1
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Ahamad S, Abdulla M, Saquib M, Kamil Hussain M. Pseudo-Natural Products: Expanding chemical and biological space by surpassing natural constraints. Bioorg Chem 2024; 150:107525. [PMID: 38852308 DOI: 10.1016/j.bioorg.2024.107525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/02/2024] [Indexed: 06/11/2024]
Abstract
This review explores the recent advancements in the design and synthesis of pseudo-natural products (pseudo-NPs) by employing innovative principles and strategies, heralding a transformative era in chemistry and biology. Pseudo-NPs, produced through in silico fragmentation and the de novo recombination of natural product fragments, reveal compounds endowed with distinct biological activities. Their advantage lies in transcending natural product structures, fostering diverse possibilities. Research in this area over the past decade has yielded unconventional combinations of natural product fragments, leading to the identification of novel compounds possessing unique scaffolds and biological significance, thereby contributing to the discovery of new therapeutics. The pseudo-NPs exert potent biological effects through various signaling pathways. In chemical biology and medicinal chemistry, designing pseudo-NPs is an important strategy, harnessing molecular hybridization and bioinspired synthesis to generate diverse compounds with remarkable biological activities, underscoring their immense potential in drug discovery and development.
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Affiliation(s)
- Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, India.
| | - Mohd Abdulla
- Babasaheb Bhimrao Ambedkar University, Lucknow-226025, India
| | - Mohammad Saquib
- Department of Chemistry, University of Allahabad, Prayagraj (Allahabad), 211002, UP, India; Department of Chemistry, G. R. P. B. Degree College, P. R. S. University, Prayagraj (Allahabad), 211010, UP, India.
| | - Mohd Kamil Hussain
- Department of Chemistry, Govt. Raza P.G. College, Rampur-244901, UP, India.
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2
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Yao M, Wang H, Wang Z, Song C, Sa X, Du W, Ye M, Qiao X. Construct Phenylethanoid Glycosides Harnessing Biosynthetic Networks, Protein Engineering and One-Pot Multienzyme Cascades. Angew Chem Int Ed Engl 2024; 63:e202402546. [PMID: 38616162 DOI: 10.1002/anie.202402546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
Phenylethanoid glycosides (PhGs) exhibit a multitude of structural variations linked to diverse pharmacological activities. Assembling various PhGs via multienzyme cascades represents a concise strategy over traditional synthetic methods. However, the challenge lies in identifying a comprehensive set of catalytic enzymes. This study explores biosynthetic PhG reconstruction from natural precursors, aiming to replicate and amplify their structural diversity. We discovered 12 catalytic enzymes, including four novel 6'-OH glycosyltransferases and three new polyphenol oxidases, revealing the intricate network in PhG biosynthesis. Subsequently, the crystal structure of CmGT3 (2.62 Å) was obtained, guiding the identification of conserved residue 144# as a critical determinant for sugar donor specificity. Engineering this residue in PhG glycosyltransferases (FsGT61, CmGT3, and FsGT6) altered their sugar donor recognition. Finally, a one-pot multienzyme cascade was established, where the combined action of glycosyltransferases and acyltransferases boosted conversion rates by up to 12.6-fold. This cascade facilitated the reconstruction of 26 PhGs with conversion rates ranging from 5-100 %, and 20 additional PhGs detectable by mass spectrometry. PhGs with extra glycosyl and hydroxyl modules demonstrated notable liver cell protection. This work not only provides catalytic tools for PhG biosynthesis, but also serves as a proof-of-concept for cell-free enzymatic construction of diverse natural products.
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Affiliation(s)
- Mingju Yao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Haotian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Zilong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Chenglin Song
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Xiaolin Sa
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Wei Du
- Agilent Technologies, 3 Wangjing North Road, Beijing, 100102, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
- Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
- Peking University-Yunnan Baiyao International Medical Research Center, 38 Xueyuan Road, Beijing, 100191, China
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3
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Grigalunas M, Patil S, Krzyzanowski A, Pahl A, Flegel J, Schölermann B, Xie J, Sievers S, Ziegler S, Waldmann H. Unprecedented Combination of Polyketide Natural Product Fragments Identifies the New Hedgehog Signaling Pathway Inhibitor Grismonone. Chemistry 2022; 28:e202202164. [PMID: 36083197 PMCID: PMC10091983 DOI: 10.1002/chem.202202164] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Pseudo-natural products (pseudo-NPs) are de novo combinations of natural product (NP) fragments that define novel bioactive chemotypes. For their discovery, new design principles are being sought. Previously, pseudo-NPs were synthesized by the combination of fragments originating from biosynthetically unrelated NPs to guarantee structural novelty and novel bioactivity. We report the combination of fragments from biosynthetically related NPs in novel arrangements to yield a novel chemotype with activity not shared by the guiding fragments. We describe the synthesis of the polyketide pseudo-NP grismonone and identify it as a structurally novel and potent inhibitor of Hedgehog signaling. The insight that the de novo combination of fragments derived from biosynthetically related NPs may also yield new biologically relevant compound classes with unexpected bioactivity may be considered a chemical extension or diversion of existing biosynthetic pathways and greatly expands the opportunities for exploration of biologically relevant chemical space by means of the pseudo-NP principle.
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Affiliation(s)
- Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sohan Patil
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Adrian Krzyzanowski
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Jana Flegel
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Beate Schölermann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Jianing Xie
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
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4
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Li Y, Cheng S, Tian Y, Zhang Y, Zhao Y. Recent ring distortion reactions for diversifying complex natural products. Nat Prod Rep 2022; 39:1970-1992. [PMID: 35972343 DOI: 10.1039/d2np00027j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2013-2022.Chemical diversification of natural products is an efficient way to generate natural product-like compounds for modern drug discovery programs. Utilizing ring-distortion reactions for diversifying natural products would directly alter the core ring systems of small molecules and lead to the production of structurally complex and diverse compounds for high-throughput screening. We review the ring distortion reactions recently used in complexity-to-diversity (CtD) and pseudo natural products (pseudo-NPs) strategies for diversifying complex natural products. The core ring structures of natural products are altered via ring expansion, ring cleavage, ring edge-fusion, ring spiro-fusion, ring rearrangement, and ring contraction. These reactions can rapidly provide natural product-like collections with properties suitable for a wide variety of biological and medicinal applications. The challenges and limitations of current ring distortion reactions are critically assessed, and avenues for future improvements of this rapidly expanding field are discussed. We also provide a toolbox for chemists for the application of ring distortion reactions to access natural product-like molecules.
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Affiliation(s)
- Yu Li
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yun Tian
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yanan Zhang
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China.
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5
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Niggemeyer G, Knyazeva A, Gasper R, Corkery D, Bodenbinder P, Holstein JJ, Sievers S, Wu Y, Waldmann H. Synthesis of 20‐Membered Macrocyclic Pseudo‐Natural Products Yields Inducers of LC3 Lipidation. Angew Chem Int Ed Engl 2022; 61:e202114328. [PMID: 34978373 PMCID: PMC9303634 DOI: 10.1002/anie.202114328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Indexed: 01/02/2023]
Abstract
Design and synthesis of pseudo‐natural products (PNPs) through recombination of natural product (NP) fragments in unprecedented arrangements enables the discovery of novel biologically relevant chemical matter. With a view to wider coverage of NP‐inspired chemical and biological space, we describe the combination of this principle with macrocycle formation. PNP‐macrocycles were synthesized efficiently in a stereoselective one‐pot procedure including the 1,3‐dipolar cycloadditions of different dipolarophiles with dimeric cinchona alkaloid‐derived azomethine ylides formed in situ. The 20‐membered bis‐cycloadducts embody 18 stereocenters and an additional fragment‐sized NP‐structure. After further functionalization, a collection of 163 macrocyclic PNPs was obtained. Biological investigation revealed potent inducers of the lipidation of the microtubule associated protein 1 light chain 3 (LC3) protein, which plays a prominent role in various autophagy‐related processes.
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Affiliation(s)
- Georg Niggemeyer
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Anastasia Knyazeva
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology Crystallography and Biophysics Unit Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Dale Corkery
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Pia Bodenbinder
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Julian J. Holstein
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS) Otto-Hahn-Strasse 11 44221 Dortmund Germany
| | - Yao‐Wen Wu
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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6
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Abstract
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Natural products
are the result of Nature’s exploration
of biologically relevant chemical space through evolution and an invaluable
source of bioactive small molecules for chemical biology and medicinal
chemistry. Novel concepts for the discovery of new bioactive compound
classes based on natural product structure may enable exploration
of wider biologically relevant chemical space. The pseudo-natural
product concept merges the relevance of natural product structure
with efficient exploration of chemical space by means of fragment-based
compound development to inspire the discovery of new bioactive chemical
matter through de novo combination of natural product
fragments in unprecedented arrangements. The novel scaffolds retain
the biological relevance of natural products but are not obtainable
through known biosynthetic pathways which can lead to new chemotypes
that may have unexpected or unprecedented bioactivities. Herein, we
cover the workflow of pseudo-natural product design and development,
highlight recent examples, and discuss a cheminformatic analysis in
which a significant portion of biologically active synthetic compounds
were found to be pseudo-natural products. We compare the concept to
natural evolution and discuss pseudo-natural products as the human-made
equivalent, i.e. the chemical evolution of natural product structure.
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Affiliation(s)
- Michael Grigalunas
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn Strasse 11, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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7
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Dridi H, Santulli G, Gambardella J, Jankauskas SS, Yuan Q, Yang J, Reiken S, Wang X, Wronska A, Liu X, Lacampagne A, Marks AR. IP3 receptor orchestrates maladaptive vascular responses in heart failure. J Clin Invest 2022; 132:e152859. [PMID: 35166236 PMCID: PMC8843748 DOI: 10.1172/jci152859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/21/2021] [Indexed: 12/02/2022] Open
Abstract
Patients with heart failure (HF) have augmented vascular tone, which increases cardiac workload, impairing ventricular output and promoting further myocardial dysfunction. The molecular mechanisms underlying the maladaptive vascular responses observed in HF are not fully understood. Vascular smooth muscle cells (VSMCs) control vasoconstriction via a Ca2+-dependent process, in which the type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) on the sarcoplasmic reticulum (SR) plays a major role. To dissect the mechanistic contribution of intracellular Ca2+ release to the increased vascular tone observed in HF, we analyzed the remodeling of IP3R1 in aortic tissues from patients with HF and from controls. VSMC IP3R1 channels from patients with HF and HF mice were hyperphosphorylated by both serine and tyrosine kinases. VSMCs isolated from IP3R1VSMC-/- mice exhibited blunted Ca2+ responses to angiotensin II (ATII) and norepinephrine compared with control VSMCs. IP3R1VSMC-/- mice displayed significantly reduced responses to ATII, both in vivo and ex vivo. HF IP3R1VSMC-/- mice developed significantly less afterload compared with HF IP3R1fl/fl mice and exhibited significantly attenuated progression toward decompensated HF and reduced interstitial fibrosis. Ca2+-dependent phosphorylation of the MLC by MLCK activated VSMC contraction. MLC phosphorylation was markedly increased in VSMCs from patients with HF and HF mice but reduced in VSMCs from HF IP3R1VSMC-/- mice and HF WT mice treated with ML-7. Taken together, our data indicate that VSMC IP3R1 is a major effector of increased vascular tone, which contributes to increased cardiac afterload and decompensation in HF.
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MESH Headings
- Animals
- Calcium Signaling
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/physiopathology
- Humans
- Inositol 1,4,5-Trisphosphate Receptors/genetics
- Inositol 1,4,5-Trisphosphate Receptors/metabolism
- Mice
- Mice, Knockout
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/physiopathology
- Myocytes, Smooth Muscle/metabolism
- Vasoconstriction
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Affiliation(s)
- Haikel Dridi
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Gaetano Santulli
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, New York, New York, USA
- Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Neuroimmunology and Inflammation, Albert Einstein College of Medicine, New York, New York, USA
| | - Jessica Gambardella
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, New York, New York, USA
- International Translational Research and Medical Education (ITME) Consortium, Department of Advanced Biomedical Science, “Federico II” University, Naples, Italy
| | - Stanislovas S. Jankauskas
- Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, New York, New York, USA
- Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Neuroimmunology and Inflammation, Albert Einstein College of Medicine, New York, New York, USA
| | - Qi Yuan
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Jingyi Yang
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Steven Reiken
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Xujun Wang
- Department of Medicine, Division of Cardiology, Albert Einstein College of Medicine, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, New York, New York, USA
- Department of Molecular Pharmacology, Einstein-Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Einstein Institute for Neuroimmunology and Inflammation, Albert Einstein College of Medicine, New York, New York, USA
| | - Anetta Wronska
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Xiaoping Liu
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Alain Lacampagne
- PhyMedExp, University of Montpellier, CNRS, INSERM, CHRU Montpellier, Montpellier, France
| | - Andrew R. Marks
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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Niggemeyer G, Knyazeva A, Gasper R, Corkery D, Bodenbinder P, Holstein JJ, Sievers S, Wu Y, Waldmann H. Synthesis of 20‐Membered Macrocyclic Pseudo‐Natural Products Yields Inducers of LC3 Lipidation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Georg Niggemeyer
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Anastasia Knyazeva
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Raphael Gasper
- Max Planck Institute of Molecular Physiology Crystallography and Biophysics Unit Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Dale Corkery
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Pia Bodenbinder
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Julian J. Holstein
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center (COMAS) Otto-Hahn-Strasse 11 44221 Dortmund Germany
| | - Yao‐Wen Wu
- Umeå University Department of Chemistry 90187 Umeå Sweden
- Umeå University Umeå Center for Microbial Research 90187 Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry, Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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9
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Morphological profiling by means of the Cell Painting assay enables identification of tubulin-targeting compounds. Cell Chem Biol 2021; 29:1053-1064.e3. [PMID: 34968420 DOI: 10.1016/j.chembiol.2021.12.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022]
Abstract
In phenotypic compound discovery, conclusive identification of cellular targets and mode of action are often impaired by off-target binding. In particular, microtubules are frequently targeted in cellular assays. However, in vitro tubulin binding assays do not correctly reflect the cellular context, and conclusive high-throughput phenotypic assays monitoring tubulin binding are scarce, such that tubulin binding is rarely identified. We report that morphological profiling using the Cell Painting assay (CPA) can efficiently detect tubulin modulators in compound collections with a high throughput, including annotated reference compounds and unannotated compound classes with unrelated chemotypes and scaffolds. Small-molecule tubulin binders share similar CPA fingerprints, which enables prediction and experimental validation of microtubule-binding activity. Our findings suggest that CPA or a related morphological profiling approach will be an invaluable addition to small-molecule discovery programs in chemical biology and medicinal chemistry, enabling early identification of one of the most frequently observed off-target activities.
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10
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Gally JM, Pahl A, Czodrowski P, Waldmann H. Pseudonatural Products Occur Frequently in Biologically Relevant Compounds. J Chem Inf Model 2021; 61:5458-5468. [PMID: 34669418 PMCID: PMC8611719 DOI: 10.1021/acs.jcim.1c01084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
A new methodology
for classifying fragment combinations and characterizing
pseudonatural products (PNPs) is described. The source code is based
on open-source tools and is organized as a Python package. Tasks can
be executed individually or within the context of scalable, robust
workflows. First, structures are standardized and duplicate entries
are filtered out. Then, molecules are probed for the presence of predefined
fragments. For molecules with more than one match, fragment combinations
are classified. The algorithm considers the pairwise relative position
of fragments within the molecule (fused atoms, linkers, intermediary
rings), resulting in 18 different possible fragment combination categories.
Finally, all combinations for a given molecule are assembled into
a fragment combination graph, with fragments as nodes and combination
types as edges. This workflow was applied to characterize PNPs in
the ChEMBL database via comparison of fragment combination graphs
with natural product (NP) references, represented by the Dictionary
of Natural Products. The Murcko fragments extracted from 2000 structures
previously described were used to define NP fragments. The results
indicate that ca. 23% of the biologically relevant compounds listed
in ChEMBL comply to the PNP definition and that, therefore, PNPs occur
frequently among known biologically relevant small molecules. The
majority (>95%) of PNPs contain two to four fragments, mainly (>95%)
distributed in five different combination types. These findings may
provide guidance for the design of new PNPs.
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Affiliation(s)
- José-Manuel Gally
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Axel Pahl
- Compound Management and Screening Center, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Paul Czodrowski
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
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11
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Burhop A, Bag S, Grigalunas M, Woitalla S, Bodenbinder P, Brieger L, Strohmann C, Pahl A, Sievers S, Waldmann H. Synthesis of Indofulvin Pseudo-Natural Products Yields a New Autophagy Inhibitor Chemotype. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102042. [PMID: 34346568 PMCID: PMC8498912 DOI: 10.1002/advs.202102042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/14/2021] [Indexed: 06/01/2023]
Abstract
Chemical and biological limitations in bioactive compound design based on natural product (NP) structure can be overcome by the combination of NP-derived fragments in unprecedented arrangements to afford "pseudo-natural products" (pseudo-NPs). A new pseudo-NP design principle is described, i.e., the combination of NP-fragments by transformations that are not part of current biosynthesis pathways. A collection of indofulvin pseudo-NPs is obtained from 2-hydroxyethyl-indoles and ketones derived from the fragment-sized NP griseofulvin by means of an iso-oxa-Pictet-Spengler reaction. Cheminformatic analysis indicates that the indofulvins reside in an area of chemical space sparsely covered by NPs, drugs, and drug-like compounds and they may combine favorable properties of these compound classes. Biological evaluation of the compound collection in different cell-based assays and the unbiased high content cell painting assay reveal that the indofulvins define a new autophagy inhibitor chemotype that targets mitochondrial respiration.
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Affiliation(s)
- Annina Burhop
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
| | - Sukdev Bag
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Michael Grigalunas
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
| | - Sophie Woitalla
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
| | - Pia Bodenbinder
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
| | - Lukas Brieger
- Technical University DortmundFaculty of ChemistryInorganic ChemistryDortmund44227Germany
| | - Carsten Strohmann
- Technical University DortmundFaculty of ChemistryInorganic ChemistryDortmund44227Germany
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Compound Management and Screening CenterDortmund44227Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular PhysiologyDepartment of Chemical BiologyDortmund44227Germany
- Technical University DortmundFaculty of ChemistryChemical BiologyDortmund44227Germany
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12
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Yildirim O, Grigalunas M, Brieger L, Strohmann C, Antonchick AP, Waldmann H. Dynamic Catalytic Highly Enantioselective 1,3-Dipolar Cycloadditions. Angew Chem Int Ed Engl 2021; 60:20012-20020. [PMID: 34236754 PMCID: PMC8456807 DOI: 10.1002/anie.202108072] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/06/2021] [Indexed: 11/06/2022]
Abstract
In dynamic covalent chemistry, reactions follow a thermodynamically controlled pathway through equilibria. Reversible covalent‐bond formation and breaking in a dynamic process enables the interconversion of products formed under kinetic control to thermodynamically more stable isomers. Notably, enantioselective catalysis of dynamic transformations has not been reported and applied in complex molecule synthesis. We describe the discovery of dynamic covalent enantioselective metal‐complex‐catalyzed 1,3‐dipolar cycloaddition reactions. We have developed a stereodivergent tandem synthesis of structurally and stereochemically complex molecules that generates eight stereocenters with high diastereo‐ and enantioselectivity through asymmetric reversible bond formation in a dynamic process in two consecutive Ag‐catalyzed 1,3‐dipolar cycloadditions of azomethine ylides with electron‐poor olefins. Time‐dependent reversible dynamic covalent‐bond formation gives enantiodivergent and diastereodivergent access to structurally complex double cycloadducts with high selectivity from a common set of reagents.
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Affiliation(s)
- Okan Yildirim
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technichal University Dortmund, Faculty of Chemistry, Chemical Biology, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Michael Grigalunas
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Lukas Brieger
- Technichal University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Carsten Strohmann
- Technichal University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Andrey P Antonchick
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technichal University Dortmund, Faculty of Chemistry, Chemical Biology, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany.,Nottingham Trent University, Department of Chemistry and Forensics, Cifton Lane, NG11 8NS, Nottingham, UK
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technichal University Dortmund, Faculty of Chemistry, Chemical Biology, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
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13
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Yildirim O, Grigalunas M, Brieger L, Strohmann C, Antonchick AP, Waldmann H. Dynamic Catalytic Highly Enantioselective 1,3‐Dipolar Cycloadditions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Okan Yildirim
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technichal University Dortmund Faculty of Chemistry Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Michael Grigalunas
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Lukas Brieger
- Technichal University Dortmund Faculty of Chemistry Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Carsten Strohmann
- Technichal University Dortmund Faculty of Chemistry Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Andrey P. Antonchick
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technichal University Dortmund Faculty of Chemistry Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
- Nottingham Trent University Department of Chemistry and Forensics Cifton Lane NG11 8NS Nottingham UK
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technichal University Dortmund Faculty of Chemistry Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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14
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products-Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021; 60:15705-15723. [PMID: 33644925 PMCID: PMC8360037 DOI: 10.1002/anie.202016575] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/27/2021] [Indexed: 01/05/2023]
Abstract
Pseudo-natural products (PNPs) combine natural product (NP) fragments in novel arrangements not accessible by current biosynthesis pathways. As such they can be regarded as non-biogenic fusions of NP-derived fragments. They inherit key biological characteristics of the guiding natural product, such as chemical and physiological properties, yet define small molecule chemotypes with unprecedented or unexpected bioactivity. We iterate the design principles underpinning PNP scaffolds and highlight their syntheses and biological investigations. We provide a cheminformatic analysis of PNP collections assessing their molecular properties and shape diversity. We propose and discuss how the iterative analysis of NP structure, design, synthesis, and biological evaluation of PNPs can be regarded as a human-driven branch of the evolution of natural products, that is, a chemical evolution of natural product structure.
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Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: School of Physical and Chemical SciencesUniversity of CanterburyPrivate Bag 4800Christchurch8140New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Current address: Department of ChemistryTechnical University of Denmark, kemitorvet 2072800 Kgs.LyngbyDenmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular PhysiologyOtto-Hahn Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTU Dortmund UniversityOtto-Hahn Strasse 4a44227DortmundGermany
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15
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Yuan S, Yue YL, Zhang DQ, Zhang JY, Yu B, Liu HM. Synthesis of new tetracyclic benzodiazepine-fused isoindolinones using recyclable mesoporous silica nanoparticles. Chem Commun (Camb) 2021; 56:11461-11464. [PMID: 32853306 DOI: 10.1039/d0cc04875e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pseudo natural products (NPs) feature structural novelty and diversity and thus are a new source of lead compounds for drug discovery. We first report the mesoporous silica nanoparticles (MSNs)-catalyzed de novo combination of benzodiazepine and isoindolinone, giving tetracyclic benzodiazepine-fused isoindolinone pseudo natural products (21 examples, 55-91% yields). The work also demonstrates that MSNs are efficient acidic catalysts for multi-component reactions.
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Affiliation(s)
- Shuo Yuan
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou 450001, China.
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16
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Alonso F, Galilea A, Mañez PA, Acebedo SL, Cabrera GM, Otero M, Barquero AA, Ramírez JA. Beyond Pseudo-natural Products: Sequential Ugi/Pictet-Spengler Reactions Leading to Steroidal Pyrazinoisoquinolines That Trigger Caspase-Independent Death in HepG2 Cells. ChemMedChem 2021; 16:1945-1955. [PMID: 33682316 DOI: 10.1002/cmdc.202100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/27/2021] [Indexed: 01/05/2023]
Abstract
In this work, we describe how stereochemically complex polycyclic compounds can be generated by applying a synthetic sequence comprising an intramolecular Ugi reaction followed by a Pictet-Spengler cyclization on steroid-derived scaffolds. The resulting compounds, which combine a fragment derived from a natural product and a scaffold not found in nature. are both structurally distinct and globally similar to natural products at the same time, and interrogate an alternative region of the chemical space. One of the new compounds showed significant antiproliferative activity on HepG2 cells through a caspase-independent cell-death mechanism, an appealing feature when new antitumor compounds are searched.
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Affiliation(s)
- Fernando Alonso
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Agustín Galilea
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Pau Arroyo Mañez
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Departamento de Química Orgánica de la Facultad de Farmacia, Universitat de València, Valencia, 46100, Spain
| | - Sofía L Acebedo
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Gabriela M Cabrera
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Marcelo Otero
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET - Universidad de Buenos Aires and Instituto de Física de Buenos Aires (IFIBA), Ciudad Universitaria, Buenos Aires, 1428, Argentina
| | - Andrea A Barquero
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Departamento de Química Biológica, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Instituto de Quimica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina
| | - Javier A Ramírez
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
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17
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Grigalunas M, Burhop A, Zinken S, Pahl A, Gally JM, Wild N, Mantel Y, Sievers S, Foley DJ, Scheel R, Strohmann C, Antonchick AP, Waldmann H. Natural product fragment combination to performance-diverse pseudo-natural products. Nat Commun 2021; 12:1883. [PMID: 33767198 PMCID: PMC7994817 DOI: 10.1038/s41467-021-22174-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Natural product structure and fragment-based compound development inspire pseudo-natural product design through different combinations of a given natural product fragment set to compound classes expected to be chemically and biologically diverse. We describe the synthetic combination of the fragment-sized natural products quinine, quinidine, sinomenine, and griseofulvin with chromanone or indole-containing fragments to provide a 244-member pseudo-natural product collection. Cheminformatic analyses reveal that the resulting eight pseudo-natural product classes are chemically diverse and share both drug- and natural product-like properties. Unbiased biological evaluation by cell painting demonstrates that bioactivity of pseudo-natural products, guiding natural products, and fragments differ and that combination of different fragments dominates establishment of unique bioactivity. Identification of phenotypic fragment dominance enables design of compound classes with correctly predicted bioactivity. The results demonstrate that fusion of natural product fragments in different combinations and arrangements can provide chemically and biologically diverse pseudo-natural product classes for wider exploration of biologically relevant chemical space.
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Affiliation(s)
- Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Annina Burhop
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Sarah Zinken
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - José-Manuel Gally
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Niklas Wild
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Yannik Mantel
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Daniel J Foley
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- College of Science, University of Canterbury, Canterbury, New Zealand
| | - Rebecca Scheel
- Technical University Dortmund, Faculty of Chemistry and Inorganic Chemistry, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry and Inorganic Chemistry, Dortmund, Germany
| | - Andrey P Antonchick
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- College of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
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18
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Karageorgis G, Foley DJ, Laraia L, Brakmann S, Waldmann H. Pseudo Natural Products—Chemical Evolution of Natural Product Structure. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016575] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- George Karageorgis
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
| | - Daniel J. Foley
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Current address: School of Physical and Chemical Sciences University of Canterbury Private Bag 4800 Christchurch 8140 New Zealand
| | - Luca Laraia
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Current address: Department of Chemistry Technical University of Denmark, kemitorvet 207 2800 Kgs. Lyngby Denmark
| | - Susanne Brakmann
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Strasse 4a 44227 Dortmund Germany
| | - Herbert Waldmann
- Max-Planck Institute of Molecular Physiology Otto-Hahn Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn Strasse 4a 44227 Dortmund Germany
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19
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Abstract
It is well established that medicinal chemists should depart from the flat, sp2-dominated nature of traditional drugs and incorporate complexities of bioactive natural products, such as sp3-richness, 3D topology and chirality. There is a gray area, however, in the relevance of newly developed chemical scaffolds that exhibit these complexities but do not correlate to anything observed in nature. This can leave synthetic methodologists searching for structural similarities between their newly developed products and known natural products in search of justification. This article offers a perspective on how these types of complex 'abiotic' scaffolds can be appreciated purely on the basis of their structural novelty, and identifies the unique advantages arising when a complex chemical entity unrecognized by nature is introduced to biological systems.
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20
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Liu J, Cremosnik GS, Otte F, Pahl A, Sievers S, Strohmann C, Waldmann H. Design, Synthesis, and Biological Evaluation of Chemically and Biologically Diverse Pyrroquinoline Pseudo Natural Products. Angew Chem Int Ed Engl 2021; 60:4648-4656. [PMID: 33200868 PMCID: PMC7986669 DOI: 10.1002/anie.202013731] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/27/2022]
Abstract
Natural product (NP) structures are a rich source of inspiration for the discovery of new biologically relevant chemical matter. In natural product inspired pseudo‐NPs, NP‐derived fragments are combined de novo in unprecedented arrangements. Described here is the design and synthesis of a 155‐member pyrroquinoline pseudo‐NP collection in which fragments characteristic of the tetrahydroquinoline and pyrrolidine NP classes are combined with eight different connectivities and regioisomeric arrangements. Cheminformatic analysis and biological evaluation of the compound collection by means of phenotyping in the morphological “cell painting” assay followed by principal component analysis revealed that the pseudo‐NP classes are chemically diverse and that bioactivity patterns differ markedly, and are dependent on connectivity and regioisomeric arrangement of the fragments.
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Affiliation(s)
- Jie Liu
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University Dortmund, Faculty of Chemistry, Chemical Biology, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Gregor S Cremosnik
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Felix Otte
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Compound Management and Screening Center, Dortmund, Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Compound Management and Screening Center, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry, Inorganic Chemistry, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.,Technical University Dortmund, Faculty of Chemistry, Chemical Biology, Otto-Hahn-Strasse 6, 44221, Dortmund, Germany
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21
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Liu J, Cremosnik GS, Otte F, Pahl A, Sievers S, Strohmann C, Waldmann H. Design, Synthesis, and Biological Evaluation of Chemically and Biologically Diverse Pyrroquinoline Pseudo Natural Products. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013731] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jie Liu
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Gregor S. Cremosnik
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Felix Otte
- Technical University Dortmund Faculty of Chemistry Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Compound Management and Screening Center Dortmund Germany
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Compound Management and Screening Center Dortmund Germany
| | - Carsten Strohmann
- Technical University Dortmund Faculty of Chemistry Inorganic Chemistry Otto-Hahn-Strasse 6 44221 Dortmund Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Department of Chemical Biology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Technical University Dortmund Faculty of Chemistry Chemical Biology Otto-Hahn-Strasse 6 44221 Dortmund Germany
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22
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Foley DJ, Zinken S, Corkery D, Laraia L, Pahl A, Wu Y, Waldmann H. Phenotyping Reveals Targets of a Pseudo-Natural-Product Autophagy Inhibitor. Angew Chem Int Ed Engl 2020; 59:12470-12476. [PMID: 32108411 PMCID: PMC7383971 DOI: 10.1002/anie.202000364] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/25/2020] [Indexed: 12/26/2022]
Abstract
Pseudo-natural-product (NP) design combines natural product fragments to provide unprecedented NP-inspired compounds not accessible by biosynthesis, but endowed with biological relevance. Since the bioactivity of pseudo-NPs may be unprecedented or unexpected, they are best evaluated in target agnostic cell-based assays monitoring entire cellular programs or complex phenotypes. Here, the Cinchona alkaloid scaffold was merged with the indole ring system to synthesize indocinchona alkaloids by Pd-catalyzed annulation. Exploration of indocinchona alkaloid bioactivities in phenotypic assays revealed a novel class of azaindole-containing autophagy inhibitors, the azaquindoles. Subsequent characterization of the most potent compound, azaquindole-1, in the morphological cell painting assay, guided target identification efforts. In contrast to the parent Cinchona alkaloids, azaquindoles selectively inhibit starvation- and rapamycin-induced autophagy by targeting the lipid kinase VPS34.
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Affiliation(s)
- Daniel J. Foley
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Current address: School of Physical and Chemical SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Sarah Zinken
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundDortmundGermany
| | - Dale Corkery
- Department of ChemistryUmeå Centre for Microbial ResearchUmeå UniversityUmeåSweden
| | - Luca Laraia
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Current address: Department of ChemistryTechnical University of DenmarkCopenhagenDenmark
| | - Axel Pahl
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Compound Management and Screening CentreDortmundGermany
| | - Yao‐Wen Wu
- Department of ChemistryUmeå Centre for Microbial ResearchUmeå UniversityUmeåSweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular PhysiologyDortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundDortmundGermany
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23
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Grigalunas M, Burhop A, Christoforow A, Waldmann H. Pseudo-natural products and natural product-inspired methods in chemical biology and drug discovery. Curr Opin Chem Biol 2020; 56:111-118. [PMID: 32362382 DOI: 10.1016/j.cbpa.2019.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 11/20/2022]
Abstract
Through evolution, nature has provided natural products (NPs) as a rich source of diverse bioactive material. Many drug discovery programs have used nature as an inspiration for the design of NP-like compound classes. These concepts are guided by the prevalidated biological relevance of NPs while going beyond the limitations of nature to produce chemical matter that could have unexpected or novel bioactivities. Herein, we discuss, compare, and highlight recent examples of NP-inspired methods with a focus on the pseudo-NP concept.
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Affiliation(s)
- Michael Grigalunas
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Annina Burhop
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
| | - Andreas Christoforow
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany.
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24
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Reckzeh ES, Waldmann H. Development of Glucose Transporter (GLUT) Inhibitors. European J Org Chem 2020; 2020:2321-2329. [PMID: 32421048 PMCID: PMC7217229 DOI: 10.1002/ejoc.201901353] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Indexed: 12/11/2022]
Abstract
The discovery of novel compound classes endowed with biological activity is at the heart of chemical biology and medicinal chemistry research. This enables novel biological insights and inspires new approaches to the treatment of diseases. Cancer cells frequently exhibit altered glycolysis and glucose metabolism and an increased glucose demand. Thus, targeting glucose uptake and metabolism may open up novel opportunities for the discovery of compounds that differentiate between normal and malignant cells. This review discusses the different chemical approaches to the development of novel inhibitors of glucose uptake through facilitative glucose transporters (GLUTs), and focusses on the most advanced and potent inhibitor classes known to date. GLUT inhibitors may find application not only in the treatment of cancer, but also of other proliferative diseases that exhibit glucose addiction.
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Affiliation(s)
- Elena S. Reckzeh
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto‐Hahn‐Str. 1144227DortmundGermany
- Department Chemistry and Chemical BiologyTU Dortmund UniversityOtto‐Hahn‐Str. 4a44227DortmundGermany
| | - Herbert Waldmann
- Department of Chemical BiologyMax Planck Institute of Molecular PhysiologyOtto‐Hahn‐Str. 1144227DortmundGermany
- Department Chemistry and Chemical BiologyTU Dortmund UniversityOtto‐Hahn‐Str. 4a44227DortmundGermany
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25
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Foley DJ, Zinken S, Corkery D, Laraia L, Pahl A, Wu Y, Waldmann H. Phenotyping Reveals Targets of a Pseudo‐Natural‐Product Autophagy Inhibitor. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000364] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Daniel J. Foley
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Current address: School of Physical and Chemical Sciences University of Canterbury Christchurch New Zealand
| | - Sarah Zinken
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Dortmund Germany
| | - Dale Corkery
- Department of Chemistry Umeå Centre for Microbial Research Umeå University Umeå Sweden
| | - Luca Laraia
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Current address: Department of Chemistry Technical University of Denmark Copenhagen Denmark
| | - Axel Pahl
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Compound Management and Screening Centre Dortmund Germany
| | - Yao‐Wen Wu
- Department of Chemistry Umeå Centre for Microbial Research Umeå University Umeå Sweden
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Dortmund Germany
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26
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Lowe RA, Taylor D, Chibale K, Nelson A, Marsden SP. Synthesis and evaluation of the performance of a small molecule library based on diverse tropane-related scaffolds. Bioorg Med Chem 2020; 28:115442. [PMID: 32209295 DOI: 10.1016/j.bmc.2020.115442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/02/2020] [Accepted: 03/12/2020] [Indexed: 12/20/2022]
Abstract
A unified synthetic approach was developed that enabled the synthesis of diverse tropane-related scaffolds. The key intermediates that were exploited were cycloadducts formed by reaction between 3-hydroxy-pyridinium salts and vinyl sulfones or sulfonamides. The diverse tropane-related scaffolds were formed by addition of substituents to, cyclisation reactions of, and fusion of additional ring(s) to the key bicyclic intermediates. A set of 53 screening compounds was designed, synthesised and evaluated in order to determine the biological relevance of the scaffolds accessible using the synthetic approach. Two inhibitors of Hedgehog signalling, and four compounds with weak activity against the parasite P. falciparum, were discovered. Three of the active compounds may be considered to be indotropane or pyrrotropane pseudo natural products in which a tropane is fused with a fragment from another natural product class. It was concluded that the unified synthetic approach had yielded diverse scaffolds suitable for the design of performance-diverse screening libraries.
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Affiliation(s)
- Robert A Lowe
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | - Dale Taylor
- H3D Drug Discovery and Development Center, University of Cape Town, Private Bag, Rondebosch 7700, South Africa
| | - Kelly Chibale
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council, Drug Discovery and Development Research Unit, University of Cape Town, Rondebosch 7701, South Africa
| | - Adam Nelson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
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27
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Karageorgis G, Foley DJ, Laraia L, Waldmann H. Principle and design of pseudo-natural products. Nat Chem 2020; 12:227-235. [PMID: 32015480 DOI: 10.1038/s41557-019-0411-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 12/16/2019] [Indexed: 01/01/2023]
Abstract
Natural products (NPs) are a significant source of inspiration towards the discovery of new bioactive compounds based on novel molecular scaffolds. However, there are currently only a small number of guiding synthetic strategies available to generate novel NP-inspired scaffolds, limiting both the number and types of compounds accessible. In this Perspective, we discuss a design approach for the preparation of biologically relevant small-molecule libraries, harnessing the unprecedented combination of NP-derived fragments as an overarching strategy for the synthesis of new bioactive compounds. These novel 'pseudo-natural product' classes retain the biological relevance of NPs, yet exhibit structures and bioactivities not accessible to nature or through the use of existing design strategies. We also analyse selected pseudo-NP libraries using chemoinformatic tools, to assess their molecular shape diversity and properties. To facilitate the exploration of biologically relevant chemical space, we identify design principles and connectivity patterns that would provide access to unprecedented pseudo-NP classes, offering new opportunities for bioactive small-molecule discovery.
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Affiliation(s)
- George Karageorgis
- Department of Chemical Biology, Max-Planck Institute for Molecular Physiology, Dortmund, Germany.,School of Chemistry, University of Leeds, Leeds, UK
| | - Daniel J Foley
- Department of Chemical Biology, Max-Planck Institute for Molecular Physiology, Dortmund, Germany.,College of Science, University of Canterbury, Canterbury, New Zealand
| | - Luca Laraia
- Department of Chemical Biology, Max-Planck Institute for Molecular Physiology, Dortmund, Germany.,Department of Chemistry, Technical University of Denmark, Copenhagen, Denmark
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck Institute for Molecular Physiology, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, Technical University, Dortmund, Germany.
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28
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Cremosnik GS, Liu J, Waldmann H. Guided by evolution: from biology oriented synthesis to pseudo natural products. Nat Prod Rep 2020; 37:1497-1510. [DOI: 10.1039/d0np00015a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review provides an overview and historical context to two concepts for the design of natural product-inspired compound libraries and highlights the used synthetic methodologies.
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Affiliation(s)
- Gregor S. Cremosnik
- Department of Chemical Biology
- Max-Planck-Institute of Molecular Physiology
- 44227 Dortmund
- Germany
| | - Jie Liu
- Department of Chemical Biology
- Max-Planck-Institute of Molecular Physiology
- 44227 Dortmund
- Germany
- Faculty of Chemistry and Chemical Biology
| | - Herbert Waldmann
- Department of Chemical Biology
- Max-Planck-Institute of Molecular Physiology
- 44227 Dortmund
- Germany
- Faculty of Chemistry and Chemical Biology
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29
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Johnson EO, Hung DT. A Point of Inflection and Reflection on Systems Chemical Biology. ACS Chem Biol 2019; 14:2497-2511. [PMID: 31613592 DOI: 10.1021/acschembio.9b00714] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For the past several decades, chemical biologists have been leveraging chemical principles for understanding biology, tackling disease, and biomanufacturing, while systems biologists have holistically applied computation and genome-scale experimental tools to the same problems. About a decade ago, the benefit of combining the philosophies of chemical biology with systems biology into systems chemical biology was advocated, with the potential to systematically understand the way small molecules affect biological systems. Recently, there has been an explosion in new technologies that permit massive expansion in the scale of biological experimentation, increase access to more diverse chemical space, and enable powerful computational interpretation of large datasets. Fueled by these rapidly increasing capabilities, systems chemical biology is now at an inflection point, poised to enter a new era of more holistic and integrated scientific discovery. Systems chemical biology is primed to reveal an integrated understanding of fundamental biology and to discover new chemical probes to comprehensively dissect and systematically understand that biology, thereby providing a path to novel strategies for discovering therapeutics, designing drug combinations, avoiding toxicity, and harnessing beneficial polypharmacology. In this Review, we examine the emergence of new capabilities driving us to this inflection point in systems chemical biology, and highlight holistic approaches and opportunities that are arising from integrating chemical biology with a systems-level understanding of the intersection of biology and chemistry.
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Affiliation(s)
- Eachan O. Johnson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Deborah T. Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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30
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Liu M, Quinn RJ. Fragment-based screening with natural products for novel anti-parasitic disease drug discovery. Expert Opin Drug Discov 2019; 14:1283-1295. [PMID: 31512943 PMCID: PMC6816479 DOI: 10.1080/17460441.2019.1653849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 08/06/2019] [Indexed: 12/30/2022]
Abstract
Introduction: Fragment-based drug discovery can identify relatively simple compounds with low binding affinity due to fewer binding interactions with protein targets. FBDD reduces the library size and provides simpler starting points for subsequent chemical optimization of initial hits. A much greater proportion of chemical space can be sampled in fragment-based screening compared to larger molecules with typical molecular weights (MWs) of 250-500 g mol-1 used in high-throughput screening (HTS) libraries. Areas covered: The authors cover the role of natural products in fragment-based drug discovery against parasitic disease targets. They review the approaches to develop fragment-based libraries either using natural products or natural product-like compounds. The authors present approaches to fragment-based drug discovery against parasitic diseases and compare these libraries with the 3D attributes of natural products. Expert opinion: To effectively use the three-dimensional properties and the chemical diversity of natural products in fragment-based drug discovery against parasitic diseases, there needs to be a mind-shift. Library design, in the medicinal chemistry area, has acknowledged that escaping flat-land is very important to increase the chances of clinical success. Attempts to increase sp3 richness in fragment libraries are acknowledged. Sufficient low molecular weight natural products are known to create true natural product fragment libraries.
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Affiliation(s)
- Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Ronald J. Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
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31
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Ceballos J, Schwalfenberg M, Karageorgis G, Reckzeh ES, Sievers S, Ostermann C, Pahl A, Sellstedt M, Nowacki J, Carnero Corrales MA, Wilke J, Laraia L, Tschapalda K, Metz M, Sehr DA, Brand S, Winklhofer K, Janning P, Ziegler S, Waldmann H. Synthesis of Indomorphan Pseudo-Natural Product Inhibitors of Glucose Transporters GLUT-1 and -3. Angew Chem Int Ed Engl 2019; 58:17016-17025. [PMID: 31469221 PMCID: PMC6900016 DOI: 10.1002/anie.201909518] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/12/2019] [Indexed: 12/22/2022]
Abstract
Bioactive compound design based on natural product (NP) structure may be limited because of partial coverage of NP-like chemical space and biological target space. These limitations can be overcome by combining NP-centered strategies with fragment-based compound design through combination of NP-derived fragments to afford structurally unprecedented "pseudo-natural products" (pseudo-NPs). The design, synthesis, and biological evaluation of a collection of indomorphan pseudo-NPs that combine biosynthetically unrelated indole- and morphan-alkaloid fragments are described. Indomorphane derivative Glupin was identified as a potent inhibitor of glucose uptake by selectively targeting and upregulating glucose transporters GLUT-1 and GLUT-3. Glupin suppresses glycolysis, reduces the levels of glucose-derived metabolites, and attenuates the growth of various cancer cell lines. Our findings underscore the importance of dual GLUT-1 and GLUT-3 inhibition to efficiently suppress tumor cell growth and the cellular rescue mechanism, which counteracts glucose scarcity.
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Affiliation(s)
- Javier Ceballos
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Current address: Laboratory of Catalysis and Organic SynthesisEPFL SB ISIC LCSO, BCH 42211015LausanneSwitzerland
| | - Melanie Schwalfenberg
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - George Karageorgis
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Current address: School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Elena S. Reckzeh
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundOtto-Hahn-Strasse 644227DortmundGermany
| | - Sonja Sievers
- Compound Management and Screening Center, DortmundOtto-Hahn-Strasse 1144227DortmundGermany
| | - Claude Ostermann
- Compound Management and Screening Center, DortmundOtto-Hahn-Strasse 1144227DortmundGermany
| | - Axel Pahl
- Compound Management and Screening Center, DortmundOtto-Hahn-Strasse 1144227DortmundGermany
| | - Magnus Sellstedt
- Department of ChemistryUmeå University901 87UmeåSweden
- Current address: Clinical Chemistry, Laboratory MedicineUniversity Hospital of Umeå901 85UmeåSweden
| | - Jessica Nowacki
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Marjorie A. Carnero Corrales
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Julian Wilke
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundOtto-Hahn-Strasse 644227DortmundGermany
| | - Luca Laraia
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Current address: Department of ChemistryTechnical University of DenmarkKemitorvet, Bygning 2072800Kgs LyngbyDenmark
| | - Kirsten Tschapalda
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Malte Metz
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Dominik A. Sehr
- Department of Molecular Cell BiologyInstitute of Biochemistry and PathobiochemistryRuhr University Bochum44801BochumGermany
| | - Silke Brand
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Konstanze Winklhofer
- Department of Molecular Cell BiologyInstitute of Biochemistry and PathobiochemistryRuhr University Bochum44801BochumGermany
| | - Petra Janning
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Slava Ziegler
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
| | - Herbert Waldmann
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Strasse 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundOtto-Hahn-Strasse 644227DortmundGermany
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32
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Ceballos J, Schwalfenberg M, Karageorgis G, Reckzeh ES, Sievers S, Ostermann C, Pahl A, Sellstedt M, Nowacki J, Carnero Corrales MA, Wilke J, Laraia L, Tschapalda K, Metz M, Sehr DA, Brand S, Winklhofer K, Janning P, Ziegler S, Waldmann H. Synthesis of Indomorphan Pseudo‐Natural Product Inhibitors of Glucose Transporters GLUT‐1 and ‐3. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909518] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Javier Ceballos
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Current address: Laboratory of Catalysis and Organic SynthesisEPFL SB ISIC LCSO, BCH 4221 1015 Lausanne Switzerland
| | - Melanie Schwalfenberg
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - George Karageorgis
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Current address: School of ChemistryUniversity of Leeds Leeds LS2 9JT UK
| | - Elena S. Reckzeh
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical BiologyTechnical University Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Dortmund Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Claude Ostermann
- Compound Management and Screening Center, Dortmund Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Axel Pahl
- Compound Management and Screening Center, Dortmund Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Magnus Sellstedt
- Department of ChemistryUmeå University 901 87 Umeå Sweden
- Current address: Clinical Chemistry, Laboratory MedicineUniversity Hospital of Umeå 901 85 Umeå Sweden
| | - Jessica Nowacki
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Marjorie A. Carnero Corrales
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Julian Wilke
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical BiologyTechnical University Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
| | - Luca Laraia
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Current address: Department of ChemistryTechnical University of Denmark Kemitorvet, Bygning 207 2800 Kgs Lyngby Denmark
| | - Kirsten Tschapalda
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Malte Metz
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Dominik A. Sehr
- Department of Molecular Cell BiologyInstitute of Biochemistry and PathobiochemistryRuhr University Bochum 44801 Bochum Germany
| | - Silke Brand
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Konstanze Winklhofer
- Department of Molecular Cell BiologyInstitute of Biochemistry and PathobiochemistryRuhr University Bochum 44801 Bochum Germany
| | - Petra Janning
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Slava Ziegler
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical BiologyMax-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical BiologyTechnical University Dortmund Otto-Hahn-Strasse 6 44227 Dortmund Germany
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33
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Christoforow A, Wilke J, Binici A, Pahl A, Ostermann C, Sievers S, Waldmann H. Design, Synthesis, and Phenotypic Profiling of Pyrano-Furo-Pyridone Pseudo Natural Products. Angew Chem Int Ed Engl 2019; 58:14715-14723. [PMID: 31339620 PMCID: PMC7687248 DOI: 10.1002/anie.201907853] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/23/2019] [Indexed: 11/23/2022]
Abstract
Natural products (NPs) inspire the design and synthesis of novel biologically relevant chemical matter, for instance through biology-oriented synthesis (BIOS). However, BIOS is limited by the partial coverage of NP-like chemical space by the guiding NPs. The design and synthesis of "pseudo NPs" overcomes these limitations by combining NP-inspired strategies with fragment-based compound design through de novo combination of NP-derived fragments to unprecedented compound classes not accessible through biosynthesis. We describe the development and biological evaluation of pyrano-furo-pyridone (PFP) pseudo NPs, which combine pyridone- and dihydropyran NP fragments in three isomeric arrangements. Cheminformatic analysis indicates that the PFPs reside in an area of NP-like chemical space not covered by existing NPs but rather by drugs and related compounds. Phenotypic profiling in a target-agnostic "cell painting" assay revealed that PFPs induce formation of reactive oxygen species and are structurally novel inhibitors of mitochondrial complex I.
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Affiliation(s)
- Andreas Christoforow
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundOtto-Hahn-Straße 644227DortmundGermany
| | - Julian Wilke
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundOtto-Hahn-Straße 644227DortmundGermany
| | - Aylin Binici
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundOtto-Hahn-Straße 644227DortmundGermany
| | - Axel Pahl
- Compound Management and Screening Center, DortmundOtto-Hahn-Str. 1144227DortmundGermany
| | - Claude Ostermann
- Compound Management and Screening Center, DortmundOtto-Hahn-Str. 1144227DortmundGermany
| | - Sonja Sievers
- Compound Management and Screening Center, DortmundOtto-Hahn-Str. 1144227DortmundGermany
| | - Herbert Waldmann
- Department of Chemical BiologyMax-Planck-Institute of Molecular PhysiologyOtto-Hahn-Straße 1144227DortmundGermany
- Faculty of Chemistry and Chemical BiologyTechnical University DortmundOtto-Hahn-Straße 644227DortmundGermany
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34
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Christoforow A, Wilke J, Binici A, Pahl A, Ostermann C, Sievers S, Waldmann H. Design, Synthesis, and Phenotypic Profiling of Pyrano‐Furo‐Pyridone Pseudo Natural Products. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907853] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andreas Christoforow
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Julian Wilke
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Aylin Binici
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Axel Pahl
- Compound Management and Screening Center, Dortmund Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Claude Ostermann
- Compound Management and Screening Center, Dortmund Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Dortmund Otto-Hahn-Str. 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology Max-Planck-Institute of Molecular Physiology Otto-Hahn-Straße 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technical University Dortmund Otto-Hahn-Straße 6 44227 Dortmund Germany
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