) Charting angiosperm chemistry: Evolutionary perspective on specialized metabolites peflected in chemical property space. J. Nat. Prod. 82: 798-812. II Henz Ryen A., Buonfiglio R., Backlund A., Kogej T. (2019) Structural classification and scaffold diversity of sesquiterpene lactones in the angiosperms. (Manuscript, submitted) III Henz Ryen A., Göls T., Steinmetz J., Tahir A., Jakobsson P.-J., Backlund A., Urban E., Glasl-Tazreiter S. (2019) Bisabolane ses- quiterpenes from the leaves of Lindera benzoin reduce prostaglandin E2 formation in A549 cells. (Manuscript, submitted) Reprints were made with permission from the respective publishers. List of Papers not included in this thesis Yang L., Chai C.-Z., Yan Y., Duan Y.-D.,
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